Atomistry » Nickel » PDB 5tvr-5xgz » 5xf9
Atomistry »
  Nickel »
    PDB 5tvr-5xgz »
      5xf9 »

Nickel in PDB 5xf9: Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State

Protein crystallography data

The structure of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State, PDB code: 5xf9 was solved by Y.Shomura, M.Taketa, H.Nakashima, H.Tai, H.Nakagawa, Y.Ikeda, M.Ishii, Y.Igarashi, H.Nishihara, K.S.Yoon, S.Ogo, S.Hirota, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.04 / 2.58
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.590, 190.090, 124.580, 90.00, 109.44, 90.00
R / Rfree (%) 19.7 / 24.4

Other elements in 5xf9:

The structure of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 38 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State (pdb code 5xf9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State, PDB code: 5xf9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5xf9

Go back to Nickel Binding Sites List in 5xf9
Nickel binding site 1 out of 2 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized 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 Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni502

b:43.9
occ:1.00
OE1 D:GLU32 2.2 44.8 1.0
OE2 D:GLU32 2.2 41.7 1.0
SG D:CYS462 2.3 43.0 1.0
SG D:CYS465 2.3 36.2 1.0
SG D:CYS83 2.3 39.0 1.0
SG D:CYS80 2.4 43.0 1.0
CD D:GLU32 2.5 43.3 1.0
FE D:FCO501 2.9 32.9 1.0
CB D:CYS462 3.1 39.4 1.0
CB D:CYS80 3.5 37.6 1.0
CB D:CYS83 3.5 34.0 1.0
CB D:CYS465 3.7 35.2 1.0
CA D:CYS462 3.8 38.8 1.0
N D:CYS465 3.9 36.5 1.0
CG D:GLU32 4.0 43.1 1.0
C1 D:FCO501 4.0 31.5 1.0
C2 D:FCO501 4.0 31.8 1.0
N D:CYS83 4.3 30.3 1.0
CA D:CYS465 4.4 35.1 1.0
C3 D:FCO501 4.4 31.4 1.0
NH2 D:ARG396 4.5 41.6 1.0
C D:CYS462 4.5 37.3 1.0
CA D:CYS83 4.6 31.5 1.0
CB D:SER464 4.7 42.7 1.0
O D:CYS462 4.9 38.0 1.0
CA D:CYS80 4.9 35.1 1.0
N2 D:FCO501 4.9 31.3 1.0
CZ D:ARG396 4.9 38.2 1.0
CB D:GLU32 4.9 42.1 1.0
CB D:ILE82 4.9 30.4 1.0
N D:ILE82 5.0 29.8 1.0
C D:SER464 5.0 37.7 1.0
N1 D:FCO501 5.0 33.1 1.0

Nickel binding site 2 out of 2 in 5xf9

Go back to Nickel Binding Sites List in 5xf9
Nickel binding site 2 out of 2 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized 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 Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni502

b:44.2
occ:1.00
OE2 H:GLU32 2.2 45.9 1.0
OE1 H:GLU32 2.2 47.7 1.0
SG H:CYS462 2.3 39.8 1.0
SG H:CYS83 2.3 41.0 1.0
SG H:CYS80 2.4 41.5 1.0
SG H:CYS465 2.4 35.4 1.0
CD H:GLU32 2.5 48.3 1.0
FE H:FCO501 2.9 34.0 1.0
CB H:CYS462 3.1 39.7 1.0
CB H:CYS80 3.5 37.8 1.0
CB H:CYS83 3.5 36.9 1.0
CB H:CYS465 3.7 35.9 1.0
CA H:CYS462 3.8 39.3 1.0
CG H:GLU32 4.0 46.6 1.0
N H:CYS465 4.0 35.5 1.0
C2 H:FCO501 4.0 31.8 1.0
C1 H:FCO501 4.1 35.9 1.0
N H:CYS83 4.3 32.3 1.0
C3 H:FCO501 4.3 36.2 1.0
CA H:CYS465 4.4 35.5 1.0
NH1 H:ARG396 4.5 39.8 1.0
C H:CYS462 4.5 38.7 1.0
CA H:CYS83 4.6 34.3 1.0
CB H:SER464 4.7 37.6 1.0
CZ H:ARG396 4.8 38.5 1.0
CA H:CYS80 4.9 35.0 1.0
CB H:ILE82 4.9 33.1 1.0
O H:CYS462 4.9 36.3 1.0
CB H:GLU32 4.9 44.7 1.0
N1 H:FCO501 5.0 36.2 1.0
N2 H:FCO501 5.0 31.0 1.0
C H:SER464 5.0 36.0 1.0

Reference:

Y.Shomura, M.Taketa, H.Nakashima, H.Tai, H.Nakagawa, Y.Ikeda, M.Ishii, Y.Igarashi, H.Nishihara, K.S.Yoon, S.Ogo, S.Hirota, Y.Higuchi. Structural Basis of the Redox Switches in the Nad(+)-Reducing Soluble [Nife]-Hydrogenase Science V. 357 928 2017.
ISSN: ESSN 1095-9203
PubMed: 28860386
DOI: 10.1126/SCIENCE.AAN4497
Page generated: Wed Dec 16 01:49:55 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy