Magnesium 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:

Chlorine (Cl) 4 atoms
Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T, PDB code: 8cjy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8cjy

Go back to Magnesium Binding Sites List in 8cjy
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg607

b:32.9
occ:1.00
 O A:HOH900 2.0 35.8 1.0
O A:HOH784 2.1 26.4 1.0
O A:HOH811 2.1 27.7 1.0
O A:HOH897 2.1 29.7 1.0
O A:HOH835 2.1 30.7 1.0
O A:LEU218 2.1 29.1 1.0
C A:LEU218 3.2 29.8 1.0
HA A:LEU218 3.3 31.6 1.0
CA A:LEU218 3.7 26.3 1.0
OD2 A:ASP263 4.0 29.4 1.0
HG23 A:VAL225 4.1 27.6 1.0
O A:ALA220 4.1 29.1 1.0
O A:HOH862 4.2 28.8 1.0
HB3 A:LEU218 4.2 28.8 1.0
O A:LYS223 4.2 28.1 1.0
OD1 A:ASP263 4.2 29.7 1.0
O A:ALA217 4.2 26.0 1.0
HA A:ASN219 4.3 39.2 1.0
N A:ASN219 4.3 30.1 1.0
HD23 A:LEU218 4.4 38.8 1.0
CG A:ASP263 4.6 30.4 1.0
CB A:LEU218 4.6 23.9 1.0
O A:GLY261 4.6 30.0 1.0
CA A:ASN219 4.7 32.7 1.0
HD22 A:LEU218 4.8 38.8 1.0
H A:ALA220 4.9 33.8 1.0
N A:LEU218 4.9 26.9 1.0
C A:ASN219 4.9 32.5 1.0
N A:ALA220 4.9 28.2 1.0
CG2 A:VAL225 5.0 23.0 1.0
CD2 A:LEU218 5.0 32.3 1.0

Magnesium binding site 2 out of 4 in 8cjy

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg609

b:28.8
occ:1.00
 OD1 A:ASP42 2.0 34.0 1.0
OD1 A:ASN40 2.0 27.9 1.0
O A:HOH814 2.1 29.4 1.0
O A:HOH932 2.1 33.9 1.0
O A:HOH852 2.1 29.7 1.0
O A:HOH843 2.1 31.7 1.0
CG A:ASP42 3.2 37.2 1.0
CG A:ASN40 3.2 29.9 1.0
H A:ASN40 3.2 29.3 1.0
HD21 A:ASN40 3.6 34.8 1.0
OD2 A:ASP42 3.7 45.0 1.0
ND2 A:ASN40 3.8 28.9 1.0
HB3 A:ASP63 3.9 31.3 1.0
HB2 A:ASP63 4.0 31.3 1.0
HA A:ASP42 4.0 37.0 1.0
O A:HOH968 4.1 44.6 1.0
N A:ASN40 4.1 24.4 1.0
O A:HOH743 4.1 37.8 1.0
O B:HOH788 4.2 40.3 1.0
OD1 B:ASN452 4.2 36.9 1.0
HB3 B:ASN452 4.3 29.4 1.0
O A:ASN40 4.3 27.1 1.0
OD2 A:ASP63 4.3 30.0 1.0
CB A:ASP63 4.4 26.1 1.0
CB A:ASP42 4.4 28.9 1.0
O A:HOH888 4.4 43.5 1.0
CB A:ASN40 4.4 25.1 1.0
C A:ASN40 4.5 27.1 1.0
HA A:CYS39 4.5 30.3 1.0
CA A:ASN40 4.5 26.1 1.0
CG B:ASN452 4.6 31.2 1.0
CA A:ASP42 4.6 30.8 1.0
HD22 A:ASN40 4.7 34.8 1.0
HB3 A:ASP42 4.7 34.6 1.0
O B:HOH895 4.7 28.4 1.0
HB2 A:CYS39 4.7 51.8 1.0
HB3 A:ASN40 4.8 30.2 1.0
HE2 A:LYS45 4.9 42.8 0.5
CG A:ASP63 4.9 32.0 1.0
N A:ASP42 4.9 29.6 1.0
HE2 A:LYS45 4.9 42.8 0.5
CB B:ASN452 4.9 24.5 1.0
H B:GLY453 4.9 27.9 1.0
H A:ASP42 5.0 35.6 1.0

Magnesium binding site 3 out of 4 in 8cjy

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg607

b:32.5
occ:1.00
 O B:HOH793 2.0 24.4 1.0
O B:HOH879 2.1 32.3 1.0
O B:HOH897 2.1 34.5 1.0
O B:HOH744 2.1 29.2 1.0
O B:HOH813 2.1 29.4 1.0
O B:LEU218 2.2 32.5 1.0
C B:LEU218 3.3 26.9 1.0
HA B:LEU218 3.3 29.2 1.0
CA B:LEU218 3.8 24.4 1.0
OD2 B:ASP263 3.9 26.7 1.0
O B:HOH740 4.0 28.9 1.0
O B:ALA220 4.0 29.1 1.0
HG23 B:VAL225 4.1 29.7 1.0
O B:LYS223 4.2 26.6 1.0
OD1 B:ASP263 4.2 28.0 1.0
O B:ALA217 4.3 25.2 1.0
HB3 B:LEU218 4.3 30.1 1.0
N B:ASN219 4.4 27.7 1.0
HA B:ASN219 4.4 36.7 1.0
HD23 B:LEU218 4.5 33.9 1.0
CG B:ASP263 4.5 31.9 1.0
O B:GLY261 4.6 27.3 1.0
CB B:LEU218 4.7 25.1 1.0
HD22 B:LEU218 4.8 33.9 1.0
HA B:PRO221 4.8 37.0 1.0
CA B:ASN219 4.8 30.6 1.0
H B:ALA220 4.9 34.0 1.0
C B:ASN219 4.9 34.1 1.0
C B:ALA220 4.9 32.2 1.0
HG21 B:VAL225 4.9 29.7 1.0
N B:ALA220 5.0 28.3 1.0
N B:LEU218 5.0 23.5 1.0
CG2 B:VAL225 5.0 24.8 1.0

Magnesium binding site 4 out of 4 in 8cjy

Go back to Magnesium Binding Sites List in 8cjy
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg609

b:37.6
occ:1.00
 O B:HOH960 2.0 45.2 1.0
O B:HOH859 2.1 35.8 1.0
O B:HOH907 2.1 36.4 1.0
O B:HOH734 2.1 42.1 1.0
OD1 B:ASP42 2.1 43.7 1.0
OD1 B:ASN40 2.1 30.4 1.0
CG B:ASN40 3.2 31.8 1.0
H B:ASN40 3.3 34.4 1.0
CG B:ASP42 3.3 42.1 1.0
HD21 B:ASN40 3.4 46.0 1.0
ND2 B:ASN40 3.7 38.4 1.0
OD2 B:ASP42 3.9 47.0 1.0
HA B:ASP42 4.0 44.1 1.0
N B:ASN40 4.1 28.7 1.0
O A:HOH741 4.1 41.0 1.0
HB3 B:ASP63 4.2 39.8 1.0
OD2 B:ASP63 4.3 34.4 1.0
O B:ASN40 4.3 27.2 1.0
HB3 A:ASN452 4.4 36.2 1.0
CB B:ASN40 4.4 26.7 1.0
HB3 B:CYS39 4.4 51.5 1.0
CB B:ASP42 4.5 38.2 1.0
HA B:CYS39 4.5 37.6 1.0
HB2 B:ASP63 4.5 39.8 1.0
HD22 B:ASN40 4.6 46.0 1.0
CG A:ASN452 4.6 35.2 1.0
C B:ASN40 4.6 25.1 1.0
CA B:ASN40 4.6 28.1 1.0
ND2 A:ASN452 4.6 41.1 1.0
CA B:ASP42 4.6 36.8 1.0
OD1 A:ASN452 4.7 38.8 1.0
HD21 A:ASN452 4.7 49.3 1.0
CB B:ASP63 4.8 33.1 1.0
HB3 B:ASP42 4.8 45.8 1.0
HB3 B:ASN40 4.8 32.1 1.0
HD22 A:ASN452 4.8 49.3 1.0
H A:GLY453 4.9 29.9 1.0
N B:ASP42 4.9 32.9 1.0
H B:ASP42 4.9 39.5 1.0
HD2 B:LYS45 4.9 54.9 1.0
O A:HOH945 5.0 40.6 1.0
CB A:ASN452 5.0 30.1 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: Thu Oct 3 22:38:27 2024

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