Chlorine in PDB 8cjy: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T

Enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T:
1.12.7.2;

Protein crystallography data

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T, PDB code: 8cjy was solved by C.Brocks, 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) 39.33 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.73, 72.29, 103.04, 90, 96.95, 90
R / Rfree (%) 16.4 / 18.7

Other elements in 8cjy:

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Iron (Fe) 40 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T (pdb code 8cjy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T, PDB code: 8cjy:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8cjy

Go back to Chlorine Binding Sites List in 8cjy
Chlorine binding site 1 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl610

b:38.5
occ:1.00
 H A:ALA406 2.5 33.3 1.0
HB3 A:ASP404 2.7 38.7 1.0
HD2 A:PRO405 2.7 42.8 1.0
O A:HOH987 3.1 42.7 1.0
HE3 A:LYS264 3.1 57.1 1.0
HB2 A:ALA406 3.2 37.6 1.0
HB3 A:ALA406 3.2 37.6 1.0
HE1 A:PHE266 3.2 36.2 1.0
N A:ALA406 3.3 27.7 1.0
CD A:PRO405 3.4 35.7 1.0
HG2 A:PRO405 3.5 43.0 1.0
N A:PRO405 3.5 33.4 1.0
CB A:ALA406 3.6 31.4 1.0
CB A:ASP404 3.6 32.2 1.0
C A:ASP404 3.8 33.1 1.0
HZ1 A:LYS264 3.9 76.3 1.0
CE A:LYS264 4.0 47.6 1.0
CG A:PRO405 4.0 35.8 1.0
HA A:ASP404 4.0 37.0 1.0
CA A:ASP404 4.0 30.9 1.0
HB2 A:ASP404 4.0 38.7 1.0
CA A:ALA406 4.1 27.5 1.0
CE1 A:PHE266 4.1 30.1 1.0
HE2 A:LYS264 4.1 57.1 1.0
HZ A:PHE266 4.2 34.1 1.0
HD3 A:PRO405 4.2 42.8 1.0
NZ A:LYS264 4.3 63.6 1.0
C A:PRO405 4.3 34.0 1.0
CA A:PRO405 4.4 32.7 1.0
O A:ASP404 4.4 30.7 1.0
HB1 A:ALA406 4.4 37.6 1.0
HZ2 A:LYS264 4.5 76.3 1.0
CG A:ASP404 4.5 42.8 1.0
CZ A:PHE266 4.6 28.4 1.0
H A:MET407 4.6 35.1 1.0
HA A:ALA406 4.6 33.0 1.0
OD1 A:ASP404 4.7 46.0 1.0
HG3 A:PRO405 4.7 43.0 1.0
CB A:PRO405 4.8 39.7 1.0

Chlorine binding site 2 out of 4 in 8cjy

Go back to Chlorine Binding Sites List in 8cjy
Chlorine binding site 2 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl611

b:50.7
occ:1.00
 HD2 A:PRO365 2.8 38.5 1.0
H A:GLN366 2.9 31.9 1.0
HB3 A:ARG364 3.0 32.0 1.0
HH11 A:ARG364 3.3 40.7 1.0
HB2 A:GLN366 3.4 43.5 1.0
HZ A:PHE570 3.5 37.8 1.0
CD A:PRO365 3.7 32.0 1.0
HG3 A:GLN366 3.7 43.6 1.0
HE21 A:GLN366 3.7 63.1 1.0
N A:GLN366 3.8 26.6 1.0
HD3 A:ARG364 3.8 36.2 1.0
CB A:ARG364 3.8 26.7 1.0
N A:PRO365 3.9 29.7 1.0
HG2 A:ARG364 3.9 29.1 1.0
HB2 A:PRO365 3.9 35.9 1.0
O A:HOH982 4.1 35.2 1.0
CB A:GLN366 4.1 36.2 1.0
NH1 A:ARG364 4.1 33.9 1.0
C A:ARG364 4.2 28.0 1.0
HA A:ARG364 4.2 31.1 1.0
CG A:ARG364 4.3 24.3 1.0
CG A:GLN366 4.3 36.3 1.0
NE2 A:GLN366 4.3 52.6 1.0
HD3 A:PRO365 4.3 38.5 1.0
CA A:ARG364 4.4 25.9 1.0
CZ A:PHE570 4.4 31.5 1.0
HH12 A:ARG364 4.4 40.7 1.0
HG2 A:PRO365 4.5 38.7 1.0
CB A:PRO365 4.5 29.9 1.0
CD A:ARG364 4.5 30.1 1.0
CG A:PRO365 4.5 32.2 1.0
HB2 A:ARG364 4.5 32.0 1.0
CA A:GLN366 4.6 28.3 1.0
CA A:PRO365 4.6 27.9 1.0
C A:PRO365 4.7 29.5 1.0
CD A:GLN366 4.7 52.9 1.0
HE22 A:GLN366 4.9 63.1 1.0
O A:ARG364 4.9 25.8 1.0
HB3 A:GLN366 4.9 43.5 1.0
HE1 A:PHE570 5.0 34.7 1.0

Chlorine binding site 3 out of 4 in 8cjy

Go back to Chlorine Binding Sites List in 8cjy
Chlorine binding site 3 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl610

b:35.9
occ:1.00
 H B:ALA406 2.5 29.1 1.0
HB3 B:ASP404 2.7 31.9 1.0
O B:HOH969 2.9 40.6 1.0
HD2 B:PRO405 3.0 39.4 1.0
HB2 B:ALA406 3.0 35.5 1.0
HB3 B:ALA406 3.2 35.5 1.0
HE1 B:PHE266 3.2 27.0 1.0
N B:ALA406 3.4 24.2 1.0
HE3 B:LYS264 3.4 54.4 1.0
CB B:ALA406 3.5 29.6 1.0
HG2 B:PRO405 3.5 40.5 1.0
CB B:ASP404 3.6 26.6 1.0
N B:PRO405 3.6 29.3 1.0
CD B:PRO405 3.6 32.8 1.0
C B:ASP404 3.8 27.8 1.0
HZ2 B:LYS264 3.8 65.6 1.0
HB2 B:ASP404 4.0 31.9 1.0
HA B:ASP404 4.0 30.2 1.0
HZ1 B:LYS264 4.0 65.6 1.0
CA B:ALA406 4.0 26.8 1.0
CA B:ASP404 4.0 25.1 1.0
CG B:PRO405 4.1 33.7 1.0
CE1 B:PHE266 4.1 22.5 1.0
HZ B:PHE266 4.1 31.1 1.0
CE B:LYS264 4.2 45.3 1.0
NZ B:LYS264 4.2 54.7 1.0
C B:PRO405 4.4 25.8 1.0
HB1 B:ALA406 4.4 35.5 1.0
O B:ASP404 4.5 27.2 1.0
CA B:PRO405 4.5 29.9 1.0
O B:HOH924 4.5 50.2 1.0
HD3 B:PRO405 4.5 39.4 1.0
CZ B:PHE266 4.5 25.9 1.0
CG B:ASP404 4.6 35.3 1.0
HA B:ALA406 4.6 32.2 1.0
H B:MET407 4.6 28.0 1.0
HD2 B:LYS264 4.7 42.4 1.0
HG3 B:PRO405 4.8 40.5 1.0
HE2 B:LYS264 4.8 54.4 1.0
OD1 B:ASP404 4.9 39.5 1.0
CB B:PRO405 5.0 34.7 1.0

Chlorine binding site 4 out of 4 in 8cjy

Go back to Chlorine Binding Sites List in 8cjy
Chlorine binding site 4 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl611

b:42.7
occ:1.00
 H B:GLN366 2.5 30.6 1.0
HD2 B:PRO365 2.8 35.3 1.0
HB3 B:ARG364 2.9 33.3 1.0
HG2 B:GLN366 3.0 53.9 1.0
HB2 B:GLN366 3.1 43.5 1.0
N B:GLN366 3.4 25.5 1.0
HZ B:PHE570 3.4 37.4 1.0
HH11 B:ARG364 3.4 64.6 1.0
HD3 B:ARG364 3.6 40.1 1.0
CG B:GLN366 3.6 44.9 1.0
CD B:PRO365 3.6 29.4 1.0
HG3 B:GLN366 3.6 53.9 1.0
N B:PRO365 3.6 32.1 1.0
CB B:GLN366 3.7 36.2 1.0
HB2 B:PRO365 3.7 35.3 1.0
CB B:ARG364 3.8 27.8 1.0
HG2 B:ARG364 4.0 30.6 1.0
C B:ARG364 4.0 31.4 1.0
CA B:GLN366 4.1 27.1 1.0
HG2 B:PRO365 4.1 42.9 1.0
NH1 B:ARG364 4.2 53.9 1.0
CG B:ARG364 4.2 25.5 1.0
CG B:PRO365 4.2 35.7 1.0
HA B:ARG364 4.2 32.9 1.0
CB B:PRO365 4.2 29.4 1.0
CZ B:PHE570 4.3 31.1 1.0
CA B:PRO365 4.3 31.3 1.0
C B:PRO365 4.3 25.6 1.0
CA B:ARG364 4.3 27.4 1.0
CD B:ARG364 4.3 33.4 1.0
HD3 B:PRO365 4.3 35.3 1.0
HE3 B:LYS573 4.4 63.8 1.0
HB2 B:ARG364 4.5 33.3 1.0
O B:HOH999 4.5 41.1 1.0
HH12 B:ARG364 4.5 64.6 1.0
HB3 B:GLN366 4.6 43.5 1.0
H B:MET367 4.7 31.0 1.0
HE2 B:PHE570 4.7 37.7 1.0
O B:ARG364 4.7 26.7 1.0
HG2 B:MET367 4.8 31.8 1.0
HE2 B:LYS573 4.9 63.8 1.0
HA B:GLN366 4.9 32.5 1.0
C B:GLN366 4.9 27.3 1.0
HD2 B:ARG364 4.9 40.1 1.0
CE2 B:PHE570 5.0 31.4 1.0
CD B:GLN366 5.0 54.5 1.0

Reference:

C.Brocks, C.K.Das, J.Duan, S.Yadav, U.P.Apfel, S.Ghosh, E.Hofmann, M.Winkler, V.Engelbrecht, L.V.Schafer, T.Happe. A Dynamic Water Channel Affects O2 Stability in [Fefe] Hydrogenases. Chemsuschem 01365 2023.
ISSN: ESSN 1864-564X
PubMed: 37830175
DOI: 10.1002/CSSC.202301365
Page generated: Tue Jul 30 08:00:45 2024

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