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Nickel in PDB 6gal: Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10

Enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10

All present enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10:
1.12.99.6;

Protein crystallography data

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10, PDB code: 6gal was solved by S.B.Carr, F.A.Armstrong, R.M.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.12 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.906, 95.224, 183.910, 90.00, 90.00, 90.00
R / Rfree (%) 12 / 14.7

Other elements in 6gal:

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 24 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10 (pdb code 6gal). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10, PDB code: 6gal:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6gal

Go back to Nickel Binding Sites List in 6gal
Nickel binding site 1 out of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni601

b:9.2
occ:1.00
NI L:EJ2601 0.0 9.2 1.0
H L:EJ2601 1.6 8.1 1.0
SG L:CYS576 2.1 11.3 1.0
SG L:CYS76 2.2 8.3 1.0
SG L:CYS79 2.3 7.5 1.0
SG L:CYS579 2.4 7.9 1.0
FE L:EJ2601 2.6 7.0 1.0
H L:CYS79 2.9 7.5 1.0
HB2 L:CYS76 3.1 7.3 1.0
CB L:CYS76 3.1 7.2 1.0
HB3 L:CYS76 3.1 7.2 1.0
CB L:CYS576 3.3 8.5 1.0
HB2 L:CYS579 3.3 6.1 1.0
HB3 L:CYS576 3.4 8.8 1.0
HB2 L:CYS576 3.4 8.6 1.0
HB3 L:CYS79 3.4 7.8 1.0
CB L:CYS79 3.5 7.5 1.0
CB L:CYS579 3.5 6.1 1.0
C1 L:EJ2601 3.6 6.8 1.0
N L:CYS79 3.8 7.8 1.0
HB L:VAL78 3.8 8.5 1.0
C2 L:EJ2601 3.8 6.2 1.0
H L:CYS579 3.9 6.1 1.0
HD2 L:ARG509 4.0 8.5 1.0
HB3 L:CYS579 4.2 6.5 1.0
HH11 L:ARG509 4.2 8.7 1.0
CA L:CYS79 4.2 8.0 1.0
C3 L:EJ2601 4.2 7.3 1.0
HB2 L:CYS79 4.3 7.6 1.0
O L:HOH895 4.3 30.7 1.0
NH1 L:ARG509 4.3 9.3 1.0
H L:VAL78 4.3 7.0 1.0
HE2 L:HIS83 4.4 7.3 0.0
CA L:CYS76 4.5 6.7 1.0
HH12 L:ARG509 4.5 9.1 1.0
CA L:CYS579 4.5 6.2 1.0
N1 L:EJ2601 4.6 6.8 1.0
CZ L:ARG509 4.6 8.0 1.0
N L:CYS579 4.6 5.8 1.0
CA L:CYS576 4.6 7.7 1.0
HG3 L:GLN28 4.7 12.8 1.0
HA L:CYS579 4.7 6.1 1.0
NE L:ARG509 4.7 8.1 1.0
CB L:VAL78 4.7 8.6 1.0
CD L:ARG509 4.7 8.6 1.0
HA L:CYS76 4.7 6.8 1.0
N2 L:EJ2601 4.8 6.3 1.0
HA L:CYS576 4.8 7.7 1.0
C L:VAL78 4.9 8.5 1.0
HD3 L:ARG509 4.9 8.3 1.0
HA L:CYS79 4.9 8.1 1.0

Nickel binding site 2 out of 2 in 6gal

Go back to Nickel Binding Sites List in 6gal
Nickel binding site 2 out of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni602

b:9.5
occ:1.00
NI M:EJ2602 0.0 9.5 1.0
H M:EJ2602 1.6 8.7 1.0
SG M:CYS576 2.2 11.4 1.0
SG M:CYS76 2.3 8.8 1.0
SG M:CYS79 2.3 8.4 1.0
SG M:CYS579 2.5 8.2 1.0
FE M:EJ2602 2.6 7.8 1.0
H M:CYS79 2.9 8.1 1.0
CB M:CYS76 3.1 8.4 1.0
HB2 M:CYS76 3.1 8.3 1.0
HB3 M:CYS76 3.1 8.2 1.0
CB M:CYS576 3.3 8.7 1.0
HB2 M:CYS579 3.3 7.1 1.0
HB3 M:CYS576 3.3 8.6 1.0
HB2 M:CYS576 3.4 8.6 1.0
HB3 M:CYS79 3.4 8.2 1.0
CB M:CYS79 3.5 8.1 1.0
CB M:CYS579 3.5 7.3 1.0
C1 M:EJ2602 3.6 8.0 1.0
C2 M:EJ2602 3.7 6.9 1.0
N M:CYS79 3.8 7.9 1.0
HB M:VAL78 3.8 9.1 1.0
H M:CYS579 3.9 6.4 1.0
HD2 M:ARG509 4.0 8.5 1.0
O M:HOH881 4.1 35.6 1.0
HB3 M:CYS579 4.2 7.4 1.0
CA M:CYS79 4.2 8.4 1.0
HH11 M:ARG509 4.2 9.3 1.0
C3 M:EJ2602 4.2 8.2 1.0
HB2 M:CYS79 4.3 8.1 1.0
NH1 M:ARG509 4.3 10.1 1.0
H M:VAL78 4.3 7.7 1.0
HE2 M:HIS83 4.4 7.6 0.0
CA M:CYS76 4.5 7.1 1.0
CA M:CYS579 4.5 6.8 1.0
N M:CYS579 4.6 6.4 1.0
HH12 M:ARG509 4.6 9.8 1.0
N1 M:EJ2602 4.6 7.6 1.0
CZ M:ARG509 4.6 9.5 1.0
CA M:CYS576 4.6 6.6 1.0
HA M:CYS579 4.7 6.6 1.0
HG3 M:GLN28 4.7 11.9 1.0
N2 M:EJ2602 4.7 7.5 1.0
CB M:VAL78 4.7 9.2 1.0
CD M:ARG509 4.7 8.4 1.0
HA M:CYS76 4.7 7.2 1.0
NE M:ARG509 4.8 8.8 1.0
HA M:CYS576 4.8 6.5 1.0
C M:VAL78 4.8 8.4 1.0
HD3 M:ARG509 5.0 8.6 1.0
HA M:CYS79 5.0 8.8 1.0

Reference:

R.M.Evans, P.A.Ash, S.E.Beaton, E.J.Brooke, K.A.Vincent, S.B.Carr, F.A.Armstrong. Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J. Am. Chem. Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798
Page generated: Thu Oct 10 08:28:45 2024

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