Chlorine 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
Magnesium (Mg) 1 atom
Nickel (Ni) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total only one binding site of Chlorine was determined in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State, PDB code: 8w6x:

Chlorine binding site 1 out of 1 in 8w6x

Go back to Chlorine Binding Sites List in 8w6x
Chlorine binding site 1 out of 1 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 Chlorine with other atoms in the Cl 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:Cl610

b:21.1
occ:0.85
 HH12 L:ARG377 1.9 10.5 0.4
DH12 L:ARG377 1.9 13.8 0.6
HA L:ALA375 2.9 15.8 1.0
NH1 L:ARG377 2.9 10.4 1.0
HA3 L:GLY507 2.9 16.3 1.0
HB2 L:SER516 2.9 5.6 1.0
D1 L:HOH938 3.0 20.1 1.0
HB3 L:SER516 3.0 14.8 1.0
HD2 L:PRO376 3.0 13.4 1.0
HB1 L:ALA375 3.2 7.0 1.0
O L:PRO508 3.2 10.8 1.0
DH22 L:ARG377 3.2 5.8 0.9
HH22 L:ARG377 3.2 20.6 0.1
O L:TRP504 3.3 10.9 1.0
C L:GLY507 3.3 10.3 1.0
O L:GLY507 3.3 11.5 1.0
D L:GLY507 3.4 22.7 0.1
H L:GLY507 3.4 5.0 0.9
DH11 L:ARG377 3.4 11.5 0.7
HH11 L:ARG377 3.4 10.8 0.3
CA L:GLY507 3.4 10.2 1.0
CB L:SER516 3.5 10.4 1.0
O L:THR503 3.5 9.9 1.0
N L:GLY507 3.7 9.7 1.0
CA L:ALA375 3.7 9.6 1.0
O L:HOH938 3.8 8.2 1.0
CD L:PRO376 3.8 10.6 1.0
CZ L:ARG377 3.8 10.4 1.0
NH2 L:ARG377 3.9 10.7 1.0
CB L:ALA375 3.9 10.7 1.0
N L:PRO508 4.0 10.1 1.0
HD3 L:PRO376 4.0 16.2 1.0
HA L:SER516 4.0 7.9 1.0
HD2 L:PRO517 4.1 8.0 1.0
HA L:TRP504 4.1 6.6 1.0
C L:TRP504 4.1 9.4 1.0
D2 L:HOH938 4.2 24.8 1.0
N L:PRO376 4.2 9.6 1.0
HD3 L:PRO517 4.2 12.4 1.0
C L:ALA375 4.2 10.3 1.0
O L:PRO376 4.2 9.5 1.0
C L:PRO508 4.3 10.5 1.0
HB3 L:ALA375 4.3 18.5 1.0
CA L:SER516 4.4 10.1 1.0
HD2 L:PRO508 4.4 8.4 1.0
HA2 L:GLY507 4.5 5.2 1.0
DG L:SER516 4.5 6.5 0.7
HG L:SER516 4.5 16.3 0.3
OG L:SER516 4.6 11.3 1.0
O L:LYS374 4.6 9.6 1.0
CA L:TRP504 4.6 8.6 1.0
CD L:PRO517 4.6 9.7 1.0
C L:THR503 4.7 9.6 1.0
CA L:PRO508 4.7 11.1 1.0
C L:LEU506 4.8 10.4 1.0
CD L:PRO508 4.8 9.6 1.0
HB2 L:ALA375 4.8 10.9 1.0
HH21 L:ARG377 4.9 12.4 0.3
DH21 L:ARG377 4.9 10.6 0.7
N L:ALA375 5.0 10.7 1.0

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: Tue Jul 30 13:48:13 2024

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