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Magnesium in PDB 8aln: Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom

Enzymatic activity of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom

All present enzymatic activity of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom:
1.12.7.2;

Protein crystallography data

The structure of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom, PDB code: 8aln 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) 47.10 / 1.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.86, 71.85, 103.23, 90, 97.47, 90
R / Rfree (%) 14.9 / 17.5

Other elements in 8aln:

The structure of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom (pdb code 8aln). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom, PDB code: 8aln:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8aln

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Magnesium binding site 1 out of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:28.5
occ:1.00
 O A:HOH985 2.0 32.1 1.0
O A:HOH820 2.1 25.0 1.0
O A:HOH952 2.1 27.1 1.0
O A:HOH909 2.1 26.1 1.0
O A:LEU218 2.1 26.7 1.0
O A:HOH840 2.2 27.8 1.0
C A:LEU218 3.2 26.3 1.0
CA A:LEU218 3.8 25.6 1.0
O A:HOH1208 4.0 46.0 1.0
O A:ALA220 4.0 28.6 1.0
OD2 A:ASP263 4.0 28.3 1.0
O A:HOH836 4.2 25.1 1.0
O A:ALA217 4.2 24.9 1.0
O A:LYS223 4.3 26.6 1.0
N A:ASN219 4.3 26.8 1.0
OD1 A:ASP263 4.4 28.7 1.0
O A:HOH757 4.6 42.9 1.0
CB A:LEU218 4.6 24.4 1.0
O A:GLY261 4.6 27.7 1.0
CG A:ASP263 4.6 26.9 1.0
CA A:ASN219 4.7 27.6 1.0
C A:ASN219 4.8 28.7 1.0
N A:ALA220 4.9 28.5 1.0
N A:LEU218 4.9 25.1 1.0
C A:ALA220 4.9 28.7 1.0

Magnesium binding site 2 out of 6 in 8aln

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Magnesium binding site 2 out of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:24.0
occ:1.00
 OD1 A:ASP42 2.0 26.2 1.0
OD1 A:ASN40 2.0 22.7 1.0
O A:HOH788 2.0 23.0 1.0
O A:HOH998 2.1 23.7 1.0
O A:HOH900 2.1 32.4 1.0
O A:HOH971 2.1 26.4 1.0
CG A:ASP42 3.1 27.4 1.0
CG A:ASN40 3.2 21.1 1.0
OD2 A:ASP42 3.6 32.8 1.0
ND2 A:ASN40 3.9 21.1 1.0
O A:HOH704 3.9 31.2 1.0
N A:ASN40 4.0 22.5 1.0
O A:ASN40 4.2 23.2 1.0
O B:HOH785 4.2 26.6 1.0
OD2 A:ASP63 4.3 23.9 1.0
O A:HOH1062 4.3 43.9 1.0
OD1 B:ASN452 4.3 30.3 1.0
CB A:ASP42 4.4 25.3 1.0
CB A:ASN40 4.4 21.5 1.0
CB A:ASP63 4.4 22.8 1.0
C A:ASN40 4.5 21.6 1.0
CA A:ASN40 4.5 22.0 1.0
CG B:ASN452 4.5 26.0 1.0
CA A:ASP42 4.6 23.7 1.0
O B:HOH1056 4.8 30.0 1.0
N A:ASP42 4.8 22.4 1.0
CB B:ASN452 4.8 22.2 1.0
CG A:ASP63 4.9 23.4 1.0

Magnesium binding site 3 out of 6 in 8aln

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Magnesium binding site 3 out of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg612

b:58.7
occ:1.00
 O A:HOH1055 2.0 52.6 1.0
O A:HOH940 2.1 48.5 1.0
O A:HOH1090 2.1 64.5 1.0
NE2 A:HIS565 2.1 47.8 1.0
OG A:SER320 2.2 32.1 1.0
O A:HOH710 3.0 58.1 1.0
CE1 A:HIS565 3.1 47.5 1.0
CD2 A:HIS565 3.2 46.9 1.0
CB A:SER320 3.3 29.6 1.0
ND1 A:HIS569 4.0 31.1 1.0
O A:HOH835 4.0 34.4 1.0
OE2 A:GLU282 4.1 42.4 1.0
ND1 A:HIS565 4.2 47.7 1.0
CD A:GLU282 4.3 40.1 1.0
CG A:HIS565 4.3 46.3 1.0
CE1 A:HIS569 4.5 31.1 1.0
OE1 A:GLU282 4.5 39.1 1.0
CA A:SER320 4.6 27.8 1.0
N A:SER320 4.7 27.7 1.0
CG A:HIS569 4.8 30.3 1.0

Magnesium binding site 4 out of 6 in 8aln

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Magnesium binding site 4 out of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:27.4
occ:1.00
 O B:HOH867 2.1 24.2 1.0
O B:HOH1010 2.1 29.9 1.0
O B:HOH825 2.1 23.2 1.0
O B:HOH856 2.1 26.7 1.0
O B:HOH945 2.1 26.1 1.0
O B:LEU218 2.2 27.4 1.0
C B:LEU218 3.2 24.8 1.0
CA B:LEU218 3.8 23.1 1.0
OD2 B:ASP263 4.0 24.6 1.0
O B:ALA220 4.1 28.2 1.0
O B:HOH1232 4.1 43.1 1.0
O B:HOH842 4.2 24.7 1.0
OD1 B:ASP263 4.3 25.4 1.0
O B:ALA217 4.3 23.3 1.0
O B:LYS223 4.3 26.1 1.0
N B:ASN219 4.4 26.6 1.0
O B:GLY261 4.5 25.4 1.0
CG B:ASP263 4.6 23.0 1.0
CB B:LEU218 4.6 23.3 1.0
CA B:ASN219 4.7 28.9 1.0
O B:HOH1146 4.8 56.7 1.0
C B:ASN219 4.9 29.2 1.0
N B:LEU218 4.9 24.3 1.0
N B:ALA220 4.9 27.3 1.0
C B:ALA220 5.0 27.9 1.0

Magnesium binding site 5 out of 6 in 8aln

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Magnesium binding site 5 out of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg610

b:32.5
occ:1.00
 OD1 B:ASN40 1.9 32.4 1.0
O B:HOH1077 2.0 33.3 1.0
O B:HOH1067 2.1 31.5 1.0
O B:HOH713 2.1 32.9 1.0
O B:HOH824 2.1 31.0 1.0
OD1 B:ASP42 2.2 41.5 1.0
CG B:ASN40 3.0 31.6 1.0
CG B:ASP42 3.3 42.1 1.0
ND2 B:ASN40 3.6 33.8 1.0
OD2 B:ASP42 3.7 43.1 1.0
O B:HOH1138 3.7 49.9 1.0
N B:ASN40 3.9 27.6 1.0
O B:HOH721 4.1 30.4 1.0
OD2 B:ASP63 4.1 38.0 1.0
CB B:ASN40 4.3 29.1 1.0
O A:HOH881 4.3 29.0 1.0
OD1 A:ASN452 4.3 37.5 1.0
O B:ASN40 4.4 27.5 1.0
CG A:ASN452 4.5 32.8 1.0
CA B:ASN40 4.5 27.7 1.0
CB B:ASP63 4.5 37.1 1.0
CB B:ASP42 4.6 39.6 1.0
C B:ASN40 4.6 26.5 1.0
CG B:ASP63 4.8 37.8 1.0
ND2 A:ASN452 4.8 33.4 1.0
CA B:ASP42 4.9 36.4 1.0
CB A:ASN452 4.9 27.9 1.0

Magnesium binding site 6 out of 6 in 8aln

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Magnesium binding site 6 out of 6 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.34 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg611

b:58.4
occ:1.00
 O B:HOH895 2.1 32.5 1.0
O B:HOH799 2.1 35.0 1.0
O B:HOH1261 2.2 51.7 1.0
O B:HOH974 2.2 28.0 1.0
O B:HOH782 3.9 49.5 1.0
OD1 B:ASN309 4.0 24.6 1.0
O B:ASP187 4.2 25.6 1.0
O B:THR188 4.3 21.2 1.0
OD1 B:ASN189 4.4 28.4 1.0
C B:THR188 4.6 19.5 1.0
C B:ASP187 4.7 22.8 1.0
CG B:ASN309 4.7 23.2 1.0
O B:HOH944 4.8 45.7 1.0
O B:HOH1230 4.9 54.9 1.0
CA B:THR188 4.9 20.8 1.0

Reference:

J.Duan, A.Hemschemeier, D.J.Burr, S.T.Stripp, E.Hofmann, T.Happe. Cyanide Binding to [Fefe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway. Angew.Chem.Int.Ed.Engl. 2022.
ISSN: ESSN 1521-3773
PubMed: 36464641
DOI: 10.1002/ANIE.202216903
Page generated: Thu Oct 3 18:08:59 2024

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