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Nickel in PDB 3myr: Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State

Enzymatic activity of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State

All present enzymatic activity of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State, PDB code: 3myr was solved by H.Ogata, P.Kellers, W.Lubitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 205.750, 216.960, 119.800, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 16.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State (pdb code 3myr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State, PDB code: 3myr:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 3myr

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Nickel binding site 1 out of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni2005

b:22.3
occ:1.00
NI B:NFV2005 0.0 22.3 1.0
O4 B:NFV2005 1.9 20.0 1.0
SG B:CYS1555 2.2 24.4 1.0
SG B:CYS1061 2.3 23.9 1.0
SG B:CYS1064 2.6 21.7 1.0
SG B:CYS1558 2.6 20.1 1.0
FE B:NFV2005 3.0 16.3 1.0
CB B:CYS1061 3.0 22.1 1.0
CB B:CYS1555 3.2 18.2 1.0
CB B:CYS1558 3.6 16.8 1.0
N B:CYS1064 3.7 19.3 1.0
CB B:CYS1064 3.9 18.2 1.0
C3 B:NFV2005 4.0 20.9 1.0
C2 B:NFV2005 4.3 13.9 1.0
CA B:CYS1064 4.3 20.5 1.0
N B:CYS1558 4.3 16.1 1.0
C1 B:NFV2005 4.4 19.5 1.0
CB B:VAL1063 4.4 21.9 1.0
CA B:CYS1061 4.5 20.2 1.0
CA B:CYS1558 4.5 17.7 1.0
CA B:CYS1555 4.6 18.7 1.0
NH1 B:ARG1487 4.7 24.0 1.0
C B:VAL1063 4.7 20.4 1.0
N B:VAL1063 4.8 21.6 1.0
CD B:ARG1487 4.8 14.6 1.0
N3 B:NFV2005 4.8 16.9 1.0
CZ B:ARG1487 4.8 23.2 1.0
CG B:GLU1014 4.8 20.6 1.0
NE B:ARG1487 4.9 19.9 1.0
C B:CYS1061 4.9 19.2 1.0
CA B:VAL1063 4.9 18.7 1.0

Nickel binding site 2 out of 4 in 3myr

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Nickel binding site 2 out of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni2005

b:22.7
occ:1.00
NI D:NFV2005 0.0 22.7 1.0
O4 D:NFV2005 1.9 19.3 1.0
SG D:CYS1555 2.2 30.9 1.0
SG D:CYS1061 2.2 29.6 1.0
SG D:CYS1558 2.6 24.3 1.0
SG D:CYS1064 2.7 24.6 1.0
FE D:NFV2005 3.0 18.2 1.0
CB D:CYS1061 3.0 25.7 1.0
CB D:CYS1555 3.2 26.9 1.0
CB D:CYS1558 3.6 25.5 1.0
N D:CYS1064 3.7 25.5 1.0
CB D:CYS1064 3.8 26.2 1.0
C3 D:NFV2005 4.0 18.7 1.0
C1 D:NFV2005 4.3 13.8 1.0
CA D:CYS1064 4.4 26.0 1.0
CB D:VAL1063 4.4 28.2 1.0
N D:CYS1558 4.4 25.6 1.0
C2 D:NFV2005 4.4 17.3 1.0
CA D:CYS1061 4.4 25.1 1.0
CA D:CYS1558 4.5 25.8 1.0
CA D:CYS1555 4.6 27.7 1.0
C D:VAL1063 4.8 27.4 1.0
NH1 D:ARG1487 4.8 25.4 1.0
CG D:GLU1014 4.8 24.4 1.0
N D:VAL1063 4.8 25.8 1.0
C D:CYS1061 4.9 25.1 1.0
CZ D:ARG1487 4.9 26.0 1.0
CD D:ARG1487 4.9 26.5 1.0
CA D:VAL1063 4.9 25.8 1.0
NE D:ARG1487 4.9 24.4 1.0
N3 D:NFV2005 4.9 15.4 1.0

Nickel binding site 3 out of 4 in 3myr

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Nickel binding site 3 out of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni2005

b:22.1
occ:1.00
NI F:NFV2005 0.0 22.1 1.0
O4 F:NFV2005 1.9 21.3 1.0
SG F:CYS1061 2.2 29.8 1.0
SG F:CYS1555 2.3 30.5 1.0
SG F:CYS1064 2.6 25.3 1.0
SG F:CYS1558 2.7 25.0 1.0
FE F:NFV2005 3.0 18.9 1.0
CB F:CYS1061 3.0 25.7 1.0
CB F:CYS1555 3.2 24.7 1.0
CB F:CYS1558 3.6 26.4 1.0
N F:CYS1064 3.7 25.3 1.0
CB F:CYS1064 3.8 24.3 1.0
C3 F:NFV2005 3.9 21.3 1.0
C2 F:NFV2005 4.3 18.9 1.0
CA F:CYS1064 4.3 26.5 1.0
C1 F:NFV2005 4.3 18.9 1.0
CB F:VAL1063 4.4 28.7 1.0
CA F:CYS1061 4.5 25.4 1.0
N F:CYS1558 4.5 26.9 1.0
CA F:CYS1558 4.5 26.1 1.0
NH1 F:ARG1487 4.6 24.9 1.0
CA F:CYS1555 4.6 26.1 1.0
N3 F:NFV2005 4.7 16.4 1.0
C F:VAL1063 4.8 27.5 1.0
CG F:GLU1014 4.8 26.1 1.0
N F:VAL1063 4.8 27.4 1.0
CD F:ARG1487 4.8 20.2 1.0
CZ F:ARG1487 4.8 27.2 1.0
NE F:ARG1487 4.9 24.9 1.0
C F:CYS1061 4.9 25.9 1.0
CA F:VAL1063 4.9 27.4 1.0
CB F:GLU1014 5.0 25.1 1.0

Nickel binding site 4 out of 4 in 3myr

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Nickel binding site 4 out of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni2005

b:20.5
occ:1.00
NI H:NFV2005 0.0 20.5 1.0
O4 H:NFV2005 1.9 18.0 1.0
SG H:CYS1061 2.2 23.4 1.0
SG H:CYS1555 2.3 26.4 1.0
SG H:CYS1064 2.5 24.1 1.0
SG H:CYS1558 2.6 20.9 1.0
CB H:CYS1061 3.0 21.3 1.0
FE H:NFV2005 3.0 16.8 1.0
CB H:CYS1555 3.3 23.7 1.0
CB H:CYS1558 3.6 22.1 1.0
N H:CYS1064 3.7 21.5 1.0
CB H:CYS1064 3.8 21.3 1.0
C3 H:NFV2005 4.0 15.7 1.0
C2 H:NFV2005 4.2 19.1 1.0
CA H:CYS1064 4.3 23.6 1.0
N H:CYS1558 4.3 21.1 1.0
C1 H:NFV2005 4.3 22.3 1.0
CB H:VAL1063 4.4 23.9 1.0
CA H:CYS1061 4.5 20.9 1.0
CA H:CYS1558 4.5 21.8 1.0
NH1 H:ARG1487 4.6 24.6 1.0
CA H:CYS1555 4.7 24.6 1.0
N H:VAL1063 4.7 22.4 1.0
C H:VAL1063 4.7 24.1 1.0
CD H:ARG1487 4.8 20.0 1.0
N3 H:NFV2005 4.9 13.6 1.0
CA H:VAL1063 4.9 23.2 1.0
CG H:GLU1014 4.9 22.9 1.0
C H:CYS1061 4.9 23.7 1.0
CZ H:ARG1487 4.9 25.2 1.0
NE H:ARG1487 4.9 20.4 1.0

Reference:

H.Ogata, P.Kellers, W.Lubitz. The Crystal Structure of the [Nife] Hydrogenase From the Photosynthetic Bacterium Allochromatium Vinosum: Characterization of the Oxidized Enzyme (Ni-A State). J.Mol.Biol. V. 402 428 2010.
ISSN: ISSN 0022-2836
PubMed: 20673834
DOI: 10.1016/J.JMB.2010.07.041
Page generated: Fri Sep 25 08:28:46 2020
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