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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: Thu Oct 10 08:49:28 2024

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