Cobalt in PDB 8khq: Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine
Protein crystallography data
The structure of Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine, PDB code: 8khq
was solved by
J.Wang,
K.Ye,
X.Y.Wang,
W.P.Yan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.70 /
2.69
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.262,
119.114,
412.429,
90,
90,
90
|
R / Rfree (%)
|
20.1 /
24.3
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine
(pdb code 8khq). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the
Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine, PDB code: 8khq:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 8khq
Go back to
Cobalt Binding Sites List in 8khq
Cobalt binding site 1 out
of 4 in the Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co801
b:57.4
occ:1.00
|
NE2
|
A:HIS162
|
2.2
|
48.6
|
1.0
|
SG
|
A:CYS803
|
2.2
|
61.8
|
1.0
|
O
|
A:HOH940
|
2.2
|
69.3
|
1.0
|
NE2
|
A:HIS166
|
2.3
|
57.5
|
1.0
|
NE2
|
A:HIS71
|
2.3
|
60.4
|
1.0
|
NE2
|
A:HIS802
|
2.5
|
58.6
|
1.0
|
CE1
|
A:HIS162
|
3.0
|
54.5
|
1.0
|
CE1
|
A:HIS166
|
3.1
|
54.9
|
1.0
|
CD2
|
A:HIS71
|
3.1
|
52.2
|
1.0
|
CD2
|
A:HIS162
|
3.2
|
50.1
|
1.0
|
CE1
|
A:HIS71
|
3.3
|
55.7
|
1.0
|
CD2
|
A:HIS166
|
3.3
|
48.9
|
1.0
|
CD2
|
A:HIS802
|
3.4
|
54.8
|
1.0
|
CB
|
A:CYS803
|
3.4
|
69.0
|
1.0
|
CE1
|
A:HIS802
|
3.5
|
53.8
|
1.0
|
ND1
|
A:HIS162
|
4.2
|
51.7
|
1.0
|
ND1
|
A:HIS166
|
4.3
|
53.0
|
1.0
|
CG
|
A:HIS162
|
4.3
|
47.7
|
1.0
|
CG
|
A:HIS71
|
4.3
|
50.5
|
1.0
|
ND1
|
A:HIS71
|
4.4
|
56.4
|
1.0
|
CG
|
A:HIS166
|
4.4
|
48.6
|
1.0
|
CG
|
A:HIS802
|
4.6
|
56.1
|
1.0
|
ND1
|
A:HIS802
|
4.6
|
57.9
|
1.0
|
CA
|
A:CYS803
|
4.8
|
76.2
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 8khq
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Cobalt Binding Sites List in 8khq
Cobalt binding site 2 out
of 4 in the Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co801
b:55.6
occ:1.00
|
NE2
|
B:HIS162
|
2.2
|
45.6
|
1.0
|
NE2
|
B:HIS166
|
2.3
|
49.8
|
1.0
|
NE2
|
B:HIS71
|
2.3
|
53.8
|
1.0
|
O
|
B:HOH928
|
2.3
|
53.2
|
1.0
|
NE2
|
B:HIS802
|
2.3
|
72.1
|
1.0
|
SG
|
B:CYS803
|
2.6
|
72.5
|
1.0
|
CE1
|
B:HIS162
|
3.0
|
45.6
|
1.0
|
CD2
|
B:HIS71
|
3.1
|
52.0
|
1.0
|
CE1
|
B:HIS166
|
3.1
|
47.0
|
1.0
|
CD2
|
B:HIS162
|
3.3
|
46.8
|
1.0
|
CE1
|
B:HIS802
|
3.3
|
72.1
|
1.0
|
CD2
|
B:HIS802
|
3.3
|
72.1
|
1.0
|
CD2
|
B:HIS166
|
3.3
|
46.7
|
1.0
|
CE1
|
B:HIS71
|
3.4
|
55.9
|
1.0
|
CB
|
B:CYS803
|
3.6
|
72.2
|
1.0
|
ND1
|
B:HIS162
|
4.2
|
50.2
|
1.0
|
ND1
|
B:HIS166
|
4.3
|
49.7
|
1.0
|
CG
|
B:HIS71
|
4.3
|
55.2
|
1.0
|
CG
|
B:HIS162
|
4.3
|
49.8
|
1.0
|
ND1
|
B:HIS802
|
4.4
|
72.0
|
1.0
|
CG
|
B:HIS166
|
4.4
|
42.2
|
1.0
|
ND1
|
B:HIS71
|
4.4
|
56.3
|
1.0
|
CG
|
B:HIS802
|
4.4
|
72.0
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 8khq
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Cobalt Binding Sites List in 8khq
Cobalt binding site 3 out
of 4 in the Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co801
b:61.5
occ:1.00
|
NE2
|
C:HIS162
|
2.2
|
51.9
|
1.0
|
NE2
|
C:HIS166
|
2.2
|
58.5
|
1.0
|
NE2
|
C:HIS71
|
2.3
|
60.6
|
1.0
|
NE2
|
C:HIS802
|
2.4
|
72.8
|
1.0
|
SG
|
C:CYS803
|
2.6
|
72.7
|
1.0
|
CE1
|
C:HIS166
|
3.1
|
59.3
|
1.0
|
CE1
|
C:HIS162
|
3.1
|
57.6
|
1.0
|
CD2
|
C:HIS71
|
3.1
|
53.4
|
1.0
|
CD2
|
C:HIS162
|
3.2
|
51.5
|
1.0
|
CD2
|
C:HIS166
|
3.3
|
54.6
|
1.0
|
CD2
|
C:HIS802
|
3.3
|
72.8
|
1.0
|
CE1
|
C:HIS71
|
3.4
|
56.6
|
1.0
|
CE1
|
C:HIS802
|
3.4
|
72.8
|
1.0
|
CB
|
C:CYS803
|
3.6
|
72.6
|
1.0
|
ND1
|
C:HIS162
|
4.2
|
57.0
|
1.0
|
ND1
|
C:HIS166
|
4.2
|
53.6
|
1.0
|
CG
|
C:HIS162
|
4.3
|
51.5
|
1.0
|
CG
|
C:HIS71
|
4.3
|
58.4
|
1.0
|
CG
|
C:HIS166
|
4.4
|
54.7
|
1.0
|
ND1
|
C:HIS71
|
4.4
|
62.3
|
1.0
|
ND1
|
C:HIS802
|
4.5
|
72.7
|
1.0
|
CG
|
C:HIS802
|
4.5
|
72.7
|
1.0
|
OH
|
C:TYR406
|
4.9
|
56.3
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 8khq
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Cobalt Binding Sites List in 8khq
Cobalt binding site 4 out
of 4 in the Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Bifunctional Sulfoxide Synthase OVOA_TH2 in Complex with Histidine and Cysteine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co801
b:89.2
occ:1.00
|
NE2
|
D:HIS162
|
2.2
|
84.4
|
1.0
|
SG
|
D:CYS803
|
2.3
|
93.6
|
1.0
|
NE2
|
D:HIS71
|
2.3
|
90.0
|
1.0
|
NE2
|
D:HIS802
|
2.3
|
98.5
|
1.0
|
NE2
|
D:HIS166
|
2.4
|
106.1
|
1.0
|
CE1
|
D:HIS162
|
3.0
|
87.3
|
1.0
|
CE1
|
D:HIS802
|
3.0
|
94.6
|
1.0
|
CD2
|
D:HIS71
|
3.2
|
97.9
|
1.0
|
CE1
|
D:HIS71
|
3.3
|
93.8
|
1.0
|
CD2
|
D:HIS162
|
3.3
|
86.5
|
1.0
|
CE1
|
D:HIS166
|
3.4
|
101.9
|
1.0
|
CD2
|
D:HIS166
|
3.4
|
95.9
|
1.0
|
CD2
|
D:HIS802
|
3.5
|
100.2
|
1.0
|
CB
|
D:CYS803
|
3.7
|
109.5
|
1.0
|
ND1
|
D:HIS162
|
4.1
|
86.8
|
1.0
|
ND1
|
D:HIS802
|
4.2
|
93.5
|
1.0
|
CG
|
D:HIS162
|
4.4
|
83.2
|
1.0
|
ND1
|
D:HIS71
|
4.4
|
94.0
|
1.0
|
CG
|
D:HIS71
|
4.4
|
90.9
|
1.0
|
ND1
|
D:HIS166
|
4.5
|
98.8
|
1.0
|
CG
|
D:HIS802
|
4.5
|
100.6
|
1.0
|
CG
|
D:HIS166
|
4.5
|
95.6
|
1.0
|
OH
|
D:TYR406
|
4.9
|
81.5
|
1.0
|
|
Reference:
X.Wang,
S.Hu,
J.Wang,
T.Zhang,
K.Ye,
A.Wen,
G.Zhu,
A.Vegas,
L.Zhang,
W.Yan,
X.Liu,
P.Liu.
Biochemical and Structural Characterization of OVOATH2: A Mononuclear Nonheme Iron Enzyme From Hydrogenimonas Thermophila For Ovothiol Biosynthesis Acs Catalysis 15417 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C04026
Page generated: Tue Jul 30 19:57:57 2024
|