Zinc in PDB 7qg4: Apo Crystal Structure of A Mutant of SN243 (D415N)
Protein crystallography data
The structure of Apo Crystal Structure of A Mutant of SN243 (D415N), PDB code: 7qg4
was solved by
S.Neun,
P.Brear,
E.Campbell,
K.Omari,
O.Wagner,
M.Hyvonen,
F.Hollfelder,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
75.77 /
2.08
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.396,
82.413,
92.077,
113.33,
90.43,
90.94
|
R / Rfree (%)
|
24.9 /
25.1
|
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
26;
Binding sites:
The binding sites of Zinc atom in the Apo Crystal Structure of A Mutant of SN243 (D415N)
(pdb code 7qg4). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 26 binding sites of Zinc where determined in the
Apo Crystal Structure of A Mutant of SN243 (D415N), PDB code: 7qg4:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 1 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn801
b:48.4
occ:1.00
|
O
|
A:HOH901
|
2.0
|
28.1
|
1.0
|
O
|
A:HOH1120
|
2.1
|
33.7
|
1.0
|
O
|
A:HOH1116
|
2.1
|
14.1
|
1.0
|
O
|
A:HOH1068
|
2.3
|
14.1
|
1.0
|
NE2
|
A:HIS505
|
2.4
|
37.2
|
1.0
|
OE1
|
A:GLU247
|
2.8
|
48.4
|
1.0
|
CE1
|
A:HIS505
|
3.3
|
36.5
|
1.0
|
CD2
|
A:HIS505
|
3.4
|
39.8
|
1.0
|
OD2
|
A:ASP504
|
3.5
|
49.7
|
1.0
|
CD
|
A:GLU247
|
4.0
|
54.3
|
1.0
|
OD1
|
A:ASP504
|
4.3
|
37.2
|
1.0
|
CG
|
A:ASP504
|
4.3
|
33.5
|
1.0
|
ND1
|
A:HIS505
|
4.4
|
25.3
|
1.0
|
CG
|
A:HIS505
|
4.5
|
30.2
|
1.0
|
OE2
|
A:GLU247
|
4.6
|
49.2
|
1.0
|
|
Zinc binding site 2 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 2 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn802
b:58.0
occ:1.00
|
O
|
A:ARG763
|
2.2
|
27.0
|
1.0
|
O
|
A:HOH999
|
2.4
|
18.3
|
1.0
|
O
|
A:THR266
|
2.5
|
23.6
|
1.0
|
O
|
A:HOH931
|
2.7
|
26.5
|
1.0
|
O
|
A:ASP760
|
2.7
|
29.5
|
1.0
|
OE1
|
A:GLN759
|
2.8
|
22.6
|
1.0
|
C
|
A:ARG763
|
3.4
|
29.5
|
1.0
|
C
|
A:ASP760
|
3.5
|
30.9
|
1.0
|
CB
|
A:GLN759
|
3.6
|
28.5
|
1.0
|
C
|
A:THR266
|
3.7
|
21.1
|
1.0
|
CD
|
A:GLN759
|
3.7
|
29.1
|
1.0
|
O
|
A:GLY765
|
3.8
|
30.2
|
1.0
|
N
|
A:ASP760
|
3.9
|
33.5
|
1.0
|
CG
|
A:GLN759
|
4.0
|
25.0
|
1.0
|
N
|
A:ARG763
|
4.2
|
21.8
|
1.0
|
C
|
A:GLN759
|
4.3
|
33.6
|
1.0
|
CA
|
A:ARG763
|
4.3
|
29.7
|
1.0
|
CA
|
A:ASP760
|
4.3
|
31.9
|
1.0
|
N
|
A:SER761
|
4.4
|
28.3
|
1.0
|
N
|
A:PRO764
|
4.4
|
24.3
|
1.0
|
CA
|
A:THR266
|
4.4
|
19.1
|
1.0
|
C
|
A:PRO764
|
4.4
|
26.4
|
1.0
|
CA
|
A:PRO764
|
4.4
|
23.0
|
1.0
|
CA
|
A:SER761
|
4.5
|
23.3
|
1.0
|
CA
|
A:GLN759
|
4.5
|
34.4
|
1.0
|
CD
|
A:PRO268
|
4.5
|
24.6
|
1.0
|
C
|
A:SER761
|
4.6
|
28.0
|
1.0
|
CB
|
A:ARG763
|
4.6
|
24.8
|
1.0
|
CB
|
A:THR266
|
4.6
|
21.3
|
1.0
|
N
|
A:GLU267
|
4.6
|
20.9
|
1.0
|
O
|
A:PRO764
|
4.7
|
23.8
|
1.0
|
OE2
|
A:GLU768
|
4.7
|
40.4
|
1.0
|
CA
|
A:GLU267
|
4.7
|
22.1
|
1.0
|
O
|
A:SER761
|
4.7
|
27.5
|
1.0
|
N
|
A:GLY765
|
4.7
|
22.7
|
1.0
|
O
|
A:GLN759
|
4.9
|
35.7
|
1.0
|
NE2
|
A:GLN759
|
4.9
|
25.0
|
1.0
|
C
|
A:GLY765
|
4.9
|
28.4
|
1.0
|
N
|
A:ASP762
|
5.0
|
24.0
|
1.0
|
|
Zinc binding site 3 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 3 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn803
b:85.9
occ:1.00
|
O
|
A:GLU67
|
2.2
|
63.8
|
1.0
|
OE1
|
A:GLU72
|
2.5
|
57.6
|
1.0
|
OD1
|
A:ASN63
|
2.5
|
62.4
|
1.0
|
OD1
|
A:ASN65
|
2.5
|
68.2
|
1.0
|
OD1
|
A:ASP69
|
2.6
|
58.3
|
1.0
|
OD1
|
A:ASP61
|
2.7
|
59.5
|
1.0
|
OE2
|
A:GLU72
|
3.0
|
57.2
|
1.0
|
CD
|
A:GLU72
|
3.1
|
57.1
|
1.0
|
CG
|
A:ASN65
|
3.2
|
62.3
|
1.0
|
CG
|
A:ASN63
|
3.4
|
59.7
|
1.0
|
C
|
A:GLU67
|
3.4
|
63.7
|
1.0
|
ND2
|
A:ASN65
|
3.6
|
65.0
|
1.0
|
N
|
A:ASP69
|
3.6
|
56.0
|
1.0
|
ND2
|
A:ASN63
|
3.6
|
51.9
|
1.0
|
CG
|
A:ASP69
|
3.7
|
60.3
|
1.0
|
CG
|
A:ASP61
|
3.8
|
64.9
|
1.0
|
CA
|
A:LEU68
|
4.0
|
58.3
|
1.0
|
N
|
A:LEU68
|
4.1
|
60.5
|
1.0
|
C
|
A:LEU68
|
4.2
|
60.8
|
1.0
|
CB
|
A:ASP69
|
4.2
|
55.6
|
1.0
|
N
|
A:GLU67
|
4.4
|
57.8
|
1.0
|
CA
|
A:ASP61
|
4.4
|
57.4
|
1.0
|
CB
|
A:ASN65
|
4.4
|
63.4
|
1.0
|
N
|
A:ASN65
|
4.5
|
59.5
|
1.0
|
CA
|
A:GLU67
|
4.5
|
67.7
|
1.0
|
CG
|
A:GLU72
|
4.5
|
53.2
|
1.0
|
CA
|
A:ASP69
|
4.5
|
54.9
|
1.0
|
CB
|
A:ASP61
|
4.5
|
59.2
|
1.0
|
OD2
|
A:ASP69
|
4.6
|
61.2
|
1.0
|
N
|
A:ASN63
|
4.7
|
60.9
|
1.0
|
OD2
|
A:ASP61
|
4.7
|
71.2
|
1.0
|
C
|
A:ASP61
|
4.7
|
58.6
|
1.0
|
CB
|
A:ASN63
|
4.8
|
54.2
|
1.0
|
N
|
A:LEU62
|
4.8
|
54.6
|
1.0
|
N
|
A:ASP64
|
4.8
|
64.1
|
1.0
|
CA
|
A:ASN65
|
4.9
|
64.4
|
1.0
|
N
|
A:GLY66
|
4.9
|
60.5
|
1.0
|
|
Zinc binding site 4 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 4 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn804
b:83.6
occ:1.00
|
NE2
|
A:HIS131
|
2.4
|
55.8
|
1.0
|
CD2
|
A:HIS131
|
3.2
|
48.0
|
1.0
|
O
|
A:HIS129
|
3.4
|
47.0
|
1.0
|
CE1
|
A:HIS131
|
3.4
|
47.8
|
1.0
|
CB
|
A:HIS129
|
3.5
|
53.3
|
1.0
|
CA
|
A:HIS129
|
4.0
|
56.0
|
1.0
|
C
|
A:HIS129
|
4.1
|
51.4
|
1.0
|
O
|
A:GLU93
|
4.1
|
53.1
|
1.0
|
CB
|
A:GLU93
|
4.2
|
50.4
|
1.0
|
CD1
|
A:ILE179
|
4.3
|
40.6
|
1.0
|
CG
|
A:HIS129
|
4.4
|
54.0
|
1.0
|
CG
|
A:GLU93
|
4.4
|
58.2
|
1.0
|
CG
|
A:HIS131
|
4.4
|
48.0
|
1.0
|
CA
|
A:GLU93
|
4.4
|
50.3
|
1.0
|
ND1
|
A:HIS131
|
4.5
|
50.0
|
1.0
|
ND1
|
A:HIS129
|
4.5
|
53.0
|
1.0
|
C
|
A:GLU93
|
4.7
|
54.7
|
1.0
|
CE
|
A:MET89
|
4.7
|
42.4
|
1.0
|
CG1
|
A:ILE179
|
4.8
|
49.9
|
1.0
|
CD2
|
A:LEU97
|
4.9
|
38.3
|
1.0
|
CB
|
A:ILE179
|
4.9
|
54.5
|
1.0
|
|
Zinc binding site 5 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 5 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn805
b:89.7
occ:1.00
|
OE1
|
A:GLU754
|
3.6
|
74.2
|
1.0
|
CG
|
A:GLU754
|
4.2
|
45.9
|
1.0
|
OD1
|
A:ASP771
|
4.3
|
42.5
|
1.0
|
OD2
|
A:ASP771
|
4.3
|
39.5
|
1.0
|
CD
|
A:GLU754
|
4.3
|
62.8
|
1.0
|
CG
|
A:ASP771
|
4.7
|
42.5
|
1.0
|
CB
|
A:GLU754
|
4.8
|
34.8
|
1.0
|
|
Zinc binding site 6 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 6 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn806
b:64.5
occ:1.00
|
OD2
|
A:ASP494
|
3.3
|
30.9
|
1.0
|
OD1
|
A:ASP494
|
3.4
|
55.5
|
1.0
|
OD2
|
A:ASP492
|
3.6
|
38.9
|
1.0
|
CG
|
A:ASP494
|
3.7
|
40.4
|
1.0
|
CG
|
A:ASP492
|
4.5
|
45.0
|
1.0
|
OD1
|
A:ASP492
|
4.6
|
57.2
|
1.0
|
CB
|
A:ASP494
|
5.0
|
35.4
|
1.0
|
|
Zinc binding site 7 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 7 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn807
b:42.0
occ:1.00
|
OE1
|
A:GLU551
|
2.1
|
40.7
|
1.0
|
OE2
|
A:GLU551
|
2.6
|
40.2
|
1.0
|
CD
|
A:GLU551
|
2.6
|
40.3
|
1.0
|
O
|
A:HOH909
|
2.8
|
25.3
|
1.0
|
O
|
A:HOH902
|
3.4
|
17.2
|
1.0
|
CG
|
A:GLU551
|
4.1
|
31.9
|
1.0
|
OE2
|
A:GLU547
|
4.3
|
33.9
|
1.0
|
CB
|
A:GLU551
|
4.6
|
32.1
|
1.0
|
|
Zinc binding site 8 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 8 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn808
b:50.3
occ:1.00
|
OE1
|
A:GLU672
|
2.0
|
50.1
|
1.0
|
NE2
|
A:HIS603
|
2.0
|
28.9
|
1.0
|
CE1
|
A:HIS603
|
2.9
|
33.7
|
1.0
|
CD
|
A:GLU672
|
2.9
|
45.4
|
1.0
|
CD2
|
A:HIS603
|
3.1
|
28.2
|
1.0
|
OE2
|
A:GLU672
|
3.2
|
42.0
|
1.0
|
ND1
|
A:HIS603
|
4.0
|
31.1
|
1.0
|
CG
|
A:HIS603
|
4.2
|
32.8
|
1.0
|
CG
|
A:GLU672
|
4.3
|
34.2
|
1.0
|
NE1
|
A:TRP658
|
4.3
|
24.7
|
1.0
|
CZ2
|
A:TRP658
|
4.7
|
29.8
|
1.0
|
CE2
|
A:TRP658
|
4.8
|
25.0
|
1.0
|
O
|
A:SER596
|
4.9
|
49.0
|
1.0
|
|
Zinc binding site 9 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 9 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn809
b:83.1
occ:1.00
|
OE2
|
A:GLU289
|
2.4
|
54.3
|
1.0
|
O
|
A:HOH979
|
2.8
|
54.3
|
1.0
|
OE1
|
A:GLU289
|
3.1
|
47.2
|
1.0
|
CD
|
A:GLU289
|
3.1
|
50.8
|
1.0
|
OE2
|
A:GLU286
|
3.5
|
41.3
|
1.0
|
O
|
A:HOH959
|
3.6
|
42.2
|
1.0
|
OE1
|
A:GLU286
|
3.6
|
49.1
|
1.0
|
CD
|
A:GLU286
|
4.0
|
46.0
|
1.0
|
CG
|
A:GLU289
|
4.6
|
35.2
|
1.0
|
|
Zinc binding site 10 out
of 26 in 7qg4
Go back to
Zinc Binding Sites List in 7qg4
Zinc binding site 10 out
of 26 in the Apo Crystal Structure of A Mutant of SN243 (D415N)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Apo Crystal Structure of A Mutant of SN243 (D415N) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn810
b:97.8
occ:1.00
|
OD1
|
A:ASP692
|
2.1
|
55.4
|
1.0
|
OG
|
A:SER694
|
2.3
|
52.1
|
1.0
|
OD2
|
A:ASP692
|
2.6
|
60.4
|
1.0
|
CG
|
A:ASP692
|
2.7
|
54.3
|
1.0
|
CB
|
A:SER694
|
3.5
|
39.8
|
1.0
|
OE2
|
A:GLU523
|
3.6
|
61.1
|
1.0
|
CB
|
A:ASP692
|
4.2
|
44.7
|
1.0
|
N
|
A:SER694
|
4.3
|
36.3
|
1.0
|
CD
|
A:GLU523
|
4.5
|
48.2
|
1.0
|
CA
|
A:SER694
|
4.5
|
34.9
|
1.0
|
OE1
|
A:GLU523
|
4.5
|
45.0
|
1.0
|
CD
|
A:PRO693
|
4.5
|
40.8
|
1.0
|
CA
|
A:ASP692
|
4.8
|
48.1
|
1.0
|
CG
|
A:PRO693
|
4.8
|
36.3
|
1.0
|
|
Reference:
S.Neun,
P.Brear,
E.Campbell,
K.Omari,
O.Wagner,
M.Hyvonen,
F.Hollfelder.
Functional Metagenomic Screening in Microfluidic Droplets Identifies A Beta-Glucuronidase in An Unprecedented Sequence Neighbourhood To Be Published.
Page generated: Wed Oct 30 09:52:55 2024
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