Chlorine in PDB 8pvm: Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D

Enzymatic activity of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D

All present enzymatic activity of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D:
1.12.7.2;

Protein crystallography data

The structure of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D, PDB code: 8pvm was solved by J.Duan, E.Hofmann, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.06 / 1.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.65, 69.83, 102.89, 90, 102.74, 90
R / Rfree (%) 14.3 / 17.5

Other elements in 8pvm:

The structure of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Iron (Fe) 40 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D (pdb code 8pvm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D, PDB code: 8pvm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8pvm

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Chlorine binding site 1 out of 6 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl613

b:36.8
occ:1.00
 N A:GLN366 3.4 20.9 1.0
CB A:GLN366 3.6 27.4 1.0
CD A:PRO365 3.7 22.3 1.0
N A:PRO365 3.8 20.4 1.0
CB A:ARG364 3.9 18.7 1.0
CG A:GLN366 3.9 34.2 1.0
CA A:GLN366 4.1 22.4 1.0
CZ A:PHE570 4.1 20.9 1.0
C A:ARG364 4.1 18.6 1.0
CD A:ARG364 4.3 22.0 1.0
C A:PRO365 4.4 21.5 1.0
CB A:PRO365 4.4 23.1 1.0
CA A:PRO365 4.4 21.3 1.0
CA A:ARG364 4.4 18.4 1.0
CG A:ARG364 4.4 19.8 1.0
CG A:PRO365 4.4 23.6 1.0
O A:HOH1112 4.5 48.6 1.0
NH1 A:ARG364 4.7 30.2 1.0
O A:ARG364 4.8 19.4 1.0
CD A:GLN366 4.9 41.1 1.0
CE2 A:PHE570 4.9 21.0 1.0
C A:GLN366 4.9 20.4 1.0
CE1 A:PHE570 5.0 20.3 1.0
NE2 A:GLN366 5.0 43.1 1.0

Chlorine binding site 2 out of 6 in 8pvm

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Chlorine binding site 2 out of 6 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl614

b:24.9
occ:1.00
 O A:HOH1189 2.8 30.5 1.0
ND1 A:HIS511 3.0 17.8 1.0
ND2 A:ASN106 3.1 19.2 1.0
N A:HIS511 3.2 17.4 1.0
CD A:ARG382 3.5 16.4 1.0
CB A:HIS511 3.8 18.5 1.0
CG A:HIS511 3.8 18.2 1.0
CG A:ARG382 3.8 16.2 1.0
CA A:PRO510 4.0 15.4 1.0
O A:HOH937 4.0 39.0 1.0
CD2 A:LEU240 4.0 21.6 1.0
CE1 A:HIS511 4.1 18.5 1.0
CA A:HIS511 4.1 18.5 1.0
C A:PRO510 4.1 16.8 1.0
CG A:ASN106 4.1 20.3 1.0
O A:HOH893 4.2 32.9 1.0
OD1 A:ASN106 4.2 21.3 1.0
CD A:ARG103 4.6 18.0 1.0
CD1 A:LEU240 4.6 21.4 1.0
O A:HIS511 4.7 23.2 1.0
NE A:ARG103 4.7 17.8 1.0
CB A:PRO510 4.7 16.9 1.0
O A:GLN509 4.7 16.1 1.0
NE A:ARG382 4.8 15.7 1.0
CB A:ARG382 4.8 14.3 1.0
C A:HIS511 4.9 21.6 1.0
CG A:LEU240 5.0 20.0 1.0

Chlorine binding site 3 out of 6 in 8pvm

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Chlorine binding site 3 out of 6 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl615

b:25.3
occ:0.19
 N4 A:402601 0.1 11.1 0.8
C4 A:402601 1.3 12.8 0.8
OG A:SER232 2.9 16.6 1.0
N A:SER232 3.0 14.7 1.0
FE1 A:402601 3.2 14.2 0.8
CB A:SER232 3.4 15.9 1.0
C5 A:402601 3.4 15.2 0.8
CD A:PRO231 3.4 14.8 1.0
N A:PRO231 3.4 14.1 1.0
CB A:ALA230 3.5 14.0 1.0
CG A:PRO231 3.5 17.4 1.0
CB A:CYS503 3.5 14.1 1.0
CB A:PRO231 3.6 17.0 1.0
O5 A:402601 3.7 15.5 0.8
C3 A:402601 3.7 12.3 0.8
CA A:SER232 3.8 14.2 1.0
CG A:PRO354 3.8 14.0 1.0
S1 A:402601 3.8 15.1 0.8
CA A:PRO231 3.8 15.4 1.0
C A:PRO231 3.9 15.5 1.0
CA A:GLY418 3.9 14.6 1.0
C A:ALA230 4.0 14.7 1.0
CD A:PRO354 4.0 14.3 1.0
SG A:CYS503 4.2 13.5 1.0
CA A:ALA230 4.3 14.4 1.0
N A:GLY418 4.5 14.4 1.0
O3 A:402601 4.6 15.0 0.8
FE2 A:402601 4.7 16.4 0.8
O A:ALA230 4.8 16.0 1.0
CA A:CYS503 4.9 14.2 1.0
C7 A:402601 4.9 14.7 0.8
CB A:PRO354 4.9 14.1 1.0
C A:SER232 4.9 15.6 1.0
C A:CYS503 5.0 13.1 1.0

Chlorine binding site 4 out of 6 in 8pvm

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Chlorine binding site 4 out of 6 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl615

b:28.6
occ:1.00
 O B:HOH1257 3.3 42.7 1.0
N B:GLN366 3.3 16.4 1.0
CB B:GLN366 3.6 21.6 1.0
CD B:PRO365 3.7 18.9 1.0
N B:PRO365 3.7 17.1 1.0
CB B:ARG364 3.7 15.6 1.0
CG B:GLN366 3.8 27.9 1.0
CA B:GLN366 4.0 18.1 1.0
C B:ARG364 4.1 15.1 1.0
CZ B:PHE570 4.1 20.6 1.0
C B:PRO365 4.3 16.7 1.0
CA B:PRO365 4.3 17.4 1.0
CB B:PRO365 4.3 18.3 1.0
CA B:ARG364 4.3 14.5 1.0
CG B:ARG364 4.4 16.4 1.0
CD B:ARG364 4.4 18.4 1.0
CG B:PRO365 4.4 19.4 1.0
O B:HOH1219 4.4 43.4 1.0
NH1 B:ARG364 4.6 27.6 1.0
O B:ARG364 4.7 14.8 1.0
C B:GLN366 4.8 15.5 1.0
CE2 B:PHE570 4.8 19.6 1.0
N B:MET367 4.9 13.3 1.0

Chlorine binding site 5 out of 6 in 8pvm

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Chlorine binding site 5 out of 6 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl616

b:21.8
occ:1.00
 O B:HOH1190 2.8 19.2 1.0
ND1 B:HIS511 2.9 14.9 1.0
ND2 B:ASN106 2.9 21.1 1.0
N B:HIS511 3.1 13.2 1.0
CD B:ARG382 3.4 12.1 1.0
CB B:HIS511 3.6 15.2 1.0
CG B:HIS511 3.7 13.8 1.0
CG B:ARG382 3.8 12.1 1.0
CG B:ASN106 3.9 19.9 1.0
CD2 B:LEU240 3.9 15.9 1.0
CA B:PRO510 3.9 12.9 1.0
CA B:HIS511 3.9 14.5 1.0
O B:HOH898 3.9 25.8 1.0
OD1 B:ASN106 4.0 20.1 1.0
C B:PRO510 4.0 12.7 1.0
CE1 B:HIS511 4.0 15.1 1.0
O B:HOH970 4.4 25.4 1.0
O B:GLN509 4.6 12.1 1.0
CD B:ARG103 4.6 16.9 1.0
O B:HIS511 4.7 15.7 1.0
NE B:ARG103 4.7 15.4 1.0
CB B:PRO510 4.8 13.3 1.0
NE B:ARG382 4.8 12.8 1.0
CB B:ARG382 4.8 10.8 1.0
C B:HIS511 4.8 14.8 1.0
CD1 B:LEU240 4.9 14.9 1.0
CD2 B:HIS511 4.9 14.5 1.0
O B:HOH829 4.9 33.0 1.0

Chlorine binding site 6 out of 6 in 8pvm

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Chlorine binding site 6 out of 6 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl617

b:23.6
occ:0.15
 N4 B:402601 0.2 9.2 0.8
C4 B:402601 1.3 11.7 0.8
OG B:SER232 3.0 13.5 1.0
N B:SER232 3.0 11.6 1.0
FE1 B:402601 3.1 12.8 0.8
C5 B:402601 3.3 15.7 0.8
CD B:PRO231 3.3 11.9 1.0
N B:PRO231 3.4 12.5 1.0
CB B:SER232 3.5 13.0 1.0
CB B:ALA230 3.5 12.4 1.0
CB B:CYS503 3.6 11.3 1.0
CB B:PRO231 3.6 12.8 1.0
O5 B:402601 3.6 15.9 0.8
CG B:PRO231 3.6 13.2 1.0
C3 B:402601 3.6 10.6 0.8
S1 B:402601 3.7 12.8 0.8
CA B:SER232 3.8 11.7 1.0
CG B:PRO354 3.8 11.5 1.0
CA B:PRO231 3.9 12.2 1.0
CA B:GLY418 3.9 12.8 1.0
C B:PRO231 3.9 12.1 1.0
C B:ALA230 4.0 12.1 1.0
CD B:PRO354 4.1 11.3 1.0
CA B:ALA230 4.3 11.4 1.0
SG B:CYS503 4.3 12.3 1.0
N B:GLY418 4.5 12.2 1.0
O3 B:402601 4.5 12.8 0.8
FE2 B:402601 4.6 14.7 0.8
C7 B:402601 4.7 13.2 0.8
O B:ALA230 4.7 12.8 1.0
CA B:CYS503 4.9 11.0 1.0
C B:SER232 5.0 12.2 1.0

Reference:

J.Duan, A.Veliju, O.Lampret, L.Liu, S.Yadav, U.P.Apfel, F.A.Armstrong, A.Hemschemeier, E.Hofmann. Insights Into the Molecular Mechanism of Formaldehyde Inhibition of [Fefe]-Hydrogenases J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
DOI: 10.1021/JACS.3C07800
Page generated: Tue Jul 30 11:40:59 2024

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