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Nickel in PDB 1yqw: Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

Enzymatic activity of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

All present enzymatic activity of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase, PDB code: 1yqw was solved by A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.410, 99.700, 182.830, 90.00, 91.42, 90.00
R / Rfree (%) 14.6 / 18.5

Other elements in 1yqw:

The structure of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Iron (Fe) 39 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase (pdb code 1yqw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase, PDB code: 1yqw:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 1yqw

Go back to Nickel Binding Sites List in 1yqw
Nickel binding site 1 out of 3 in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ni551

b:15.0
occ:1.00
O Q:HOH564 1.8 12.2 0.3
O1 Q:PER552 1.9 14.9 1.0
O2 Q:PER552 2.1 15.9 0.7
SG Q:CYS72 2.2 11.4 1.0
SG Q:CYS543 2.3 13.9 0.7
SG Q:CYS546 2.5 11.3 1.0
SG Q:CYS75 2.5 12.0 1.0
CB Q:CYS72 2.9 9.5 1.0
FE Q:FCO550 2.9 10.2 1.0
SG Q:CYS543 3.2 13.2 0.3
CB Q:CYS543 3.3 8.8 1.0
CB Q:CYS546 3.5 9.1 1.0
CB Q:CYS75 3.6 11.0 1.0
N Q:CYS75 3.6 7.4 1.0
C1 Q:FCO550 3.9 8.1 1.0
CA Q:CYS75 4.2 10.3 1.0
C2 Q:FCO550 4.2 9.5 1.0
CA Q:CYS72 4.3 8.9 1.0
CB Q:VAL74 4.4 10.2 1.0
C3 Q:FCO550 4.4 7.4 1.0
CA Q:CYS546 4.5 10.2 1.0
N Q:CYS546 4.6 7.5 1.0
CA Q:CYS543 4.7 10.1 1.0
C Q:VAL74 4.7 8.0 1.0
N Q:VAL74 4.7 9.3 1.0
C Q:CYS72 4.8 10.3 1.0
NH1 Q:ARG476 4.8 13.8 1.0
N1 Q:FCO550 4.8 9.3 1.0
CD Q:ARG476 4.8 7.2 1.0
C Q:CYS75 4.9 9.5 1.0
CA Q:VAL74 4.9 8.3 1.0
CG Q:GLU25 4.9 10.2 1.0
O Q:CYS75 5.0 11.6 1.0
NE Q:ARG476 5.0 8.9 1.0

Nickel binding site 2 out of 3 in 1yqw

Go back to Nickel Binding Sites List in 1yqw
Nickel binding site 2 out of 3 in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni551

b:14.2
occ:1.00
O R:HOH557 1.9 9.4 0.5
O1 R:PER552 1.9 14.2 1.0
O2 R:PER552 2.1 16.3 0.5
SG R:CYS72 2.2 12.4 1.0
SG R:CYS543 2.3 12.9 0.7
SG R:CYS546 2.5 9.4 1.0
SG R:CYS75 2.5 12.0 1.0
SG R:CYS543 2.8 15.4 0.3
FE R:FCO550 2.8 9.7 1.0
CB R:CYS72 2.9 10.9 1.0
CB R:CYS543 3.2 8.1 1.0
CB R:CYS75 3.5 9.3 1.0
CB R:CYS546 3.6 9.1 1.0
N R:CYS75 3.6 8.9 1.0
C1 R:FCO550 3.9 5.5 1.0
C2 R:FCO550 4.1 7.2 1.0
CA R:CYS75 4.1 9.7 1.0
C3 R:FCO550 4.4 7.8 1.0
CA R:CYS72 4.4 11.3 1.0
CB R:VAL74 4.5 12.4 1.0
CA R:CYS546 4.5 9.3 1.0
N R:CYS546 4.6 10.5 1.0
NH1 R:ARG476 4.6 10.2 1.0
CA R:CYS543 4.7 8.9 1.0
C R:VAL74 4.7 9.2 1.0
CD R:ARG476 4.7 12.2 1.0
N1 R:FCO550 4.8 8.0 1.0
N R:VAL74 4.8 10.7 1.0
C R:CYS75 4.8 11.8 1.0
C R:CYS72 4.9 10.8 1.0
CA R:VAL74 4.9 8.5 1.0
CZ R:ARG476 4.9 12.1 1.0
NE R:ARG476 4.9 11.8 1.0
O R:CYS75 4.9 11.9 1.0

Nickel binding site 3 out of 3 in 1yqw

Go back to Nickel Binding Sites List in 1yqw
Nickel binding site 3 out of 3 in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ni551

b:15.1
occ:1.00
O S:HOH557 1.8 10.3 0.3
O1 S:PER552 1.9 12.1 1.0
O2 S:PER552 2.0 12.1 0.7
SG S:CYS72 2.1 16.2 1.0
SG S:CYS543 2.2 12.1 0.7
SG S:CYS75 2.5 12.7 1.0
SG S:CYS546 2.5 9.0 1.0
CB S:CYS72 2.9 10.0 1.0
FE S:FCO550 2.9 11.9 1.0
SG S:CYS543 3.1 11.5 0.3
CB S:CYS543 3.3 9.6 1.0
CB S:CYS546 3.5 10.3 1.0
CB S:CYS75 3.6 12.3 1.0
N S:CYS75 3.7 9.0 1.0
C1 S:FCO550 3.9 8.4 1.0
C2 S:FCO550 4.2 11.3 1.0
CA S:CYS75 4.2 10.1 1.0
CA S:CYS72 4.4 9.3 1.0
CA S:CYS546 4.4 9.9 1.0
C3 S:FCO550 4.5 13.0 1.0
N S:CYS546 4.5 10.5 1.0
CB S:VAL74 4.6 10.9 1.0
CA S:CYS543 4.7 8.6 1.0
C S:VAL74 4.8 9.0 1.0
N1 S:FCO550 4.8 9.5 1.0
C S:CYS72 4.8 9.4 1.0
CD S:ARG476 4.8 8.7 1.0
NH1 S:ARG476 4.8 18.3 1.0
C S:CYS75 4.9 12.8 1.0
N S:VAL74 4.9 10.3 1.0
O S:CYS75 4.9 13.3 1.0
CG S:GLU25 4.9 9.4 1.0
CA S:VAL74 5.0 9.9 1.0

Reference:

A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps. Structural Differences Between the Ready and Unready Oxidized States of [Nife] Hydrogenases. J.Biol.Inorg.Chem. V. 10 239 2005.
ISSN: ISSN 0949-8257
PubMed: 15803334
DOI: 10.1007/S00775-005-0632-X
Page generated: Wed Dec 16 01:16:45 2020

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