Chlorine in PDB 6ond: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced

All present enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced, PDB code: 6ond was solved by E.C.Wittenborn, S.E.Cohen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.27 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.790, 144.150, 123.690, 90.00, 98.50, 90.00
R / Rfree (%) 14.9 / 17.6

Other elements in 6ond:

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Iron (Fe) 40 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced (pdb code 6ond). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced, PDB code: 6ond:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6ond

Go back to Chlorine Binding Sites List in 6ond
Chlorine binding site 1 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl706

b:22.6
occ:1.00
 O A:HOH825 3.0 30.5 1.0
OG A:SER541 3.1 20.5 1.0
NH2 A:ARG176 3.4 16.9 1.0
CA A:GLY598 3.7 16.6 1.0
CB A:SER541 3.7 19.0 1.0
O A:HOH816 3.8 25.9 1.0
O A:VAL597 3.8 18.2 1.0
N A:GLY598 4.0 17.5 1.0
C A:VAL597 4.0 19.0 1.0
OD2 A:ASP539 4.2 23.8 1.0
CD2 A:LEU179 4.3 21.4 1.0
O A:HOH1204 4.5 41.4 1.0
CZ A:ARG176 4.6 15.2 1.0
O A:HOH1189 4.7 36.8 1.0
O A:HOH1158 4.8 26.6 1.0
C A:GLY598 5.0 16.3 1.0
O A:HOH1183 5.0 23.5 1.0
CA A:VAL597 5.0 13.8 1.0

Chlorine binding site 2 out of 5 in 6ond

Go back to Chlorine Binding Sites List in 6ond
Chlorine binding site 2 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl707

b:28.9
occ:1.00
 O A:HOH1076 2.9 39.0 1.0
O A:HOH807 3.2 22.6 1.0
NE A:ARG621 3.2 19.4 1.0
NE2 A:GLN594 3.3 31.6 1.0
NH1 A:ARG621 3.3 15.8 1.0
CD2 A:HIS617 3.5 32.8 1.0
CZ A:ARG621 3.7 20.6 1.0
O A:GLY598 3.8 14.5 1.0
OE1 A:GLN594 3.9 37.6 1.0
CG A:PRO570 3.9 23.2 1.0
O A:HOH952 4.0 18.7 1.0
CD A:GLN594 4.0 36.0 1.0
CG A:HIS617 4.4 26.4 1.0
CD A:ARG621 4.4 23.2 1.0
NE2 A:HIS617 4.5 34.8 1.0
CG A:ARG621 4.6 25.5 1.0
MG A:MG704 4.6 23.5 1.0
CB A:HIS617 4.7 21.9 1.0
O A:HOH1176 4.7 20.5 1.0
CB A:PRO570 4.7 20.3 1.0
CA A:ALA599 4.9 15.9 1.0
C A:GLY598 4.9 16.3 1.0
NH2 A:ARG621 5.0 16.7 1.0

Chlorine binding site 3 out of 5 in 6ond

Go back to Chlorine Binding Sites List in 6ond
Chlorine binding site 3 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl706

b:25.7
occ:1.00
 O B:HOH1249 2.7 38.5 1.0
OG B:SER409 3.2 30.2 1.0
N B:SER409 3.3 21.1 1.0
CB B:SER409 3.7 18.3 1.0
CA B:VAL408 3.9 23.2 0.5
CA B:VAL408 4.0 23.0 0.5
C B:VAL408 4.1 20.8 0.5
CA B:SER409 4.1 16.3 1.0
C B:VAL408 4.1 20.9 0.5
O B:HOH1033 4.2 27.8 1.0
CB B:VAL408 4.3 24.0 0.5
O B:PRO407 4.6 22.6 1.0
CG1 B:VAL408 4.6 26.9 0.5
O B:HOH897 4.6 45.9 1.0
CG1 B:VAL408 4.7 24.0 0.5
O B:HOH1246 4.7 44.0 1.0
CB B:VAL408 4.7 24.3 0.5
O B:HOH947 4.8 24.7 1.0
O B:HOH1280 4.9 37.7 1.0
CG2 B:VAL408 4.9 25.0 0.5

Chlorine binding site 4 out of 5 in 6ond

Go back to Chlorine Binding Sites List in 6ond
Chlorine binding site 4 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl707

b:24.9
occ:1.00
 O B:HOH817 3.1 29.7 1.0
OG B:SER541 3.4 17.5 1.0
O B:HOH1284 3.4 24.2 1.0
NH2 B:ARG176 3.4 18.2 1.0
CA B:GLY598 3.7 14.9 1.0
O B:HOH988 3.8 21.0 1.0
O B:VAL597 3.9 15.8 1.0
CB B:SER541 4.0 16.9 1.0
CD2 B:LEU179 4.0 24.2 1.0
N B:GLY598 4.0 16.9 1.0
C B:VAL597 4.1 16.2 1.0
OD2 B:ASP539 4.2 21.4 1.0
CZ B:ARG176 4.5 20.9 1.0
O B:HOH1023 4.7 29.3 1.0
O B:HOH886 4.8 23.5 1.0

Chlorine binding site 5 out of 5 in 6ond

Go back to Chlorine Binding Sites List in 6ond
Chlorine binding site 5 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl706

b:25.8
occ:1.00
 OG D:SER541 3.0 24.4 1.0
O D:HOH814 3.1 32.0 1.0
NH2 D:ARG176 3.4 19.9 1.0
O D:HOH849 3.7 24.3 1.0
CB D:SER541 3.7 20.7 1.0
CA D:GLY598 3.7 18.8 1.0
O D:VAL597 3.8 21.4 1.0
N D:GLY598 4.0 16.6 1.0
C D:VAL597 4.0 18.1 1.0
OD2 D:ASP539 4.1 27.9 1.0
CD2 D:LEU179 4.2 22.0 1.0
CZ D:ARG176 4.5 24.9 1.0
O D:HOH1158 4.9 32.0 1.0
CA D:VAL597 4.9 18.4 1.0
CG D:ASP539 4.9 22.4 1.0

Reference:

E.C.Wittenborn, S.E.Cohen, M.Merrouch, C.Leger, V.Fourmond, S.Dementin, C.L.Drennan. Structural Insight Into Metallocofactor Maturation in Carbon Monoxide Dehydrogenase. J.Biol.Chem. V. 294 13017 2019.
ISSN: ESSN 1083-351X
PubMed: 31296570
DOI: 10.1074/JBC.RA119.009610
Page generated: Sat Dec 12 13:27:23 2020

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