Atomistry » Nickel » PDB 6r44-6vwy » 6rp2
Atomistry »
  Nickel »
    PDB 6r44-6vwy »
      6rp2 »

Nickel in PDB 6rp2: Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1

Enzymatic activity of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1

All present enzymatic activity of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1:
1.12.99.6;

Protein crystallography data

The structure of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1, PDB code: 6rp2 was solved by S.B.Carr, F.A.Armstrong, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.07 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.720, 97.520, 183.060, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 15.9

Other elements in 6rp2:

The structure of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 also contains other interesting chemical elements:

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

Nickel Binding Sites:

The binding sites of Nickel atom in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 (pdb code 6rp2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1, PDB code: 6rp2:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6rp2

Go back to Nickel Binding Sites List in 6rp2
Nickel binding site 1 out of 2 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni603

b:16.8
occ:1.00
O L:HOH1097 1.8 16.4 1.0
OD L:CSO79 1.8 19.1 0.8
SG L:CYS576 2.0 21.9 1.0
SG L:CYS76 2.2 15.0 1.0
SG L:CYS579 2.5 11.5 1.0
SG L:CSO79 2.6 11.7 1.0
FE L:FCO602 2.9 10.9 1.0
CB L:CYS76 3.0 12.3 1.0
CB L:CYS576 3.2 14.9 1.0
CB L:CYS579 3.6 9.9 1.0
CB L:CSO79 3.8 12.0 1.0
N L:CSO79 3.8 12.0 1.0
C1 L:FCO602 3.9 11.2 1.0
C2 L:FCO602 4.1 11.2 1.0
CA L:CSO79 4.4 11.7 1.0
NH1 L:ARG509 4.4 13.2 1.0
CB L:VAL78 4.4 11.9 1.0
CA L:CYS76 4.4 11.6 1.0
N L:CYS579 4.5 9.8 1.0
C3 L:FCO602 4.5 11.3 1.0
CA L:CYS579 4.5 10.2 1.0
CA L:CYS576 4.5 11.7 1.0
CZ L:ARG509 4.8 12.0 1.0
N1 L:FCO602 4.8 11.6 1.0
C L:VAL78 4.8 11.8 1.0
NE L:ARG509 4.8 10.6 1.0
CD L:ARG509 4.8 11.1 1.0
N L:VAL78 4.9 11.2 1.0
CA L:VAL78 4.9 11.1 1.0
C L:CYS76 5.0 11.5 1.0

Nickel binding site 2 out of 2 in 6rp2

Go back to Nickel Binding Sites List in 6rp2
Nickel binding site 2 out of 2 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni602

b:16.9
occ:1.00
O M:HOH1022 1.8 15.7 1.0
OD M:CSO79 1.8 15.5 0.6
SG M:CYS576 2.0 20.3 1.0
SG M:CYS76 2.2 15.3 1.0
SG M:CYS579 2.6 11.6 1.0
SG M:CSO79 2.6 12.1 1.0
FE M:FCO601 2.9 11.1 1.0
CB M:CYS76 3.0 13.2 1.0
CB M:CYS576 3.2 14.7 1.0
CB M:CYS579 3.6 9.7 1.0
CB M:CSO79 3.8 10.6 1.0
N M:CSO79 3.8 11.3 1.0
C1 M:FCO601 3.9 12.1 1.0
C2 M:FCO601 4.1 11.5 1.0
NH1 M:ARG509 4.3 13.3 1.0
CA M:CSO79 4.4 11.1 1.0
CB M:VAL78 4.4 12.1 1.0
CA M:CYS76 4.4 11.8 1.0
C3 M:FCO601 4.5 11.2 1.0
N M:CYS579 4.5 10.3 1.0
CA M:CYS576 4.5 11.7 1.0
CA M:CYS579 4.5 10.5 1.0
CZ M:ARG509 4.7 12.4 1.0
N1 M:FCO601 4.8 12.4 1.0
C M:VAL78 4.8 11.3 1.0
NE M:ARG509 4.8 11.6 1.0
CD M:ARG509 4.8 11.3 1.0
N M:VAL78 4.9 11.5 1.0
CA M:VAL78 4.9 11.7 1.0
C M:CYS76 5.0 11.2 1.0

Reference:

L.Zhang, S.E.Beaton, S.B.Carr, F.A.Armstrong. Direct Visible Light Activation of A Surface Cysteine-Engineered [Nife]-Hydrogenase By Silver Nanoclusters Energy Environ Sci 2018.
ISSN: ESSN 1754-5706
DOI: 10.1039/C8EE02361A
Page generated: Wed Dec 16 01:53:29 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