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Nickel in PDB 8w6x: Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State

Enzymatic activity of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State

All present enzymatic activity of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State:
1.12.2.1;

Protein crystallography data

The structure of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State, PDB code: 8w6x was solved by T.Hiromoto, T.Tamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.705, 98.485, 126.86, 90, 90, 90
R / Rfree (%) 18.9 / 22

Other elements in 8w6x:

The structure of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State also contains other interesting chemical elements:

Iron (Fe) 12 atoms
Chlorine (Cl) 1 atom
Magnesium (Mg) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State (pdb code 8w6x). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State, PDB code: 8w6x:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 8w6x

Go back to Nickel Binding Sites List in 8w6x
Nickel binding site 1 out of 2 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni601

b:9.6
occ:0.68
NI L:NFU601 0.0 9.6 0.7
SG L:CYS546 1.6 10.7 0.3
OD L:CYS546 1.6 11.7 0.3
O L:OH608 1.7 8.1 0.7
SG L:CYS81 1.8 10.4 0.3
SG L:CYS81 2.2 10.3 0.7
SG L:CYS546 2.2 8.9 0.7
NI L:NFU601 2.4 11.1 0.3
SG L:CYS549 2.6 7.6 0.7
SG L:CYS84 2.7 9.3 1.0
H L:CYS84 2.7 4.5 0.8
D L:CYS84 2.7 13.9 0.2
OE1 L:GLU34 2.9 10.5 0.3
FE L:NFU601 2.9 7.8 1.0
SG L:CYS549 2.9 12.9 0.3
CB L:CYS81 3.0 8.2 0.7
HB3 L:CYS81 3.0 7.1 0.7
OE2 L:GLU34 3.1 10.0 0.3
HB2 L:CYS81 3.2 5.5 0.7
CD L:GLU34 3.2 9.9 0.3
CB L:CYS546 3.2 8.7 0.7
CB L:CYS546 3.3 8.7 0.3
HB2 L:CYS549 3.3 9.5 0.7
HB3 L:CYS546 3.3 7.5 0.7
HB3 L:CYS84 3.3 5.2 1.0
HB2 L:CYS546 3.4 10.1 0.7
CB L:CYS81 3.4 10.0 0.3
HB L:VAL83 3.4 8.6 0.7
HB L:VAL83 3.5 7.1 0.3
HB3 L:CYS546 3.5 10.1 0.3
HB3 L:CYS549 3.5 11.1 0.3
CB L:CYS84 3.5 8.8 1.0
CB L:CYS549 3.6 9.3 0.7
HB2 L:CYS81 3.7 9.6 0.3
N L:CYS84 3.7 8.1 1.0
HB2 L:CYS546 3.7 8.7 0.3
H L:CYS549 3.8 14.2 0.6
HA L:CYS81 3.9 6.5 0.3
CB L:CYS549 3.9 12.3 0.3
D L:VAL83 3.9 8.6 0.3
C1 L:NFU601 4.0 9.1 1.0
HB3 L:CYS81 4.1 11.8 0.3
HD2 L:ARG479 4.1 3.0 1.0
HG3 L:GLU34 4.1 7.7 0.7
C2 L:NFU601 4.2 8.8 1.0
CA L:CYS84 4.2 9.5 1.0
CA L:CYS81 4.2 8.7 0.3
HB3 L:GLU34 4.3 8.8 0.3
H L:VAL83 4.3 12.2 0.7
HA L:CYS546 4.3 9.2 0.3
HB3 L:CYS549 4.3 13.4 0.7
CA L:CYS546 4.4 8.1 0.3
HE2 L:HIS88 4.4 4.6 0.9
DE2 L:HIS88 4.4 20.5 0.1
C3 L:NFU601 4.4 10.0 1.0
HH11 L:ARG479 4.5 9.1 0.2
DH11 L:ARG479 4.5 5.3 0.8
CB L:VAL83 4.5 9.5 0.7
N L:CYS549 4.5 8.1 0.7
CA L:CYS81 4.5 7.9 0.7
HB2 L:CYS84 4.5 10.5 1.0
CB L:VAL83 4.5 8.6 0.3
CG L:GLU34 4.5 9.5 0.3
N L:CYS549 4.5 9.5 0.3
CA L:CYS549 4.5 8.0 0.7
NH1 L:ARG479 4.6 9.4 1.0
HB3 L:GLU34 4.6 10.4 0.7
CA L:CYS546 4.6 6.8 0.7
HG12 L:VAL83 4.7 11.7 0.7
N L:VAL83 4.7 8.2 0.3
HB2 L:CYS549 4.7 12.6 0.3
C L:VAL83 4.7 8.5 0.3
HB2 L:GLU34 4.7 9.3 0.3
HA L:CYS549 4.7 11.8 0.7
CB L:GLU34 4.8 8.9 0.3
C L:VAL83 4.8 8.1 0.7
HG12 L:VAL83 4.8 10.4 0.3
N1 L:NFU601 4.8 9.1 1.0
CZ L:ARG479 4.8 8.1 1.0
C L:CYS81 4.9 8.3 0.3
CA L:VAL83 4.9 8.4 0.3
HA L:CYS81 4.9 9.2 0.7
CA L:CYS549 4.9 10.8 0.3
NE L:ARG479 4.9 9.1 1.0
HA L:CYS546 4.9 2.5 0.7
N L:VAL83 4.9 8.8 0.7
D L:GLY82 4.9 8.8 0.1
CD L:ARG479 4.9 9.3 1.0
C L:CYS546 4.9 7.2 0.3
CA L:VAL83 4.9 8.6 0.7
HG3 L:GLU34 5.0 9.0 0.3
C L:CYS84 5.0 8.2 1.0
DH12 L:ARG479 5.0 4.0 0.5
HH12 L:ARG479 5.0 15.2 0.5
C L:CYS81 5.0 7.7 0.7
CG L:GLU34 5.0 8.6 0.7

Nickel binding site 2 out of 2 in 8w6x

Go back to Nickel Binding Sites List in 8w6x
Nickel binding site 2 out of 2 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni601

b:11.1
occ:0.32
NI L:NFU601 0.0 11.1 0.3
H L:CYS549 1.5 14.2 0.6
HB2 L:CYS549 1.7 9.5 0.7
SG L:CYS546 1.8 8.9 0.7
OE2 L:GLU34 1.8 10.0 0.3
CB L:CYS549 2.1 9.3 0.7
SG L:CYS549 2.1 12.9 0.3
N L:CYS549 2.2 8.1 0.7
SG L:CYS546 2.2 10.7 0.3
N L:CYS549 2.3 9.5 0.3
SG L:CYS549 2.3 7.6 0.7
NI L:NFU601 2.4 9.6 0.7
CA L:CYS549 2.6 8.0 0.7
HB2 L:CYS81 2.7 5.5 0.7
CB L:CYS549 2.7 12.3 0.3
HB3 L:CYS549 2.8 11.1 0.3
CD L:GLU34 2.8 9.9 0.3
HB3 L:CYS546 2.9 7.5 0.7
CB L:CYS546 3.0 8.7 0.7
HB3 L:CYS546 3.0 10.1 0.3
SG L:CYS81 3.0 10.3 0.7
CA L:CYS549 3.0 10.8 0.3
HA L:CYS549 3.1 11.8 0.7
CB L:CYS546 3.1 8.7 0.3
OE1 L:GLU34 3.1 10.5 0.3
HB3 L:CYS549 3.2 13.4 0.7
SG L:CYS81 3.2 10.4 0.3
CB L:CYS81 3.3 8.2 0.7
O L:OH608 3.3 8.1 0.7
D L:ALA548 3.3 8.3 0.5
O L:CYS546 3.4 6.2 0.3
H L:GLY550 3.4 11.1 0.4
C L:ALA548 3.4 7.7 0.7
C L:CYS546 3.4 7.2 0.3
C L:ALA548 3.5 9.4 0.3
HB3 L:ALA548 3.5 7.9 0.3
OD L:CYS546 3.5 11.7 0.3
O L:CYS546 3.5 8.5 0.7
CA L:CYS546 3.6 8.1 0.3
N L:ALA548 3.6 7.3 0.3
C L:CYS546 3.6 7.4 0.7
HB2 L:ALA548 3.7 8.6 0.7
HA L:CYS546 3.7 9.2 0.3
HB2 L:ALA548 3.7 8.9 0.3
HB2 L:CYS81 3.8 9.6 0.3
HB2 L:CYS546 3.8 10.1 0.7
HB2 L:CYS549 3.8 12.6 0.3
CA L:CYS546 3.8 6.8 0.7
HA L:CYS81 3.8 6.5 0.3
HB3 L:CYS81 3.8 7.1 0.7
CA L:ALA548 3.8 8.2 0.3
OE2 L:GLU34 3.8 8.8 0.7
H L:GLY550 3.9 9.6 0.6
HA L:CYS549 3.9 10.6 0.3
CB L:ALA548 3.9 8.0 0.3
H L:ALA548 3.9 17.4 0.6
C L:CYS549 3.9 7.9 0.7
N L:GLY550 3.9 10.3 0.3
C L:CYS549 3.9 9.9 0.3
N L:ALA548 4.0 8.7 0.7
HB1 L:ALA548 4.0 7.1 0.7
FE L:NFU601 4.0 7.8 1.0
CA L:ALA548 4.0 7.5 0.7
CB L:CYS81 4.0 10.0 0.3
N L:ILE547 4.1 8.4 0.3
HB2 L:CYS546 4.1 8.7 0.3
CB L:ALA548 4.1 8.2 0.7
HB3 L:GLU34 4.1 8.8 0.3
CG L:GLU34 4.2 9.5 0.3
HA L:CYS546 4.2 2.5 0.7
N L:GLY550 4.3 7.7 0.7
HG3 L:GLU34 4.3 7.7 0.7
C1 L:NFU601 4.3 9.1 1.0
N L:ILE547 4.3 6.7 0.7
O L:ALA548 4.3 7.5 0.7
C L:ILE547 4.4 7.7 0.3
O L:THR80 4.4 9.1 0.3
HG22 L:THR80 4.4 8.2 0.7
HB3 L:GLU34 4.4 10.4 0.7
HE2 L:HIS88 4.4 4.6 0.9
DE2 L:HIS88 4.4 20.5 0.1
HG2 L:GLU34 4.4 8.9 0.3
SG L:CYS84 4.4 9.3 1.0
CA L:CYS81 4.4 8.7 0.3
CD L:GLU34 4.5 8.8 0.7
D L:ILE547 4.5 13.5 0.1
O L:THR80 4.5 8.8 0.7
HG21 L:THR80 4.5 8.8 0.7
O L:ALA548 4.5 9.9 0.3
C L:ILE547 4.6 8.2 0.7
CA L:CYS81 4.6 7.9 0.7
HG11 L:VAL500 4.6 10.7 1.0
HA L:CYS81 4.7 9.2 0.7
CB L:GLU34 4.7 8.9 0.3
H L:ILE547 4.8 5.7 0.9
CA L:ILE547 4.8 7.7 0.3
N1 L:NFU601 4.8 9.1 1.0
CG L:GLU34 4.8 8.6 0.7
D L:CYS84 4.9 13.9 0.2
H L:CYS84 4.9 4.5 0.8
HA L:ALA548 4.9 8.4 0.3
O L:CYS549 5.0 7.1 0.7
HG3 L:GLU34 5.0 9.0 0.3
HB1 L:ALA548 5.0 7.2 0.3
CG2 L:THR80 5.0 7.3 0.7

Reference:

T.Hiromoto, K.Nishikawa, S.Inoue, H.Ogata, Y.Hori, K.Kusaka, Y.Hirano, K.Kurihara, Y.Shigeta, T.Tamada, Y.Higuchi. New Insights Into the Oxidation Process From Neutron and X-Ray Crystal Structures of An O2-Sensitive [Nife]-Hydrogenase. Chemical Science 2023.
DOI: 10.1039/D3SC02156D
Page generated: Thu Oct 10 09:48:39 2024

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