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Nickel in PDB 4urh: High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase

Enzymatic activity of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase, PDB code: 4urh was solved by A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.Delacey, P.P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.530, 99.820, 182.420, 90.00, 92.46, 90.00
R / Rfree (%) 14.164 / 18.526

Other elements in 4urh:

The structure of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Iron (Fe) 48 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase (pdb code 4urh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase, PDB code: 4urh:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4urh

Go back to Nickel Binding Sites List in 4urh
Nickel binding site 1 out of 4 in the High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ni1551

b:13.2
occ:1.00
 O Q:HOH2066 1.8 10.1 0.8
OD Q:CSX75 1.9 10.3 0.5
SG Q:CYS543 2.1 10.9 0.8
SG Q:CYS72 2.1 12.7 1.0
SG Q:CYS543 2.6 13.1 0.2
SG Q:CYS546 2.6 9.7 1.0
SG Q:CSX75 2.7 9.0 1.0
CB Q:CYS72 2.9 9.2 1.0
FE Q:FCO1550 3.0 7.9 1.0
CB Q:CYS543 3.1 10.8 0.2
CB Q:CYS543 3.2 9.5 0.8
CB Q:CYS546 3.6 7.3 1.0
N Q:CSX75 3.7 7.6 1.0
CB Q:CSX75 3.7 7.2 1.0
C1 Q:FCO1550 4.0 7.3 1.0
CA Q:CSX75 4.3 7.6 1.0
C2 Q:FCO1550 4.3 9.0 1.0
CA Q:CYS72 4.4 8.0 1.0
N Q:CYS546 4.5 7.8 1.0
CB Q:VAL74 4.5 7.1 1.0
NH1 Q:ARG476 4.5 11.3 1.0
CA Q:CYS543 4.5 7.7 1.0
C3 Q:FCO1550 4.5 8.2 1.0
CA Q:CYS546 4.5 8.2 1.0
CG Q:GLU25 4.8 9.6 1.0
N Q:VAL74 4.8 8.0 1.0
C Q:VAL74 4.8 7.2 1.0
CD Q:ARG476 4.8 7.6 1.0
N1 Q:FCO1550 4.8 8.3 1.0
CZ Q:ARG476 4.8 8.8 1.0
NE Q:ARG476 4.9 8.3 1.0
C Q:CYS72 4.9 7.3 1.0
CA Q:VAL74 4.9 6.9 1.0
CB Q:GLU25 5.0 9.3 1.0
C Q:CSX75 5.0 7.8 1.0

Nickel binding site 2 out of 4 in 4urh

Go back to Nickel Binding Sites List in 4urh
Nickel binding site 2 out of 4 in the High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni1551

b:14.7
occ:0.50
 NI R:NI1551 0.0 14.7 0.5
NI R:NI1551 0.8 14.2 0.5
SG R:CYS72 1.5 13.4 0.5
OD R:CSX75 1.9 14.7 0.2
O R:HOH2053 1.9 11.6 0.4
SG R:CYS543 2.0 9.7 0.4
OD R:CSX75 2.1 11.3 0.2
SG R:CYS543 2.1 13.3 0.4
SG R:CYS72 2.2 15.2 0.5
O R:HOH3053 2.5 12.3 0.4
SG R:CYS546 2.5 10.9 0.5
SG R:CSX75 2.6 12.1 0.5
CB R:CYS72 2.7 11.3 0.5
SG R:CYS543 2.7 14.4 0.1
SG R:CYS543 2.7 13.7 0.1
FE R:FCO1550 2.9 10.5 0.5
CB R:CYS72 3.1 13.8 0.5
CB R:CYS543 3.1 11.0 0.5
SG R:CSX75 3.2 9.7 0.5
SG R:CYS546 3.2 8.4 0.5
CB R:CYS543 3.4 8.9 0.5
CB R:CYS546 3.5 8.0 0.5
N R:CSX75 3.5 8.8 0.5
CB R:CSX75 3.6 9.5 0.5
N R:CSX75 3.7 10.5 0.5
FE R:FCO1550 3.7 8.2 0.5
CB R:VAL74 3.8 8.3 0.5
C1 R:FCO1550 3.9 10.1 0.5
CB R:CSX75 4.0 7.5 0.5
CB R:CYS546 4.1 8.0 0.5
CA R:CYS72 4.1 11.3 0.5
N R:VAL74 4.2 9.8 0.5
C2 R:FCO1550 4.2 6.8 0.5
CA R:CSX75 4.2 9.9 0.5
CG R:GLU25 4.2 9.7 0.5
CA R:CSX75 4.3 8.5 0.5
CA R:VAL74 4.3 9.9 0.5
C R:VAL74 4.4 9.4 0.5
CB R:GLU25 4.4 10.3 0.5
C3 R:FCO1550 4.5 10.3 0.5
CB R:VAL74 4.5 10.8 0.5
C R:CYS72 4.5 10.8 0.5
N R:CYS546 4.5 9.1 0.5
CA R:CYS546 4.5 9.3 0.5
CA R:CYS72 4.5 12.6 0.5
CA R:CYS543 4.5 9.0 0.5
NH1 R:ARG476 4.6 11.4 0.5
N R:CYS546 4.6 8.5 0.5
CA R:CYS543 4.6 8.2 0.5
CG2 R:VAL74 4.6 11.6 0.5
OE1 R:GLU25 4.6 12.2 0.5
CG1 R:VAL74 4.7 9.6 0.5
C1 R:FCO1550 4.7 7.8 0.5
CD R:GLU25 4.7 11.3 0.5
N R:GLY73 4.7 10.1 0.5
CD R:ARG476 4.8 10.4 0.5
N1 R:FCO1550 4.8 9.0 0.5
CZ R:ARG476 4.8 10.9 0.5
C R:VAL74 4.8 10.3 0.5
NE R:ARG476 4.8 11.0 0.5
CA R:CYS546 4.9 8.2 0.5
N R:VAL74 4.9 11.5 0.5
NH1 R:ARG476 4.9 10.5 0.5
C R:CSX75 4.9 12.1 0.5
C2 R:FCO1550 4.9 6.9 0.5
CA R:VAL74 5.0 10.3 0.5
C R:CYS72 5.0 11.6 0.5
CG R:GLU25 5.0 10.8 0.5

Nickel binding site 3 out of 4 in 4urh

Go back to Nickel Binding Sites List in 4urh
Nickel binding site 3 out of 4 in the High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni1551

b:14.2
occ:0.50
 NI R:NI1551 0.0 14.2 0.5
NI R:NI1551 0.8 14.7 0.5
O R:HOH2053 1.5 11.6 0.4
O R:HOH3053 1.8 12.3 0.4
OD R:CSX75 1.9 11.3 0.2
SG R:CYS546 2.0 10.9 0.5
FE R:FCO1550 2.1 10.5 0.5
OD R:CSX75 2.1 14.7 0.2
SG R:CYS543 2.2 9.7 0.4
SG R:CYS72 2.2 13.4 0.5
SG R:CSX75 2.3 12.1 0.5
SG R:CYS543 2.5 13.3 0.4
SG R:CYS546 2.6 8.4 0.5
SG R:CSX75 2.6 9.7 0.5
SG R:CYS543 2.8 13.7 0.1
FE R:FCO1550 2.9 8.2 0.5
CB R:CYS72 3.0 11.3 0.5
SG R:CYS72 3.0 15.2 0.5
SG R:CYS543 3.0 14.4 0.1
C1 R:FCO1550 3.1 10.1 0.5
CB R:CYS546 3.1 8.0 0.5
CB R:CYS543 3.2 11.0 0.5
CB R:CYS543 3.2 8.9 0.5
CB R:CSX75 3.4 9.5 0.5
C2 R:FCO1550 3.5 6.8 0.5
CB R:CYS72 3.5 13.8 0.5
CB R:CYS546 3.5 8.0 0.5
CB R:CSX75 3.6 7.5 0.5
C3 R:FCO1550 3.7 10.3 0.5
N R:CSX75 3.7 8.8 0.5
C1 R:FCO1550 3.9 7.8 0.5
N1 R:FCO1550 4.1 9.0 0.5
N R:CSX75 4.1 10.5 0.5
C2 R:FCO1550 4.2 6.9 0.5
CA R:CSX75 4.2 8.5 0.5
CA R:CSX75 4.3 9.9 0.5
CA R:CYS546 4.3 9.3 0.5
CD R:ARG476 4.4 10.4 0.5
NH1 R:ARG476 4.4 11.4 0.5
CA R:CYS72 4.4 11.3 0.5
CB R:VAL74 4.4 8.3 0.5
C3 R:FCO1550 4.5 8.4 0.5
N R:CYS546 4.5 8.5 0.5
N2 R:FCO1550 4.5 8.7 0.5
CA R:CYS546 4.5 8.2 0.5
N R:CYS546 4.6 9.1 0.5
NH1 R:ARG476 4.6 10.5 0.5
CA R:CYS543 4.6 8.2 0.5
CA R:CYS543 4.6 9.0 0.5
NE R:ARG476 4.7 11.0 0.5
CZ R:ARG476 4.7 10.9 0.5
C R:VAL74 4.7 9.4 0.5
O3 R:FCO1550 4.8 10.8 0.5
N R:VAL74 4.8 9.8 0.5
CD R:ARG476 4.8 9.2 0.5
N1 R:FCO1550 4.8 8.1 0.5
CZ R:ARG476 4.8 9.0 0.5
NE2 R:HIS79 4.8 9.4 0.5
NE R:ARG476 4.9 10.3 0.5
CA R:VAL74 4.9 9.9 0.5
C R:CYS72 4.9 10.8 0.5
C R:CSX75 4.9 11.0 0.5
CG R:GLU25 5.0 9.7 0.5
O R:CSX75 5.0 12.5 0.5

Nickel binding site 4 out of 4 in 4urh

Go back to Nickel Binding Sites List in 4urh
Nickel binding site 4 out of 4 in the High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of High-Resolution Structure of Partially Oxidized D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ni1551

b:17.5
occ:1.00
 O S:HOH2047 1.8 15.9 0.8
OD S:CSX75 1.9 15.0 0.5
SG S:CYS543 2.1 15.5 0.8
SG S:CYS72 2.1 16.1 1.0
SG S:CYS546 2.6 13.9 1.0
SG S:CYS543 2.6 16.5 0.2
SG S:CSX75 2.7 13.6 1.0
CB S:CYS72 2.9 13.6 1.0
FE S:FCO1550 3.0 13.2 1.0
CB S:CYS543 3.1 14.8 0.2
CB S:CYS543 3.2 12.3 0.8
CB S:CYS546 3.6 11.7 1.0
N S:CSX75 3.7 11.3 1.0
CB S:CSX75 3.7 11.5 1.0
C1 S:FCO1550 4.0 13.6 1.0
CA S:CSX75 4.3 10.8 1.0
C2 S:FCO1550 4.3 13.1 1.0
CA S:CYS72 4.4 11.6 1.0
N S:CYS546 4.5 11.2 1.0
CB S:VAL74 4.5 11.3 1.0
CA S:CYS546 4.5 12.1 1.0
CA S:CYS543 4.5 13.4 1.0
C3 S:FCO1550 4.6 13.9 1.0
NH1 S:ARG476 4.6 18.2 1.0
C S:VAL74 4.8 10.3 1.0
N S:VAL74 4.8 11.4 1.0
CG S:GLU25 4.8 13.6 1.0
CD S:ARG476 4.8 14.6 1.0
CZ S:ARG476 4.8 13.2 1.0
NE S:ARG476 4.9 14.3 1.0
C S:CYS72 4.9 12.5 1.0
N1 S:FCO1550 4.9 14.4 1.0
CA S:VAL74 4.9 12.5 1.0
C S:CSX75 5.0 11.8 1.0

Reference:

A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.De Lacey, P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps. Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures For the Elusive Unready Oxidized States. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25315838
DOI: 10.1007/S00775-014-1203-9
Page generated: Wed Oct 9 19:15:22 2024

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