Atomistry » Nickel » PDB 3u4s-446d » 3use
Atomistry »
  Nickel »
    PDB 3u4s-446d »
      3use »

Nickel in PDB 3use: Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form

Enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form

All present enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form, PDB code: 3use was solved by A.Volbeda, J.C.Fontecilla-Camps, C.Darnault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.930, 97.790, 183.290, 90.00, 90.00, 90.00
R / Rfree (%) 12 / 16.8

Other elements in 3use:

The structure of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 32 atoms
Chlorine (Cl) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form (pdb code 3use). 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 E. Coli Hydrogenase-1 in Its As-Isolated Form, PDB code: 3use:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3use

Go back to Nickel Binding Sites List in 3use
Nickel binding site 1 out of 2 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


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 E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni602

b:11.5
occ:1.00
O L:HOH701 1.9 9.7 1.0
SG L:CYS576 2.2 10.9 1.0
SG L:CYS76 2.2 9.6 1.0
O L:HOH702 2.4 10.3 0.2
SG L:CYS79 2.5 9.2 1.0
SG L:CYS579 2.6 8.6 1.0
FE L:FCO601 2.9 8.7 1.0
CB L:CYS76 3.1 9.4 1.0
CB L:CYS576 3.2 9.6 1.0
CB L:CYS79 3.6 8.0 1.0
CB L:CYS579 3.7 8.1 1.0
N L:CYS79 3.7 8.2 1.0
C1 L:FCO601 4.0 7.8 1.0
C2 L:FCO601 4.1 8.7 1.0
CA L:CYS79 4.2 8.0 1.0
NH1 L:ARG509 4.4 9.5 1.0
C3 L:FCO601 4.4 8.8 1.0
CA L:CYS76 4.5 8.7 1.0
CB L:VAL78 4.5 7.7 1.0
N L:CYS579 4.6 8.7 1.0
CZ L:ARG509 4.6 9.1 1.0
CA L:CYS576 4.6 8.8 1.0
CA L:CYS579 4.6 7.6 1.0
C L:VAL78 4.7 9.2 1.0
NE L:ARG509 4.8 8.9 1.0
CD L:ARG509 4.9 8.0 1.0
N1 L:FCO601 4.9 9.2 1.0
N L:VAL78 4.9 7.9 1.0
CA L:VAL78 4.9 9.1 1.0

Nickel binding site 2 out of 2 in 3use

Go back to Nickel Binding Sites List in 3use
Nickel binding site 2 out of 2 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


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 E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni602

b:11.7
occ:1.00
O M:HOH701 1.8 9.9 1.0
SG M:CYS576 2.2 10.0 1.0
SG M:CYS76 2.2 12.0 1.0
O M:HOH702 2.4 9.6 0.2
SG M:CYS79 2.4 8.4 1.0
SG M:CYS579 2.7 8.0 1.0
FE M:FCO601 2.9 7.9 1.0
CB M:CYS76 3.1 9.2 1.0
CB M:CYS576 3.2 8.1 1.0
CB M:CYS79 3.6 8.2 1.0
CB M:CYS579 3.7 7.3 1.0
N M:CYS79 3.7 8.2 1.0
C1 M:FCO601 4.0 8.5 1.0
C2 M:FCO601 4.1 7.1 1.0
CA M:CYS79 4.2 9.1 1.0
NH1 M:ARG509 4.3 8.1 1.0
C3 M:FCO601 4.4 8.0 1.0
CA M:CYS76 4.5 6.9 1.0
CZ M:ARG509 4.5 9.0 1.0
CB M:VAL78 4.6 10.5 1.0
CA M:CYS576 4.6 7.7 1.0
N M:CYS579 4.6 6.4 1.0
CA M:CYS579 4.6 6.3 1.0
NE M:ARG509 4.7 6.5 1.0
C M:VAL78 4.7 8.7 1.0
CD M:ARG509 4.8 6.3 1.0
N1 M:FCO601 4.9 8.5 1.0
N M:VAL78 4.9 8.3 1.0
CA M:VAL78 5.0 9.4 1.0

Reference:

A.Volbeda, P.Amara, C.Darnault, J.M.Mouesca, A.Parkin, M.M.Roessler, F.A.Armstrong, J.C.Fontecilla-Camps. X-Ray Crystallographic and Computational Studies of the O2-Tolerant [Nife]-Hydrogenase 1 From Escherichia Coli. Proc.Natl.Acad.Sci.Usa V. 109 5305 2012.
ISSN: ISSN 0027-8424
PubMed: 22431599
DOI: 10.1073/PNAS.1119806109
Page generated: Wed Dec 16 01:28:18 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