Atomistry » Nickel » PDB 5i8s-5mdj » 5jrd
Atomistry »
  Nickel »
    PDB 5i8s-5mdj »
      5jrd »

Nickel in PDB 5jrd: E. Coli Hydrogenase-1 Variant P508A

Enzymatic activity of E. Coli Hydrogenase-1 Variant P508A

All present enzymatic activity of E. Coli Hydrogenase-1 Variant P508A:
1.12.99.6;

Protein crystallography data

The structure of E. Coli Hydrogenase-1 Variant P508A, PDB code: 5jrd was solved by S.B.Carr, S.E.V.Phillips, F.A.Armstrong, R.M.Evans, E.J.Brooke, S.T.A.Islam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.69 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.691, 98.589, 185.373, 90.00, 90.00, 90.00
R / Rfree (%) 12.1 / 14.1

Other elements in 5jrd:

The structure of E. Coli Hydrogenase-1 Variant P508A also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 26 atoms
Chlorine (Cl) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the E. Coli Hydrogenase-1 Variant P508A (pdb code 5jrd). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the E. Coli Hydrogenase-1 Variant P508A, PDB code: 5jrd:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5jrd

Go back to Nickel Binding Sites List in 5jrd
Nickel binding site 1 out of 2 in the E. Coli Hydrogenase-1 Variant P508A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of E. Coli Hydrogenase-1 Variant P508A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni602

b:19.5
occ:0.80
SG L:CYS576 1.9 20.4 0.8
SG L:CYS76 1.9 19.1 0.8
O L:HOH949 2.0 10.1 1.0
OD L:CSO79 2.0 16.7 1.0
SG L:CYS579 2.5 12.3 1.0
CB L:CYS76 2.8 19.2 0.8
CB L:CYS76 2.8 17.8 0.2
SG L:CSO79 3.1 12.1 1.0
FE L:FCO601 3.2 11.3 1.0
CB L:CYS576 3.3 14.3 0.8
CB L:CYS576 3.4 10.1 0.2
SG L:CYS576 3.4 11.0 0.2
SG L:CYS76 3.4 19.9 0.2
CB L:CYS579 3.6 11.0 1.0
N L:CSO79 4.0 17.4 1.0
CA L:CYS76 4.1 14.0 0.8
C1 L:FCO601 4.2 11.2 1.0
CB L:CSO79 4.2 16.3 1.0
CA L:CYS76 4.2 13.5 0.2
N L:CYS579 4.3 10.1 1.0
CA L:CYS579 4.4 10.9 1.0
CB L:VAL78 4.5 17.7 1.0
C2 L:FCO601 4.5 11.5 1.0
CA L:CYS576 4.6 10.2 0.2
CA L:CYS576 4.6 10.7 0.8
CA L:CSO79 4.7 16.9 1.0
C3 L:FCO601 4.7 11.6 1.0
C L:CYS76 4.7 12.2 1.0
N L:VAL78 4.8 15.8 1.0
CG L:GLU28 4.8 19.1 1.0
OE1 L:GLU28 4.9 20.6 1.0
C L:VAL78 5.0 19.6 1.0
CA L:VAL78 5.0 17.1 1.0

Nickel binding site 2 out of 2 in 5jrd

Go back to Nickel Binding Sites List in 5jrd
Nickel binding site 2 out of 2 in the E. Coli Hydrogenase-1 Variant P508A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of E. Coli Hydrogenase-1 Variant P508A within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni602

b:21.2
occ:0.80
O M:HOH918 1.9 10.2 1.0
SG M:CYS576 1.9 21.9 0.8
SG M:CYS76 2.0 19.5 0.8
OD M:CSO79 2.0 18.3 1.0
SG M:CYS579 2.6 12.5 1.0
CB M:CYS76 2.8 20.4 0.8
CB M:CYS76 2.8 20.0 0.2
SG M:CSO79 3.1 12.4 1.0
FE M:FCO601 3.1 11.5 1.0
CB M:CYS576 3.3 14.9 0.8
SG M:CYS576 3.3 10.9 0.2
SG M:CYS76 3.4 22.8 0.2
CB M:CYS576 3.4 11.0 0.2
CB M:CYS579 3.6 11.2 1.0
N M:CSO79 4.0 16.5 1.0
CB M:CSO79 4.1 15.4 1.0
C1 M:FCO601 4.1 11.7 1.0
CA M:CYS76 4.2 15.0 0.8
CA M:CYS76 4.2 14.8 0.2
N M:CYS579 4.3 11.0 1.0
C2 M:FCO601 4.4 11.7 1.0
CB M:VAL78 4.4 19.0 1.0
CA M:CYS579 4.5 10.9 1.0
CA M:CYS576 4.6 11.0 0.2
CA M:CYS576 4.6 10.8 0.8
CA M:CSO79 4.6 17.0 1.0
C3 M:FCO601 4.7 10.9 1.0
C M:CYS76 4.8 12.2 1.0
N M:VAL78 4.8 16.5 1.0
CG M:GLU28 4.8 18.7 1.0
OE1 M:GLU28 4.9 20.4 1.0
C M:VAL78 4.9 19.4 1.0
CA M:VAL78 4.9 17.8 1.0
NH1 M:ARG509 5.0 17.4 1.0

Reference:

E.J.Brooke, R.M.Evans, S.T.Islam, G.M.Roberts, S.A.Wehlin, S.B.Carr, S.E.Phillips, F.A.Armstrong. Importance of the Active Site "Canopy" Residues in An O2-Tolerant [Nife]-Hydrogenase. Biochemistry V. 56 132 2017.
ISSN: ISSN 1520-4995
PubMed: 28001048
DOI: 10.1021/ACS.BIOCHEM.6B00868
Page generated: Wed Dec 16 01:41:22 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