Zinc in PDB 7pvk: X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
Protein crystallography data
The structure of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg., PDB code: 7pvk
was solved by
C.A.Schmitz,
M.Madej,
J.Potempa,
M.Sola,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
51.90 /
2.40
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.63,
103.77,
132.21,
90,
98.5,
90
|
|
R / Rfree (%)
|
19.4 /
22.3
|
Other elements in 7pvk:
The structure of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
(pdb code 7pvk). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the
X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg., PDB code: 7pvk:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 1 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn603
b:72.0
occ:1.00
|
OD1
|
A:ASP239
|
1.9
|
66.4
|
1.0
|
|
NE2
|
A:HIS416
|
1.9
|
69.6
|
1.0
|
|
OD2
|
A:ASP415
|
2.2
|
65.0
|
1.0
|
|
OD2
|
A:ASP239
|
2.4
|
67.1
|
1.0
|
|
CG
|
A:ASP239
|
2.4
|
63.5
|
1.0
|
|
CD2
|
A:HIS416
|
2.6
|
69.5
|
1.0
|
|
HD2
|
A:HIS416
|
2.6
|
83.5
|
1.0
|
|
HB2
|
A:ALA272
|
2.7
|
99.3
|
1.0
|
|
CG
|
A:ASP415
|
3.0
|
68.3
|
1.0
|
|
CE1
|
A:HIS416
|
3.0
|
70.6
|
1.0
|
|
OD1
|
A:ASP415
|
3.1
|
64.0
|
1.0
|
|
P
|
E:G1
|
3.4
|
78.9
|
1.0
|
|
HE1
|
A:HIS416
|
3.4
|
84.8
|
1.0
|
|
H
|
A:ALA272
|
3.4
|
95.3
|
1.0
|
|
CB
|
A:ALA272
|
3.6
|
82.7
|
1.0
|
|
N
|
A:ALA272
|
3.8
|
79.3
|
1.0
|
|
CG
|
A:HIS416
|
3.8
|
69.5
|
1.0
|
|
OP1
|
E:G1
|
3.8
|
80.4
|
1.0
|
|
CB
|
A:ASP239
|
3.9
|
64.4
|
1.0
|
|
HA
|
A:ALA272
|
3.9
|
90.6
|
1.0
|
|
H
|
A:ASN240
|
3.9
|
79.0
|
1.0
|
|
ND1
|
A:HIS416
|
3.9
|
69.7
|
1.0
|
|
CA
|
A:ALA272
|
4.0
|
75.4
|
1.0
|
|
HB3
|
A:ALA272
|
4.0
|
99.3
|
1.0
|
|
OD1
|
A:ASP361
|
4.1
|
68.9
|
1.0
|
|
H5''
|
E:G1
|
4.1
|
92.6
|
1.0
|
|
HA
|
A:ASP239
|
4.1
|
84.5
|
1.0
|
|
HA
|
A:ALA271
|
4.1
|
103.1
|
1.0
|
|
HB1
|
A:ALA272
|
4.2
|
99.3
|
1.0
|
|
O5'
|
E:G1
|
4.2
|
78.9
|
1.0
|
|
HB2
|
A:ASN240
|
4.2
|
83.5
|
1.0
|
|
HD3
|
A:ARG276
|
4.2
|
82.5
|
1.0
|
|
HE1
|
A:HIS500
|
4.2
|
84.9
|
1.0
|
|
HH11
|
A:ARG276
|
4.3
|
87.6
|
1.0
|
|
HB2
|
A:ASP361
|
4.3
|
83.5
|
1.0
|
|
N
|
A:ASN240
|
4.3
|
65.7
|
1.0
|
|
HB3
|
A:ASP239
|
4.3
|
77.4
|
1.0
|
|
HB2
|
A:ASP239
|
4.3
|
77.4
|
1.0
|
|
OP2
|
E:G1
|
4.4
|
79.7
|
1.0
|
|
CB
|
A:ASP415
|
4.4
|
69.8
|
1.0
|
|
CA
|
A:ASP239
|
4.4
|
70.4
|
1.0
|
|
CE1
|
A:HIS500
|
4.5
|
70.7
|
1.0
|
|
ZN
|
A:ZN604
|
4.5
|
72.4
|
1.0
|
|
C
|
A:ALA271
|
4.5
|
79.5
|
1.0
|
|
HB2
|
A:ASP415
|
4.5
|
83.8
|
1.0
|
|
CG
|
A:ASP361
|
4.6
|
65.7
|
1.0
|
|
C5'
|
E:G1
|
4.7
|
77.5
|
1.0
|
|
HB2
|
A:ARG276
|
4.7
|
80.8
|
1.0
|
|
C
|
A:ASP239
|
4.7
|
65.7
|
1.0
|
|
HD1
|
A:HIS416
|
4.8
|
83.7
|
1.0
|
|
CA
|
A:ALA271
|
4.8
|
85.9
|
1.0
|
|
HB3
|
A:ASP415
|
4.9
|
83.8
|
1.0
|
|
HA
|
A:ASN240
|
4.9
|
79.7
|
1.0
|
|
CB
|
A:ASP361
|
5.0
|
69.5
|
1.0
|
|
NH1
|
A:ARG276
|
5.0
|
72.9
|
1.0
|
|
Zinc binding site 2 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 2 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn604
b:72.4
occ:1.00
|
OD1
|
A:ASP361
|
1.7
|
68.9
|
1.0
|
|
NE2
|
A:HIS500
|
2.0
|
68.4
|
1.0
|
|
NE2
|
A:HIS365
|
2.0
|
65.9
|
1.0
|
|
OP2
|
E:G1
|
2.0
|
79.7
|
1.0
|
|
CE1
|
A:HIS500
|
2.7
|
70.7
|
1.0
|
|
CG
|
A:ASP361
|
2.7
|
65.7
|
1.0
|
|
HE1
|
A:HIS500
|
2.8
|
84.9
|
1.0
|
|
CE1
|
A:HIS365
|
2.9
|
65.3
|
1.0
|
|
CD2
|
A:HIS365
|
2.9
|
65.4
|
1.0
|
|
P
|
E:G1
|
3.0
|
78.9
|
1.0
|
|
CD2
|
A:HIS500
|
3.1
|
69.7
|
1.0
|
|
OD2
|
A:ASP361
|
3.1
|
66.0
|
1.0
|
|
HE1
|
A:HIS365
|
3.1
|
78.4
|
1.0
|
|
HD2
|
A:HIS365
|
3.2
|
78.6
|
1.0
|
|
HD22
|
A:ASN240
|
3.4
|
92.1
|
1.0
|
|
HE1
|
A:HIS416
|
3.4
|
84.8
|
1.0
|
|
HD2
|
A:HIS500
|
3.4
|
83.7
|
1.0
|
|
ND1
|
A:HIS500
|
3.8
|
68.5
|
1.0
|
|
OP1
|
E:G1
|
3.9
|
80.4
|
1.0
|
|
H5'
|
E:G1
|
4.0
|
92.6
|
1.0
|
|
ND1
|
A:HIS365
|
4.0
|
69.5
|
1.0
|
|
CE1
|
A:HIS416
|
4.0
|
70.6
|
1.0
|
|
ND2
|
A:ASN240
|
4.0
|
76.7
|
1.0
|
|
CG
|
A:HIS365
|
4.0
|
63.7
|
1.0
|
|
CG
|
A:HIS500
|
4.1
|
68.0
|
1.0
|
|
CB
|
A:ASP361
|
4.1
|
69.5
|
1.0
|
|
O5'
|
E:G1
|
4.2
|
78.9
|
1.0
|
|
HB2
|
A:ASP361
|
4.2
|
83.5
|
1.0
|
|
NE2
|
A:HIS416
|
4.2
|
69.6
|
1.0
|
|
HD21
|
A:ASN240
|
4.2
|
92.1
|
1.0
|
|
HB2
|
A:ASN240
|
4.4
|
83.5
|
1.0
|
|
C5'
|
E:G1
|
4.5
|
77.5
|
1.0
|
|
HA
|
A:ASP361
|
4.5
|
81.0
|
1.0
|
|
ZN
|
A:ZN603
|
4.5
|
72.0
|
1.0
|
|
H5''
|
E:G1
|
4.6
|
92.6
|
1.0
|
|
HD1
|
A:HIS500
|
4.6
|
82.2
|
1.0
|
|
O
|
A:ASP361
|
4.6
|
69.9
|
1.0
|
|
OD1
|
A:ASP239
|
4.6
|
66.4
|
1.0
|
|
HB3
|
A:ASP361
|
4.7
|
83.5
|
1.0
|
|
HD1
|
A:HIS365
|
4.8
|
83.5
|
1.0
|
|
CA
|
A:ASP361
|
4.8
|
67.9
|
1.0
|
|
O
|
E:HOH1002
|
4.9
|
91.1
|
1.0
|
|
C
|
A:ASP361
|
5.0
|
68.0
|
1.0
|
|
CG
|
A:ASN240
|
5.0
|
72.6
|
1.0
|
|
Zinc binding site 3 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 3 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn603
b:59.3
occ:1.00
|
HE2
|
B:HIS416
|
1.7
|
77.9
|
1.0
|
|
OP2
|
G:G1
|
1.8
|
61.5
|
1.0
|
|
OD2
|
B:ASP415
|
2.1
|
56.4
|
1.0
|
|
OD1
|
B:ASP239
|
2.1
|
55.8
|
1.0
|
|
NE2
|
B:HIS416
|
2.2
|
64.8
|
1.0
|
|
OD2
|
B:ASP239
|
2.4
|
51.4
|
1.0
|
|
CG
|
B:ASP239
|
2.5
|
53.0
|
1.0
|
|
HB2
|
B:ALA272
|
2.7
|
64.4
|
1.0
|
|
CG
|
B:ASP415
|
2.9
|
56.1
|
1.0
|
|
CE1
|
B:HIS416
|
2.9
|
60.4
|
1.0
|
|
OD1
|
B:ASP415
|
3.0
|
55.2
|
1.0
|
|
CD2
|
B:HIS416
|
3.0
|
55.4
|
1.0
|
|
HE1
|
B:HIS416
|
3.1
|
72.5
|
1.0
|
|
P
|
G:G1
|
3.3
|
64.7
|
1.0
|
|
HD2
|
B:HIS416
|
3.3
|
66.5
|
1.0
|
|
H
|
B:ALA272
|
3.4
|
65.0
|
1.0
|
|
CB
|
B:ALA272
|
3.7
|
53.6
|
1.0
|
|
H
|
B:ASN240
|
3.8
|
74.9
|
1.0
|
|
N
|
B:ALA272
|
3.8
|
54.1
|
1.0
|
|
HB2
|
B:ASN240
|
3.9
|
68.8
|
1.0
|
|
ND1
|
B:HIS416
|
3.9
|
52.3
|
1.0
|
|
H5''
|
G:G1
|
3.9
|
78.1
|
1.0
|
|
HA
|
B:ALA272
|
4.0
|
67.0
|
1.0
|
|
CG
|
B:HIS416
|
4.0
|
60.7
|
1.0
|
|
CB
|
B:ASP239
|
4.0
|
48.5
|
1.0
|
|
OP1
|
G:G1
|
4.0
|
73.2
|
1.0
|
|
CA
|
B:ALA272
|
4.1
|
55.8
|
1.0
|
|
OP3
|
G:G1
|
4.1
|
67.4
|
1.0
|
|
HB3
|
B:ALA272
|
4.1
|
64.4
|
1.0
|
|
O5'
|
G:G1
|
4.2
|
63.6
|
1.0
|
|
N
|
B:ASN240
|
4.2
|
62.4
|
1.0
|
|
HB1
|
B:ALA272
|
4.3
|
64.4
|
1.0
|
|
HA
|
B:ASP239
|
4.3
|
67.1
|
1.0
|
|
HA
|
B:ALA271
|
4.3
|
73.1
|
1.0
|
|
OD1
|
B:ASP361
|
4.3
|
62.2
|
1.0
|
|
HD3
|
B:ARG276
|
4.3
|
66.5
|
1.0
|
|
CB
|
B:ASP415
|
4.3
|
50.0
|
1.0
|
|
HB2
|
B:ASP361
|
4.4
|
74.4
|
1.0
|
|
HE1
|
B:HIS500
|
4.4
|
68.2
|
1.0
|
|
CG
|
B:ASP361
|
4.4
|
61.4
|
1.0
|
|
HB2
|
B:ASP239
|
4.4
|
58.3
|
1.0
|
|
HB2
|
B:ASP415
|
4.5
|
60.1
|
1.0
|
|
ZN
|
B:ZN610
|
4.5
|
60.2
|
1.0
|
|
HB3
|
B:ASP239
|
4.5
|
58.3
|
1.0
|
|
HH11
|
B:ARG276
|
4.5
|
76.8
|
1.0
|
|
C5'
|
G:G1
|
4.5
|
65.0
|
1.0
|
|
CA
|
B:ASP239
|
4.6
|
55.9
|
1.0
|
|
CE1
|
B:HIS500
|
4.6
|
56.8
|
1.0
|
|
NE2
|
B:HIS500
|
4.7
|
61.6
|
1.0
|
|
C
|
B:ALA271
|
4.7
|
59.7
|
1.0
|
|
C
|
B:ASP239
|
4.7
|
55.0
|
1.0
|
|
OD2
|
B:ASP361
|
4.7
|
62.1
|
1.0
|
|
CB
|
B:ASN240
|
4.7
|
57.3
|
1.0
|
|
HB3
|
B:ASP415
|
4.8
|
60.1
|
1.0
|
|
HA
|
B:ASN240
|
4.8
|
75.2
|
1.0
|
|
H5'
|
G:G1
|
4.8
|
78.1
|
1.0
|
|
CA
|
B:ASN240
|
4.9
|
62.6
|
1.0
|
|
HB2
|
B:ARG276
|
4.9
|
69.3
|
1.0
|
|
CB
|
B:ASP361
|
4.9
|
62.4
|
1.0
|
|
CA
|
B:ALA271
|
5.0
|
60.8
|
1.0
|
|
Zinc binding site 4 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 4 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn610
b:60.2
occ:1.00
|
OP1
|
G:G1
|
1.6
|
73.2
|
1.0
|
|
NE2
|
B:HIS500
|
2.0
|
61.6
|
1.0
|
|
NE2
|
B:HIS365
|
2.1
|
63.4
|
1.0
|
|
OD1
|
B:ASP361
|
2.1
|
62.2
|
1.0
|
|
OD2
|
B:ASP361
|
2.6
|
62.1
|
1.0
|
|
CG
|
B:ASP361
|
2.7
|
61.4
|
1.0
|
|
P
|
G:G1
|
2.9
|
64.7
|
1.0
|
|
CD2
|
B:HIS500
|
3.0
|
55.0
|
1.0
|
|
CD2
|
B:HIS365
|
3.0
|
60.9
|
1.0
|
|
CE1
|
B:HIS365
|
3.0
|
59.5
|
1.0
|
|
CE1
|
B:HIS500
|
3.0
|
56.8
|
1.0
|
|
HD2
|
B:HIS500
|
3.2
|
66.1
|
1.0
|
|
HD2
|
B:HIS365
|
3.2
|
72.6
|
1.0
|
|
HE1
|
B:HIS365
|
3.2
|
71.5
|
1.0
|
|
HE1
|
B:HIS500
|
3.3
|
68.2
|
1.0
|
|
HD22
|
B:ASN240
|
3.4
|
78.7
|
1.0
|
|
OP2
|
G:G1
|
3.5
|
61.5
|
1.0
|
|
HE1
|
B:HIS416
|
3.6
|
72.5
|
1.0
|
|
OP3
|
G:G1
|
3.7
|
67.4
|
1.0
|
|
O
|
G:HOH1003
|
3.7
|
113.3
|
1.0
|
|
H5'
|
G:G1
|
3.8
|
78.1
|
1.0
|
|
HE2
|
B:HIS416
|
4.0
|
77.9
|
1.0
|
|
O5'
|
G:G1
|
4.0
|
63.6
|
1.0
|
|
ND1
|
B:HIS365
|
4.1
|
62.5
|
1.0
|
|
ND1
|
B:HIS500
|
4.1
|
59.6
|
1.0
|
|
CG
|
B:HIS500
|
4.2
|
55.5
|
1.0
|
|
CG
|
B:HIS365
|
4.2
|
63.2
|
1.0
|
|
CB
|
B:ASP361
|
4.2
|
62.4
|
1.0
|
|
ND2
|
B:ASN240
|
4.2
|
65.5
|
1.0
|
|
CE1
|
B:HIS416
|
4.3
|
60.4
|
1.0
|
|
C5'
|
G:G1
|
4.3
|
65.0
|
1.0
|
|
HB2
|
B:ASN240
|
4.4
|
68.8
|
1.0
|
|
NE2
|
B:HIS416
|
4.5
|
64.8
|
1.0
|
|
ZN
|
B:ZN603
|
4.5
|
59.3
|
1.0
|
|
HB2
|
B:ASP361
|
4.5
|
74.4
|
1.0
|
|
HD21
|
B:ASN240
|
4.5
|
78.7
|
1.0
|
|
H5''
|
G:G1
|
4.5
|
78.1
|
1.0
|
|
OD1
|
B:ASP239
|
4.6
|
55.8
|
1.0
|
|
HB3
|
B:ASP361
|
4.7
|
74.4
|
1.0
|
|
HA
|
B:ASP361
|
4.7
|
74.3
|
1.0
|
|
O
|
B:ASP361
|
4.8
|
62.1
|
1.0
|
|
HD1
|
B:HIS365
|
4.9
|
75.1
|
1.0
|
|
HD1
|
B:HIS500
|
4.9
|
71.6
|
1.0
|
|
CA
|
B:ASP361
|
4.9
|
62.3
|
1.0
|
|
Zinc binding site 5 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 5 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn603
b:56.6
occ:1.00
|
OP3
|
H:G1
|
1.9
|
69.5
|
1.0
|
|
NE2
|
C:HIS416
|
2.0
|
60.7
|
1.0
|
|
OD2
|
C:ASP415
|
2.1
|
51.4
|
1.0
|
|
OD1
|
C:ASP239
|
2.1
|
60.1
|
1.0
|
|
OD2
|
C:ASP239
|
2.5
|
56.5
|
1.0
|
|
CG
|
C:ASP239
|
2.5
|
58.9
|
1.0
|
|
CD2
|
C:HIS416
|
2.6
|
55.1
|
1.0
|
|
HD2
|
C:HIS416
|
2.6
|
66.2
|
1.0
|
|
HB2
|
C:ALA272
|
2.7
|
74.5
|
1.0
|
|
CG
|
C:ASP415
|
2.9
|
56.9
|
1.0
|
|
CE1
|
C:HIS416
|
3.1
|
59.3
|
1.0
|
|
OD1
|
C:ASP415
|
3.1
|
54.4
|
1.0
|
|
P
|
H:G1
|
3.3
|
59.7
|
1.0
|
|
H
|
C:ALA272
|
3.4
|
71.9
|
1.0
|
|
HE1
|
C:HIS416
|
3.5
|
71.3
|
1.0
|
|
CB
|
C:ALA272
|
3.6
|
62.0
|
1.0
|
|
N
|
C:ALA272
|
3.8
|
59.8
|
1.0
|
|
CG
|
C:HIS416
|
3.8
|
52.8
|
1.0
|
|
OP2
|
H:G1
|
3.8
|
54.7
|
1.0
|
|
HA
|
C:ALA272
|
3.8
|
77.8
|
1.0
|
|
H
|
C:ASN240
|
4.0
|
68.5
|
1.0
|
|
CA
|
C:ALA272
|
4.0
|
64.7
|
1.0
|
|
ND1
|
C:HIS416
|
4.0
|
54.9
|
1.0
|
|
CB
|
C:ASP239
|
4.0
|
61.7
|
1.0
|
|
OD2
|
C:ASP361
|
4.1
|
58.4
|
1.0
|
|
HB3
|
C:ALA272
|
4.1
|
74.5
|
1.0
|
|
O5'
|
H:G1
|
4.1
|
56.3
|
1.0
|
|
HB1
|
C:ALA272
|
4.2
|
74.5
|
1.0
|
|
HA
|
C:ALA271
|
4.2
|
70.1
|
1.0
|
|
OP1
|
H:G1
|
4.2
|
56.1
|
1.0
|
|
HA
|
C:ASP239
|
4.2
|
81.2
|
1.0
|
|
HB2
|
C:ASN240
|
4.2
|
68.5
|
1.0
|
|
HH11
|
C:ARG276
|
4.2
|
66.6
|
1.0
|
|
HD3
|
C:ARG276
|
4.3
|
63.2
|
1.0
|
|
HE1
|
C:HIS500
|
4.3
|
64.9
|
1.0
|
|
HB2
|
C:ASP361
|
4.3
|
71.7
|
1.0
|
|
CB
|
C:ASP415
|
4.3
|
55.6
|
1.0
|
|
H5''
|
H:G1
|
4.3
|
70.7
|
1.0
|
|
N
|
C:ASN240
|
4.3
|
57.0
|
1.0
|
|
HB2
|
C:ASP415
|
4.4
|
66.8
|
1.0
|
|
HB2
|
C:ASP239
|
4.5
|
74.1
|
1.0
|
|
HB3
|
C:ASP239
|
4.5
|
74.1
|
1.0
|
|
CE1
|
C:HIS500
|
4.5
|
54.0
|
1.0
|
|
CA
|
C:ASP239
|
4.5
|
67.6
|
1.0
|
|
C
|
C:ALA271
|
4.6
|
56.7
|
1.0
|
|
ZN
|
C:ZN611
|
4.6
|
59.4
|
1.0
|
|
CG
|
C:ASP361
|
4.7
|
58.4
|
1.0
|
|
C
|
C:ASP239
|
4.7
|
65.2
|
1.0
|
|
HB3
|
C:ASP415
|
4.8
|
66.8
|
1.0
|
|
HD1
|
C:HIS416
|
4.8
|
66.0
|
1.0
|
|
C5'
|
H:G1
|
4.8
|
58.9
|
1.0
|
|
HB2
|
C:ARG276
|
4.9
|
66.6
|
1.0
|
|
CA
|
C:ALA271
|
4.9
|
58.3
|
1.0
|
|
NH1
|
C:ARG276
|
4.9
|
55.5
|
1.0
|
|
HA
|
C:ASN240
|
4.9
|
67.9
|
1.0
|
|
NE2
|
C:HIS500
|
5.0
|
54.8
|
1.0
|
|
CB
|
C:ASP361
|
5.0
|
59.7
|
1.0
|
|
ND1
|
C:HIS500
|
5.0
|
52.0
|
1.0
|
|
Zinc binding site 6 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 6 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn610
b:166.9
occ:0.53
|
NE2
|
D:HIS323
|
2.2
|
163.5
|
1.0
|
|
CE1
|
D:HIS323
|
3.2
|
166.7
|
1.0
|
|
CD2
|
D:HIS323
|
3.2
|
160.0
|
1.0
|
|
HE1
|
D:HIS323
|
3.3
|
200.1
|
1.0
|
|
HD2
|
D:HIS323
|
3.4
|
192.0
|
1.0
|
|
HB3
|
D:ARG321
|
3.7
|
80.2
|
1.0
|
|
O
|
D:ARG321
|
3.9
|
68.2
|
1.0
|
|
ND1
|
D:HIS323
|
4.3
|
159.2
|
1.0
|
|
CG
|
D:HIS323
|
4.3
|
143.9
|
1.0
|
|
HA
|
D:ARG321
|
4.3
|
81.8
|
1.0
|
|
C
|
D:ARG321
|
4.5
|
71.0
|
1.0
|
|
CB
|
D:ARG321
|
4.6
|
66.8
|
1.0
|
|
CA
|
D:ARG321
|
4.7
|
68.1
|
1.0
|
|
HG2
|
D:ARG321
|
4.8
|
85.4
|
1.0
|
|
Zinc binding site 7 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 7 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn610
b:166.9
occ:0.47
|
OE1
|
C:GLU90
|
2.0
|
147.5
|
1.0
|
|
OE2
|
C:GLU90
|
2.3
|
138.9
|
1.0
|
|
CD
|
C:GLU90
|
2.5
|
144.7
|
1.0
|
|
NE2
|
C:HIS92
|
2.6
|
64.4
|
1.0
|
|
HD2
|
C:HIS92
|
3.4
|
63.8
|
1.0
|
|
CD2
|
C:HIS92
|
3.4
|
53.1
|
1.0
|
|
CE1
|
C:HIS92
|
3.7
|
58.2
|
1.0
|
|
HE1
|
C:HIS92
|
4.0
|
69.9
|
1.0
|
|
CG
|
C:GLU90
|
4.0
|
157.1
|
1.0
|
|
HD11
|
C:ILE93
|
4.2
|
70.9
|
1.0
|
|
HB3
|
C:GLU90
|
4.4
|
174.0
|
1.0
|
|
O
|
C:HOH810
|
4.4
|
116.6
|
1.0
|
|
HG3
|
C:GLU90
|
4.4
|
188.7
|
1.0
|
|
HG2
|
C:GLU90
|
4.4
|
188.7
|
1.0
|
|
HG12
|
C:ILE93
|
4.5
|
76.1
|
1.0
|
|
CG
|
C:HIS92
|
4.6
|
60.8
|
1.0
|
|
CB
|
C:GLU90
|
4.7
|
144.9
|
1.0
|
|
ND1
|
C:HIS92
|
4.8
|
61.9
|
1.0
|
|
HB2
|
C:GLU90
|
4.8
|
174.0
|
1.0
|
|
O
|
C:HOH733
|
4.8
|
72.1
|
1.0
|
|
Zinc binding site 8 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 8 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn611
b:59.4
occ:1.00
|
OP1
|
H:G1
|
1.7
|
56.1
|
1.0
|
|
OD2
|
C:ASP361
|
1.8
|
58.4
|
1.0
|
|
NE2
|
C:HIS500
|
1.8
|
54.8
|
1.0
|
|
NE2
|
C:HIS365
|
1.9
|
59.4
|
1.0
|
|
CE1
|
C:HIS500
|
2.6
|
54.0
|
1.0
|
|
HE1
|
C:HIS500
|
2.7
|
64.9
|
1.0
|
|
CG
|
C:ASP361
|
2.7
|
58.4
|
1.0
|
|
CE1
|
C:HIS365
|
2.7
|
59.8
|
1.0
|
|
HE1
|
C:HIS365
|
2.8
|
71.3
|
1.0
|
|
P
|
H:G1
|
3.0
|
59.7
|
1.0
|
|
CD2
|
C:HIS500
|
3.0
|
55.7
|
1.0
|
|
OD1
|
C:ASP361
|
3.0
|
58.6
|
1.0
|
|
CD2
|
C:HIS365
|
3.1
|
59.6
|
1.0
|
|
OP3
|
H:G1
|
3.3
|
69.5
|
1.0
|
|
HD2
|
C:HIS365
|
3.4
|
71.1
|
1.0
|
|
HD2
|
C:HIS500
|
3.4
|
67.0
|
1.0
|
|
HD22
|
C:ASN240
|
3.6
|
72.9
|
1.0
|
|
HE1
|
C:HIS416
|
3.6
|
71.3
|
1.0
|
|
ND1
|
C:HIS500
|
3.8
|
52.0
|
1.0
|
|
H5'
|
H:G1
|
3.8
|
70.7
|
1.0
|
|
OP2
|
H:G1
|
3.9
|
54.7
|
1.0
|
|
ND1
|
C:HIS365
|
3.9
|
63.0
|
1.0
|
|
CG
|
C:HIS500
|
4.0
|
54.2
|
1.0
|
|
CG
|
C:HIS365
|
4.1
|
60.1
|
1.0
|
|
O5'
|
H:G1
|
4.1
|
56.3
|
1.0
|
|
CB
|
C:ASP361
|
4.1
|
59.7
|
1.0
|
|
ND2
|
C:ASN240
|
4.2
|
60.7
|
1.0
|
|
CE1
|
C:HIS416
|
4.2
|
59.3
|
1.0
|
|
HB2
|
C:ASP361
|
4.3
|
71.7
|
1.0
|
|
C5'
|
H:G1
|
4.3
|
58.9
|
1.0
|
|
HD21
|
C:ASN240
|
4.3
|
72.9
|
1.0
|
|
H5''
|
H:G1
|
4.3
|
70.7
|
1.0
|
|
NE2
|
C:HIS416
|
4.4
|
60.7
|
1.0
|
|
HD1
|
C:HIS500
|
4.5
|
62.5
|
1.0
|
|
O
|
C:ASP361
|
4.6
|
60.3
|
1.0
|
|
ZN
|
C:ZN603
|
4.6
|
56.6
|
1.0
|
|
HD1
|
C:HIS365
|
4.6
|
75.7
|
1.0
|
|
HB2
|
C:ASN240
|
4.6
|
68.5
|
1.0
|
|
HA
|
C:ASP361
|
4.6
|
70.0
|
1.0
|
|
OD1
|
C:ASP239
|
4.7
|
60.1
|
1.0
|
|
HB3
|
C:ASP361
|
4.7
|
71.7
|
1.0
|
|
CA
|
C:ASP361
|
4.9
|
58.3
|
1.0
|
|
O
|
C:HOH744
|
5.0
|
59.0
|
1.0
|
|
O
|
C:HOH707
|
5.0
|
54.8
|
1.0
|
|
Zinc binding site 9 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 9 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn603
b:60.1
occ:1.00
|
OP2
|
F:G1
|
1.9
|
62.8
|
1.0
|
|
OD2
|
D:ASP415
|
2.0
|
58.7
|
1.0
|
|
NE2
|
D:HIS416
|
2.1
|
66.0
|
1.0
|
|
OD1
|
D:ASP239
|
2.1
|
59.1
|
1.0
|
|
OD2
|
D:ASP239
|
2.3
|
57.1
|
1.0
|
|
CG
|
D:ASP239
|
2.5
|
56.1
|
1.0
|
|
HB2
|
D:ALA272
|
2.6
|
70.6
|
1.0
|
|
CG
|
D:ASP415
|
2.9
|
55.8
|
1.0
|
|
CE1
|
D:HIS416
|
2.9
|
66.4
|
1.0
|
|
CD2
|
D:HIS416
|
2.9
|
63.3
|
1.0
|
|
OD1
|
D:ASP415
|
3.1
|
52.8
|
1.0
|
|
HE1
|
D:HIS416
|
3.1
|
79.8
|
1.0
|
|
HD2
|
D:HIS416
|
3.2
|
76.0
|
1.0
|
|
P
|
F:G1
|
3.3
|
62.5
|
1.0
|
|
H
|
D:ALA272
|
3.3
|
76.2
|
1.0
|
|
CB
|
D:ALA272
|
3.6
|
58.8
|
1.0
|
|
N
|
D:ALA272
|
3.8
|
63.4
|
1.0
|
|
H
|
D:ASN240
|
3.9
|
64.2
|
1.0
|
|
ND1
|
D:HIS416
|
3.9
|
58.9
|
1.0
|
|
HA
|
D:ALA272
|
3.9
|
71.2
|
1.0
|
|
H5''
|
F:G1
|
3.9
|
81.7
|
1.0
|
|
CG
|
D:HIS416
|
3.9
|
63.4
|
1.0
|
|
HB2
|
D:ASN240
|
3.9
|
64.7
|
1.0
|
|
CB
|
D:ASP239
|
4.0
|
50.8
|
1.0
|
|
CA
|
D:ALA272
|
4.0
|
59.2
|
1.0
|
|
HB3
|
D:ALA272
|
4.0
|
70.6
|
1.0
|
|
OP3
|
F:G1
|
4.1
|
61.2
|
1.0
|
|
OP1
|
F:G1
|
4.1
|
60.3
|
1.0
|
|
HB1
|
D:ALA272
|
4.1
|
70.6
|
1.0
|
|
O5'
|
F:G1
|
4.2
|
59.7
|
1.0
|
|
OD1
|
D:ASP361
|
4.2
|
52.6
|
1.0
|
|
HA
|
D:ASP239
|
4.2
|
70.5
|
1.0
|
|
CB
|
D:ASP415
|
4.3
|
53.4
|
1.0
|
|
N
|
D:ASN240
|
4.3
|
53.5
|
1.0
|
|
HD3
|
D:ARG276
|
4.3
|
72.3
|
1.0
|
|
HE1
|
D:HIS500
|
4.3
|
73.0
|
1.0
|
|
HA
|
D:ALA271
|
4.3
|
72.0
|
1.0
|
|
HB2
|
D:ASP361
|
4.3
|
62.0
|
1.0
|
|
HB2
|
D:ASP415
|
4.4
|
64.2
|
1.0
|
|
CG
|
D:ASP361
|
4.4
|
52.9
|
1.0
|
|
HB2
|
D:ASP239
|
4.4
|
61.1
|
1.0
|
|
ZN
|
D:ZN608
|
4.5
|
59.2
|
1.0
|
|
HB3
|
D:ASP239
|
4.5
|
61.1
|
1.0
|
|
CE1
|
D:HIS500
|
4.5
|
60.7
|
1.0
|
|
C5'
|
F:G1
|
4.5
|
68.0
|
1.0
|
|
HH11
|
D:ARG276
|
4.5
|
80.8
|
1.0
|
|
CA
|
D:ASP239
|
4.6
|
58.7
|
1.0
|
|
HD1
|
D:HIS416
|
4.6
|
70.8
|
1.0
|
|
C
|
D:ALA271
|
4.7
|
56.9
|
1.0
|
|
HB3
|
D:ASP415
|
4.7
|
64.2
|
1.0
|
|
OD2
|
D:ASP361
|
4.7
|
54.9
|
1.0
|
|
NE2
|
D:HIS500
|
4.7
|
59.8
|
1.0
|
|
C
|
D:ASP239
|
4.8
|
53.6
|
1.0
|
|
H5'
|
F:G1
|
4.8
|
81.7
|
1.0
|
|
CB
|
D:ASN240
|
4.8
|
53.8
|
1.0
|
|
HB2
|
D:ARG276
|
4.8
|
74.6
|
1.0
|
|
HA
|
D:ASN240
|
4.9
|
64.8
|
1.0
|
|
CB
|
D:ASP361
|
4.9
|
52.0
|
1.0
|
|
CA
|
D:ASN240
|
4.9
|
53.9
|
1.0
|
|
H
|
D:HIS416
|
5.0
|
69.2
|
1.0
|
|
Zinc binding site 10 out
of 10 in 7pvk
Go back to
Zinc Binding Sites List in 7pvk
Zinc binding site 10 out
of 10 in the X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg.
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of X-Ray Structure of Dimeric Porx (T272A Mutant), in Complex with Pgpg. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn608
b:59.2
occ:1.00
|
OP1
|
F:G1
|
1.7
|
60.3
|
1.0
|
|
NE2
|
D:HIS500
|
1.9
|
59.8
|
1.0
|
|
NE2
|
D:HIS365
|
2.0
|
72.1
|
1.0
|
|
OD1
|
D:ASP361
|
2.0
|
52.6
|
1.0
|
|
CG
|
D:ASP361
|
2.7
|
52.9
|
1.0
|
|
CE1
|
D:HIS500
|
2.8
|
60.7
|
1.0
|
|
OD2
|
D:ASP361
|
2.8
|
54.9
|
1.0
|
|
CE1
|
D:HIS365
|
2.8
|
74.1
|
1.0
|
|
HE1
|
D:HIS365
|
2.9
|
89.0
|
1.0
|
|
HE1
|
D:HIS500
|
2.9
|
73.0
|
1.0
|
|
P
|
F:G1
|
3.0
|
62.5
|
1.0
|
|
CD2
|
D:HIS500
|
3.0
|
61.3
|
1.0
|
|
CD2
|
D:HIS365
|
3.1
|
73.2
|
1.0
|
|
HD2
|
D:HIS500
|
3.3
|
73.6
|
1.0
|
|
HD2
|
D:HIS365
|
3.4
|
87.9
|
1.0
|
|
HD22
|
D:ASN240
|
3.4
|
79.5
|
1.0
|
|
OP2
|
F:G1
|
3.5
|
62.8
|
1.0
|
|
HE1
|
D:HIS416
|
3.6
|
79.8
|
1.0
|
|
OP3
|
F:G1
|
3.8
|
61.2
|
1.0
|
|
O
|
F:HOH1002
|
3.8
|
88.3
|
1.0
|
|
H5'
|
F:G1
|
3.9
|
81.7
|
1.0
|
|
ND1
|
D:HIS500
|
3.9
|
60.8
|
1.0
|
|
ND1
|
D:HIS365
|
4.0
|
75.2
|
1.0
|
|
CG
|
D:HIS500
|
4.1
|
59.4
|
1.0
|
|
O5'
|
F:G1
|
4.1
|
59.7
|
1.0
|
|
CG
|
D:HIS365
|
4.1
|
71.6
|
1.0
|
|
ND2
|
D:ASN240
|
4.2
|
66.2
|
1.0
|
|
CE1
|
D:HIS416
|
4.2
|
66.4
|
1.0
|
|
CB
|
D:ASP361
|
4.2
|
52.0
|
1.0
|
|
NE2
|
D:HIS416
|
4.4
|
66.0
|
1.0
|
|
C5'
|
F:G1
|
4.4
|
68.0
|
1.0
|
|
HD21
|
D:ASN240
|
4.4
|
79.5
|
1.0
|
|
ZN
|
D:ZN603
|
4.5
|
60.1
|
1.0
|
|
HB2
|
D:ASN240
|
4.5
|
64.7
|
1.0
|
|
HB2
|
D:ASP361
|
4.5
|
62.0
|
1.0
|
|
H5''
|
F:G1
|
4.6
|
81.7
|
1.0
|
|
OD1
|
D:ASP239
|
4.6
|
59.1
|
1.0
|
|
HA
|
D:ASP361
|
4.7
|
71.4
|
1.0
|
|
HD1
|
D:HIS500
|
4.7
|
73.0
|
1.0
|
|
HD1
|
D:HIS365
|
4.7
|
90.3
|
1.0
|
|
HB3
|
D:ASP361
|
4.8
|
62.0
|
1.0
|
|
O
|
D:ASP361
|
4.8
|
57.8
|
1.0
|
|
O
|
D:HOH759
|
4.9
|
64.0
|
1.0
|
|
CA
|
D:ASP361
|
4.9
|
59.4
|
1.0
|
|
Reference:
C.Schmitz,
M.Madej,
Z.Nowakowska,
A.Cuppari,
A.Jacula,
M.Ksiazek,
K.Mikruta,
J.Wisniewski,
N.Pudelko-Malik,
A.Saran,
N.Zeytuni,
P.Mlynarz,
R.J.Lamont,
I.Uson,
V.Siksnys,
J.Potempa,
M.Sola.
Response Regulator Porx Coordinates Oligonucleotide Signalling and Gene Expression to Control the Secretion of Virulence Factors. Nucleic Acids Res. V. 50 12558 2022.
ISSN: ESSN 1362-4962
PubMed: 36464236
DOI: 10.1093/NAR/GKAC1103
Page generated: Wed Oct 30 09:22:54 2024
|
