Magnesium in PDB 8ap2: Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom

Enzymatic activity of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom

All present enzymatic activity of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom:
1.12.7.2;

Protein crystallography data

The structure of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom, PDB code: 8ap2 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) 46.13 / 1.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.07, 71.5, 102.78, 90, 100.75, 90
R / Rfree (%) 15.9 / 19.1

Other elements in 8ap2:

The structure of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom (pdb code 8ap2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom, PDB code: 8ap2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8ap2

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Magnesium binding site 1 out of 8 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:34.5
occ:1.00
 O A:HOH735 1.9 27.8 1.0
NE2 A:HIS565 1.9 35.3 1.0
O A:HOH950 2.0 39.5 1.0
O A:HOH1092 2.1 36.3 1.0
OG A:SER320 2.1 26.5 1.0
O A:HOH762 2.2 34.6 1.0
CE1 A:HIS565 2.7 35.3 1.0
CB A:SER320 3.1 24.2 1.0
CD2 A:HIS565 3.1 34.7 1.0
ND1 A:HIS569 3.9 20.0 1.0
ND1 A:HIS565 3.9 36.0 1.0
CG A:HIS565 4.2 34.4 1.0
O A:HOH754 4.4 38.2 1.0
OE2 A:GLU282 4.4 39.6 1.0
CA A:SER320 4.4 21.7 1.0
O A:HOH1263 4.4 47.5 1.0
CE1 A:HIS569 4.5 20.0 1.0
OE1 A:GLU282 4.6 35.1 1.0
CD A:GLU282 4.6 36.5 1.0
CG A:HIS569 4.7 20.2 1.0
O A:HOH1082 4.7 47.5 1.0
N A:SER320 4.7 20.3 1.0
CB A:HIS569 4.9 19.5 1.0

Magnesium binding site 2 out of 8 in 8ap2

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Magnesium binding site 2 out of 8 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:49.6
occ:1.00
 O B:HOH706 2.1 36.3 1.0
O B:HOH1187 2.1 55.4 1.0
O A:HOH871 2.1 55.0 1.0
O B:HOH1062 2.1 43.3 1.0
O A:ILE43 4.1 25.0 1.0
OD1 A:ASN44 4.1 25.2 1.0
NZ B:LYS489 4.2 34.6 1.0
OE2 B:GLU456 4.3 45.3 1.0
CE B:LYS489 4.4 32.1 1.0
CA A:ASN44 4.6 20.4 1.0
O A:HOH856 4.7 34.4 1.0
CG A:ASN44 4.9 22.8 1.0
CB A:ASN44 5.0 20.5 1.0

Magnesium binding site 3 out of 8 in 8ap2

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Magnesium binding site 3 out of 8 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg612

b:19.7
occ:1.00
 OD1 A:ASP42 2.0 19.3 1.0
O A:HOH1004 2.0 24.6 1.0
O A:HOH760 2.1 18.8 1.0
OD1 A:ASN40 2.1 19.7 1.0
O A:HOH1020 2.1 18.8 1.0
O A:HOH988 2.1 20.5 1.0
CG A:ASP42 3.1 21.3 1.0
CG A:ASN40 3.3 18.0 1.0
OD2 A:ASP42 3.6 26.0 1.0
O A:HOH730 3.9 26.5 1.0
ND2 A:ASN40 3.9 19.1 1.0
N A:ASN40 4.0 16.1 1.0
O A:HOH1098 4.2 31.8 1.0
O B:HOH827 4.2 20.2 1.0
O A:HOH980 4.2 32.0 1.0
O A:ASN40 4.3 17.5 1.0
OD2 A:ASP63 4.3 17.3 1.0
CB A:ASP63 4.4 17.7 1.0
CB A:ASP42 4.4 19.6 1.0
O A:HOH744 4.4 53.9 1.0
CB A:ASN40 4.4 17.4 1.0
CA A:ASN40 4.5 17.1 1.0
C A:ASN40 4.5 16.4 1.0
OD1 B:ASN452 4.6 25.2 1.0
CA A:ASP42 4.6 19.2 1.0
CG B:ASN452 4.7 21.6 1.0
O B:HOH1108 4.8 20.9 1.0
CG A:ASP63 4.9 18.1 1.0
N A:ASP42 4.9 18.4 1.0
CB B:ASN452 4.9 17.9 1.0
ND2 B:ASN452 5.0 22.6 1.0
CA A:CYS39 5.0 19.5 0.4
C A:CYS39 5.0 16.9 0.4

Magnesium binding site 4 out of 8 in 8ap2

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Magnesium binding site 4 out of 8 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg613

b:21.6
occ:1.00
 O A:HOH985 2.1 20.6 1.0
O A:HOH844 2.1 22.9 1.0
O A:HOH753 2.1 19.2 1.0
O A:HOH896 2.1 21.7 1.0
O A:HOH1050 2.1 28.3 1.0
O A:LEU218 2.1 21.1 1.0
C A:LEU218 3.2 20.1 1.0
CA A:LEU218 3.8 18.5 1.0
O A:ALA220 4.0 23.1 1.0
OD2 A:ASP263 4.0 21.1 1.0
O A:HOH809 4.1 20.1 1.0
O A:ALA217 4.2 20.6 1.0
O A:LYS223 4.3 20.4 1.0
OD1 A:ASP263 4.3 21.5 1.0
N A:ASN219 4.3 22.7 1.0
O A:HOH866 4.5 56.9 1.0
CG A:ASP263 4.6 20.2 1.0
CB A:LEU218 4.6 17.4 1.0
O A:GLY261 4.6 21.6 1.0
CA A:ASN219 4.7 22.8 1.0
C A:ASN219 4.9 23.5 1.0
N A:LEU218 4.9 18.3 1.0
N A:ALA220 4.9 21.5 1.0
C A:ALA220 4.9 22.5 1.0
CG2 A:VAL225 5.0 16.8 1.0

Magnesium binding site 5 out of 8 in 8ap2

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Magnesium binding site 5 out of 8 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:20.9
occ:1.00
 O B:HOH824 2.1 17.9 1.0
O B:HOH831 2.1 20.1 1.0
O B:HOH954 2.1 24.1 1.0
O B:HOH967 2.1 21.1 1.0
O B:LEU218 2.1 20.3 1.0
O B:HOH818 2.1 18.9 1.0
C B:LEU218 3.2 20.8 1.0
CA B:LEU218 3.8 19.5 1.0
OD2 B:ASP263 4.0 18.5 1.0
O B:ALA220 4.1 21.5 1.0
O B:HOH799 4.2 18.8 1.0
O B:ALA217 4.2 19.2 1.0
OD1 B:ASP263 4.3 20.7 1.0
O B:HOH1105 4.3 36.4 1.0
O B:LYS223 4.3 20.5 1.0
N B:ASN219 4.3 20.0 1.0
O B:GLY261 4.5 20.5 1.0
CG B:ASP263 4.6 18.9 1.0
CB B:LEU218 4.6 18.6 1.0
CA B:ASN219 4.7 21.8 1.0
C B:ASN219 4.9 22.7 1.0
N B:LEU218 4.9 18.9 1.0
N B:ALA220 4.9 21.4 1.0
CD2 B:LEU218 5.0 18.5 1.0
C B:ALA220 5.0 21.8 1.0

Magnesium binding site 6 out of 8 in 8ap2

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Magnesium binding site 6 out of 8 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg612

b:25.6
occ:1.00
 OD1 B:ASN40 2.0 25.2 1.0
OD1 B:ASP42 2.1 26.8 1.0
O B:HOH776 2.1 25.5 1.0
O B:HOH1042 2.1 25.1 1.0
O B:HOH975 2.1 28.1 1.0
O B:HOH960 2.1 24.8 1.0
CG B:ASP42 3.1 27.6 1.0
CG B:ASN40 3.2 23.8 1.0
OD2 B:ASP42 3.5 29.2 1.0
ND2 B:ASN40 3.8 24.1 1.0
N B:ASN40 4.0 23.5 1.0
O B:HOH863 4.0 24.9 1.0
O A:HOH916 4.1 22.2 1.0
O B:HOH1160 4.2 32.2 1.0
OD2 B:ASP63 4.2 30.1 1.0
O B:ASN40 4.3 22.4 1.0
CB B:ASN40 4.4 23.5 1.0
CB B:ASP42 4.4 26.1 1.0
ND2 A:ASN452 4.4 24.8 1.0
CA B:ASN40 4.5 22.8 1.0
C B:ASN40 4.5 22.1 1.0
CB B:ASP63 4.6 31.9 1.0
CG A:ASN452 4.6 23.0 1.0
CA B:ASP42 4.7 26.1 1.0
N B:ASP42 4.9 24.6 1.0
CG B:ASP63 4.9 31.3 1.0
OD1 A:ASN452 5.0 26.6 1.0

Magnesium binding site 7 out of 8 in 8ap2

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Magnesium binding site 7 out of 8 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg613

b:38.7
occ:1.00
 O B:HOH813 2.0 34.6 1.0
O B:HOH1157 2.1 47.6 1.0
OD1 B:ASN437 4.1 31.2 1.0
O B:PHE434 4.3 23.7 1.0
O B:HOH993 4.8 41.4 1.0
O B:HOH1266 4.9 31.4 1.0
CG B:ASN437 5.0 30.2 1.0

Magnesium binding site 8 out of 8 in 8ap2

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Magnesium binding site 8 out of 8 in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) at 1.39 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg614

b:45.6
occ:1.00
 NE2 B:HIS565 1.9 42.7 1.0
O B:HOH1063 2.1 42.8 1.0
O B:HOH1113 2.1 54.5 1.0
O B:HOH886 2.1 42.5 1.0
O B:HOH732 2.2 59.1 1.0
OG B:SER320 2.4 32.4 1.0
CE1 B:HIS565 2.9 41.9 1.0
CD2 B:HIS565 3.0 40.1 1.0
CB B:SER320 3.4 26.7 1.0
O B:HOH1119 3.8 57.6 1.0
ND1 B:HIS569 3.9 19.2 1.0
ND1 B:HIS565 4.0 40.4 1.0
CG B:HIS565 4.1 37.5 1.0
O B:HOH841 4.3 35.5 1.0
CE1 B:HIS569 4.4 19.2 1.0
OE1 B:GLU282 4.5 26.2 0.5
OE2 B:GLU282 4.6 26.1 0.5
OE1 B:GLU282 4.6 25.8 0.5
CG B:HIS569 4.7 18.9 1.0
CD B:GLU282 4.7 25.0 0.5
CA B:SER320 4.7 22.1 1.0
CD B:GLU282 4.9 25.4 0.5

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 18:12:30 2024

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