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Zinc in PDB 3ten: Holo Form of Carbon Disulfide Hydrolase

Protein crystallography data

The structure of Holo Form of Carbon Disulfide Hydrolase, PDB code: 3ten was solved by M.J.Smeulders, T.R.M.B.Barends, A.Pol, A.Scherer, M.H.Zandvoort, A.Udvarhelyi, A.Khadem, A.Menzel, J.Hermans, R.L.Shoeman, H.J.C.T.Wessels, L.P.Van Den Heuvel, L.Russ, I.Schlichting, M.S.M.Jetten, H.J.M.Op Den Camp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 204.950, 113.240, 87.140, 90.00, 90.00, 90.00
R / Rfree (%) 26.6 / 29.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Holo Form of Carbon Disulfide Hydrolase (pdb code 3ten). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Holo Form of Carbon Disulfide Hydrolase, PDB code: 3ten:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3ten

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Zinc binding site 1 out of 8 in the Holo Form of Carbon Disulfide Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Holo Form of Carbon Disulfide Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:28.6
occ:1.00
 O A:HOH206 2.0 21.8 1.0
NE2 A:HIS88 2.1 23.7 1.0
SG A:CYS35 2.2 23.9 1.0
SG A:CYS91 2.4 28.0 1.0
CD2 A:HIS88 2.9 24.3 1.0
CB A:CYS91 3.1 27.8 1.0
CE1 A:HIS88 3.2 24.0 1.0
CB A:CYS35 3.3 23.8 1.0
CA A:CYS91 3.4 27.9 1.0
N A:GLY92 3.8 28.6 1.0
CA A:GLY60 4.0 25.8 1.0
C A:CYS91 4.1 28.3 1.0
CB A:ASP37 4.1 24.4 1.0
N A:GLY60 4.1 25.7 1.0
CG A:HIS88 4.1 24.5 1.0
ND1 A:HIS88 4.3 23.7 1.0
OD2 A:ASP37 4.5 26.7 1.0
N A:CYS91 4.6 27.6 1.0
CA A:CYS35 4.7 23.6 1.0
C A:GLY60 4.8 25.9 1.0
CG A:ASP37 4.8 24.9 1.0
N A:MET93 5.0 29.6 1.0
N A:ASP37 5.0 24.2 1.0
CA A:GLY92 5.0 28.9 1.0

Zinc binding site 2 out of 8 in 3ten

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Zinc binding site 2 out of 8 in the Holo Form of Carbon Disulfide Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Holo Form of Carbon Disulfide Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn205

b:21.2
occ:1.00
 NE2 B:HIS88 2.0 23.7 1.0
O B:HOH206 2.0 14.2 1.0
SG B:CYS35 2.1 22.6 1.0
SG B:CYS91 2.3 26.9 1.0
CD2 B:HIS88 3.0 23.7 1.0
CE1 B:HIS88 3.0 24.0 1.0
CB B:CYS35 3.2 23.6 1.0
CB B:CYS91 3.3 27.7 1.0
CA B:CYS91 3.6 27.8 1.0
CB B:ASP37 3.9 24.1 1.0
N B:GLY92 3.9 28.6 1.0
OD2 B:ASP37 4.0 24.2 1.0
ND1 B:HIS88 4.1 23.7 1.0
CG B:HIS88 4.1 24.4 1.0
N B:GLY60 4.2 25.6 1.0
CA B:GLY60 4.2 25.8 1.0
C B:CYS91 4.2 28.2 1.0
CG B:ASP37 4.5 23.8 1.0
CA B:CYS35 4.6 23.6 1.0
N B:ASP37 4.7 24.1 1.0
N B:CYS91 4.8 27.6 1.0
C B:GLY60 4.9 25.9 1.0
CA B:ASP37 4.9 24.2 1.0

Zinc binding site 3 out of 8 in 3ten

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Zinc binding site 3 out of 8 in the Holo Form of Carbon Disulfide Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Holo Form of Carbon Disulfide Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn205

b:30.4
occ:1.00
 O C:HOH206 2.0 27.1 1.0
NE2 C:HIS88 2.2 23.8 1.0
SG C:CYS35 2.3 23.3 1.0
SG C:CYS91 2.3 27.8 1.0
CD2 C:HIS88 2.9 23.9 1.0
CB C:CYS91 3.1 27.9 1.0
CB C:CYS35 3.3 23.7 1.0
CE1 C:HIS88 3.3 23.8 1.0
CA C:CYS91 3.5 27.9 1.0
N C:GLY92 3.9 28.6 1.0
CB C:ASP37 4.0 24.3 1.0
CA C:GLY60 4.1 25.8 1.0
CG C:HIS88 4.1 24.4 1.0
N C:GLY60 4.1 25.7 1.0
C C:CYS91 4.2 28.3 1.0
OD2 C:ASP37 4.2 26.3 1.0
ND1 C:HIS88 4.3 23.9 1.0
CG C:ASP37 4.7 24.9 1.0
CA C:CYS35 4.7 23.6 1.0
N C:CYS91 4.7 27.5 1.0
C C:GLY60 4.8 26.0 1.0
N C:ASP37 4.9 24.1 1.0

Zinc binding site 4 out of 8 in 3ten

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Zinc binding site 4 out of 8 in the Holo Form of Carbon Disulfide Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Holo Form of Carbon Disulfide Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn205

b:22.9
occ:1.00
 O D:HOH206 2.0 18.6 1.0
NE2 D:HIS88 2.0 23.9 1.0
SG D:CYS35 2.2 22.8 1.0
SG D:CYS91 2.3 27.3 1.0
CD2 D:HIS88 3.0 23.7 1.0
CE1 D:HIS88 3.0 23.9 1.0
CB D:CYS91 3.2 27.9 1.0
CB D:CYS35 3.3 23.6 1.0
CA D:CYS91 3.5 27.9 1.0
N D:GLY92 3.8 28.6 1.0
CB D:ASP37 4.0 24.2 1.0
C D:CYS91 4.1 28.2 1.0
CG D:HIS88 4.1 24.4 1.0
ND1 D:HIS88 4.1 23.8 1.0
CA D:GLY60 4.1 25.8 1.0
N D:GLY60 4.2 25.6 1.0
OD2 D:ASP37 4.2 25.0 1.0
CG D:ASP37 4.6 24.2 1.0
N D:CYS91 4.7 27.5 1.0
CA D:CYS35 4.7 23.6 1.0
N D:ASP37 4.8 24.1 1.0
C D:GLY60 4.9 25.9 1.0
CA D:GLY92 5.0 28.9 1.0
CA D:ASP37 5.0 24.2 1.0

Zinc binding site 5 out of 8 in 3ten

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Zinc binding site 5 out of 8 in the Holo Form of Carbon Disulfide Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Holo Form of Carbon Disulfide Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn205

b:28.2
occ:1.00
 O E:HOH206 2.0 26.3 1.0
SG E:CYS35 2.2 23.4 1.0
NE2 E:HIS88 2.2 23.4 1.0
SG E:CYS91 2.2 28.1 1.0
CD2 E:HIS88 3.0 23.7 1.0
CB E:CYS91 3.2 28.1 1.0
CE1 E:HIS88 3.3 23.5 1.0
CB E:CYS35 3.3 23.6 1.0
CA E:CYS91 3.5 27.9 1.0
N E:GLY92 3.8 28.6 1.0
O E:HOH223 3.9 30.7 1.0
CB E:ASP37 4.0 24.3 1.0
CA E:GLY60 4.1 25.8 1.0
N E:GLY60 4.1 25.8 1.0
OD2 E:ASP37 4.1 26.1 1.0
C E:CYS91 4.1 28.3 1.0
CG E:HIS88 4.2 24.5 1.0
ND1 E:HIS88 4.3 23.7 1.0
CG E:ASP37 4.6 24.8 1.0
CA E:CYS35 4.7 23.6 1.0
N E:CYS91 4.7 27.6 1.0
N E:ASP37 4.8 24.1 1.0
C E:GLY60 4.9 25.9 1.0
CA E:GLY92 5.0 28.9 1.0
CA E:ASP37 5.0 24.2 1.0

Zinc binding site 6 out of 8 in 3ten

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Zinc binding site 6 out of 8 in the Holo Form of Carbon Disulfide Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Holo Form of Carbon Disulfide Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn205

b:24.0
occ:1.00
 O F:HOH206 2.0 20.5 1.0
NE2 F:HIS88 2.1 23.5 1.0
SG F:CYS35 2.1 23.7 1.0
SG F:CYS91 2.2 28.7 1.0
CE1 F:HIS88 3.0 24.0 1.0
CD2 F:HIS88 3.1 23.6 1.0
CB F:CYS91 3.2 27.9 1.0
CB F:CYS35 3.3 23.5 1.0
CA F:CYS91 3.5 27.9 1.0
CB F:ASP37 3.9 24.4 1.0
N F:GLY92 3.9 28.6 1.0
N F:GLY60 4.1 25.7 1.0
CA F:GLY60 4.1 25.8 1.0
ND1 F:HIS88 4.1 23.8 1.0
CG F:HIS88 4.2 24.4 1.0
C F:CYS91 4.2 28.3 1.0
OD2 F:ASP37 4.3 25.8 1.0
CG F:ASP37 4.5 24.6 1.0
CA F:CYS35 4.7 23.6 1.0
N F:ASP37 4.7 24.2 1.0
N F:CYS91 4.8 27.7 1.0
C F:GLY60 4.9 25.9 1.0
CA F:ASP37 4.9 24.3 1.0

Zinc binding site 7 out of 8 in 3ten

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Zinc binding site 7 out of 8 in the Holo Form of Carbon Disulfide Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Holo Form of Carbon Disulfide Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn205

b:27.3
occ:1.00
 NE2 G:HIS88 2.0 24.1 1.0
O G:HOH206 2.0 23.8 1.0
SG G:CYS35 2.2 24.2 1.0
SG G:CYS91 2.5 28.8 1.0
CD2 G:HIS88 2.9 24.2 1.0
CE1 G:HIS88 3.1 24.4 1.0
CB G:CYS35 3.2 23.6 1.0
CB G:CYS91 3.2 27.9 1.0
CA G:CYS91 3.5 27.9 1.0
N G:GLY92 3.9 28.6 1.0
CB G:ASP37 4.0 24.2 1.0
CA G:GLY60 4.0 25.8 1.0
CG G:HIS88 4.1 24.7 1.0
N G:GLY60 4.1 25.7 1.0
ND1 G:HIS88 4.1 24.0 1.0
C G:CYS91 4.2 28.3 1.0
OD2 G:ASP37 4.4 25.3 1.0
CG G:ASP37 4.6 24.5 1.0
CA G:CYS35 4.6 23.6 1.0
C G:GLY60 4.7 26.0 1.0
N G:CYS91 4.8 27.7 1.0
N G:ASP37 4.9 24.2 1.0

Zinc binding site 8 out of 8 in 3ten

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Zinc binding site 8 out of 8 in the Holo Form of Carbon Disulfide Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Holo Form of Carbon Disulfide Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn205

b:27.8
occ:1.00
 O H:HOH206 2.0 23.9 1.0
NE2 H:HIS88 2.1 23.1 1.0
SG H:CYS91 2.3 27.6 1.0
SG H:CYS35 2.3 24.2 1.0
CD2 H:HIS88 3.0 23.4 1.0
CE1 H:HIS88 3.1 23.6 1.0
CB H:CYS91 3.1 28.0 1.0
CB H:CYS35 3.3 23.8 1.0
CA H:CYS91 3.4 27.9 1.0
N H:GLY92 3.8 28.6 1.0
CB H:ASP37 4.1 24.4 1.0
C H:CYS91 4.1 28.3 1.0
CA H:GLY60 4.1 25.8 1.0
CG H:HIS88 4.1 24.4 1.0
N H:GLY60 4.2 25.7 1.0
ND1 H:HIS88 4.2 23.6 1.0
OD2 H:ASP37 4.6 25.2 1.0
N H:CYS91 4.6 27.6 1.0
CG H:ASP37 4.8 24.4 1.0
CA H:CYS35 4.8 23.7 1.0
C H:GLY60 4.8 26.0 1.0
N H:ASP37 4.9 24.1 1.0
CA H:GLY92 5.0 28.9 1.0

Reference:

M.J.Smeulders, T.R.Barends, A.Pol, A.Scherer, M.H.Zandvoort, A.Udvarhelyi, A.F.Khadem, A.Menzel, J.Hermans, R.L.Shoeman, H.J.Wessels, L.P.Van Den Heuvel, L.Russ, I.Schlichting, M.S.Jetten, H.J.Op Den Camp. Evolution of A New Enzyme For Carbon Disulphide Conversion By An Acidothermophilic Archaeon. Nature V. 478 412 2011.
ISSN: ISSN 0028-0836
PubMed: 22012399
DOI: 10.1038/NATURE10464
Page generated: Sat Oct 26 16:30:21 2024

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