Zinc in PDB 5jf1: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin:
3.5.1.88;
Protein crystallography data
The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin, PDB code: 5jf1
was solved by
S.Fieulaine,
C.Giglione,
T.Meinnel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.41 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.840,
66.160,
88.860,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.1 /
19.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
(pdb code 5jf1). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin, PDB code: 5jf1:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5jf1
Go back to
Zinc Binding Sites List in 5jf1
Zinc binding site 1 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn303
b:18.1
occ:1.00
|
OD3
|
A:OCS131
|
1.9
|
20.9
|
1.0
|
O2
|
A:BB2301
|
2.1
|
20.2
|
1.0
|
NE2
|
A:HIS174
|
2.1
|
14.0
|
1.0
|
NE2
|
A:HIS178
|
2.1
|
17.3
|
1.0
|
O4
|
A:BB2301
|
2.3
|
27.3
|
1.0
|
N1
|
A:BB2301
|
2.6
|
25.3
|
1.0
|
C3
|
A:BB2301
|
2.7
|
24.3
|
1.0
|
CD2
|
A:HIS174
|
3.0
|
11.7
|
1.0
|
CD2
|
A:HIS178
|
3.1
|
15.9
|
1.0
|
CE1
|
A:HIS178
|
3.1
|
16.6
|
1.0
|
CE1
|
A:HIS174
|
3.1
|
13.6
|
1.0
|
SG
|
A:OCS131
|
3.2
|
19.1
|
1.0
|
OD2
|
A:OCS131
|
3.2
|
18.5
|
1.0
|
NE2
|
A:GLN77
|
3.3
|
16.3
|
1.0
|
O
|
A:HOH518
|
3.8
|
16.3
|
1.0
|
OD1
|
A:OCS131
|
4.0
|
19.9
|
1.0
|
CD
|
A:GLN77
|
4.0
|
14.2
|
1.0
|
CB
|
A:OCS131
|
4.1
|
18.1
|
1.0
|
C5
|
A:BB2301
|
4.1
|
23.1
|
1.0
|
CG
|
A:HIS174
|
4.1
|
11.4
|
1.0
|
OE1
|
A:GLN77
|
4.2
|
14.3
|
1.0
|
ND1
|
A:HIS178
|
4.2
|
15.6
|
1.0
|
ND1
|
A:HIS174
|
4.2
|
13.3
|
1.0
|
CG
|
A:HIS178
|
4.2
|
14.7
|
1.0
|
OE2
|
A:GLU175
|
4.2
|
22.6
|
1.0
|
C6
|
A:BB2301
|
4.4
|
22.1
|
1.0
|
CA
|
A:OCS131
|
4.5
|
16.9
|
1.0
|
OE1
|
A:GLU175
|
4.6
|
22.9
|
1.0
|
C7
|
A:BB2301
|
4.6
|
21.8
|
1.0
|
O
|
A:HOH507
|
4.6
|
15.3
|
1.0
|
CD
|
A:GLU175
|
4.8
|
18.1
|
1.0
|
N
|
A:LEU132
|
4.9
|
16.9
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5jf1
Go back to
Zinc Binding Sites List in 5jf1
Zinc binding site 2 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn304
b:21.2
occ:1.00
|
NE2
|
A:HIS55
|
2.1
|
16.3
|
1.0
|
O
|
A:HOH586
|
2.3
|
28.1
|
1.0
|
CD2
|
A:HIS55
|
3.1
|
15.3
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
15.5
|
1.0
|
NE2
|
A:GLN51
|
4.1
|
22.1
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
14.9
|
1.0
|
CG
|
A:HIS55
|
4.2
|
14.1
|
1.0
|
O
|
A:HOH606
|
4.4
|
46.7
|
1.0
|
CG
|
A:GLN51
|
4.7
|
18.5
|
1.0
|
CG
|
A:MET61
|
4.8
|
27.5
|
1.0
|
CD
|
A:GLN51
|
4.8
|
20.5
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5jf1
Go back to
Zinc Binding Sites List in 5jf1
Zinc binding site 3 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn305
b:26.0
occ:1.00
|
NE2
|
A:HIS118
|
2.0
|
13.3
|
1.0
|
O
|
A:HOH593
|
2.3
|
34.1
|
1.0
|
O
|
A:HOH584
|
2.4
|
43.3
|
1.0
|
CD2
|
A:HIS118
|
3.0
|
12.2
|
1.0
|
CE1
|
A:HIS118
|
3.1
|
13.5
|
1.0
|
CG
|
A:HIS118
|
4.1
|
11.9
|
1.0
|
ND1
|
A:HIS118
|
4.1
|
12.7
|
1.0
|
O
|
A:HOH504
|
4.3
|
14.8
|
1.0
|
O
|
A:HOH542
|
4.5
|
23.4
|
1.0
|
CE1
|
A:HIS145
|
4.9
|
13.1
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5jf1
Go back to
Zinc Binding Sites List in 5jf1
Zinc binding site 4 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn306
b:19.8
occ:1.00
|
OE2
|
A:GLU190
|
1.9
|
26.3
|
1.0
|
O
|
A:HOH441
|
2.0
|
15.7
|
1.0
|
O
|
A:HOH475
|
2.2
|
13.3
|
1.0
|
CD
|
A:GLU190
|
2.6
|
27.9
|
1.0
|
OE1
|
A:GLU190
|
2.7
|
27.0
|
1.0
|
O
|
A:HOH418
|
3.7
|
41.5
|
1.0
|
O
|
A:HOH462
|
4.1
|
13.4
|
1.0
|
CG
|
A:GLU190
|
4.1
|
27.3
|
1.0
|
O
|
A:TYR185
|
4.2
|
14.1
|
1.0
|
O
|
A:ILE188
|
4.5
|
16.7
|
1.0
|
CA
|
A:GLU190
|
4.7
|
24.9
|
1.0
|
CB
|
A:GLU190
|
4.7
|
25.8
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5jf1
Go back to
Zinc Binding Sites List in 5jf1
Zinc binding site 5 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn307
b:17.5
occ:1.00
|
O
|
A:HOH504
|
1.8
|
14.8
|
1.0
|
O
|
A:ACT302
|
2.1
|
17.9
|
1.0
|
NE2
|
A:HIS145
|
2.1
|
13.9
|
1.0
|
C
|
A:ACT302
|
2.7
|
19.2
|
1.0
|
OXT
|
A:ACT302
|
2.7
|
20.8
|
1.0
|
CD2
|
A:HIS145
|
3.0
|
12.7
|
1.0
|
CE1
|
A:HIS145
|
3.1
|
13.1
|
1.0
|
O
|
A:HOH560
|
4.0
|
26.6
|
1.0
|
CH3
|
A:ACT302
|
4.2
|
19.8
|
1.0
|
CG
|
A:HIS145
|
4.2
|
12.8
|
1.0
|
ND1
|
A:HIS145
|
4.2
|
13.3
|
1.0
|
O
|
A:HOH430
|
4.2
|
26.9
|
1.0
|
CD2
|
A:HIS118
|
4.5
|
12.2
|
1.0
|
NE2
|
A:HIS118
|
4.9
|
13.3
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5jf1
Go back to
Zinc Binding Sites List in 5jf1
Zinc binding site 6 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn308
b:50.1
occ:1.00
|
NE2
|
A:HIS12
|
2.2
|
25.4
|
1.0
|
O
|
A:HOH414
|
2.3
|
31.1
|
1.0
|
O
|
A:HOH474
|
2.3
|
29.9
|
1.0
|
OD1
|
A:ASP18
|
2.4
|
22.0
|
1.0
|
O
|
A:HOH569
|
2.4
|
34.4
|
1.0
|
OD2
|
A:ASP18
|
2.5
|
20.8
|
1.0
|
CG
|
A:ASP18
|
2.7
|
20.3
|
1.0
|
CE1
|
A:HIS12
|
2.9
|
24.7
|
1.0
|
O
|
A:HOH619
|
3.2
|
25.6
|
1.0
|
CD2
|
A:HIS12
|
3.3
|
24.5
|
1.0
|
OD1
|
A:ASP15
|
3.9
|
22.2
|
1.0
|
O
|
A:LEU13
|
3.9
|
18.3
|
1.0
|
ND1
|
A:HIS12
|
4.1
|
25.4
|
1.0
|
CB
|
A:ASP18
|
4.2
|
19.0
|
1.0
|
CG
|
A:ASP15
|
4.3
|
22.2
|
1.0
|
CG
|
A:HIS12
|
4.4
|
23.5
|
1.0
|
OD2
|
A:ASP15
|
4.4
|
25.4
|
1.0
|
O
|
A:HOH624
|
4.4
|
41.3
|
1.0
|
O
|
A:HOH405
|
4.5
|
30.7
|
1.0
|
N
|
A:ASP15
|
4.5
|
17.4
|
1.0
|
N
|
A:ASP18
|
4.7
|
17.9
|
1.0
|
CA
|
A:ASP18
|
4.8
|
18.5
|
1.0
|
CA
|
A:ILE14
|
4.8
|
17.1
|
1.0
|
C
|
A:LEU13
|
4.9
|
18.5
|
1.0
|
O
|
A:HOH592
|
5.0
|
25.0
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5jf1
Go back to
Zinc Binding Sites List in 5jf1
Zinc binding site 7 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn309
b:54.4
occ:1.00
|
OE2
|
A:GLU47
|
2.3
|
32.4
|
1.0
|
O
|
A:HOH576
|
2.3
|
47.1
|
1.0
|
OE1
|
A:GLU43
|
2.7
|
42.6
|
1.0
|
CD
|
A:GLU47
|
3.1
|
26.6
|
1.0
|
OE1
|
A:GLU47
|
3.2
|
26.9
|
1.0
|
CD
|
A:GLU43
|
3.3
|
37.0
|
1.0
|
CG
|
A:GLU43
|
3.7
|
29.4
|
1.0
|
O
|
A:HOH404
|
3.9
|
40.5
|
1.0
|
NZ
|
A:LYS155
|
3.9
|
33.5
|
1.0
|
OE2
|
A:GLU43
|
4.2
|
45.1
|
1.0
|
CE
|
A:LYS155
|
4.4
|
31.5
|
1.0
|
CG
|
A:GLU47
|
4.5
|
21.6
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5jf1
Go back to
Zinc Binding Sites List in 5jf1
Zinc binding site 8 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Actinonin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn310
b:31.7
occ:1.00
|
OE2
|
A:GLU151
|
2.2
|
17.9
|
1.0
|
O
|
A:HOH557
|
2.6
|
34.1
|
1.0
|
CD
|
A:GLU151
|
2.9
|
18.5
|
1.0
|
OE1
|
A:GLU151
|
2.9
|
19.6
|
1.0
|
NZ
|
A:LYS159
|
3.8
|
23.6
|
1.0
|
NH2
|
A:ARG161
|
4.0
|
23.7
|
1.0
|
NE
|
A:ARG161
|
4.0
|
22.5
|
1.0
|
CG
|
A:GLU151
|
4.4
|
16.2
|
1.0
|
CZ
|
A:ARG161
|
4.4
|
24.1
|
1.0
|
CE
|
A:LYS159
|
4.5
|
21.6
|
1.0
|
CG1
|
A:VAL116
|
4.9
|
17.1
|
1.0
|
CD
|
A:ARG161
|
5.0
|
22.2
|
1.0
|
|
Reference:
S.Fieulaine,
R.Alves De Sousa,
L.Maigre,
K.Hamiche,
M.Alimi,
J.M.Bolla,
A.Taleb,
A.Denis,
J.M.Pages,
I.Artaud,
T.Meinnel,
C.Giglione.
A Unique Peptide Deformylase Platform to Rationally Design and Challenge Novel Active Compounds. Sci Rep V. 6 35429 2016.
ISSN: ESSN 2045-2322
PubMed: 27762275
DOI: 10.1038/SREP35429
Page generated: Sun Oct 27 18:48:28 2024
|