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Nickel in PDB 5xlf: Crystal Structure of Aerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase

Enzymatic activity of Crystal Structure of Aerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase

All present enzymatic activity of Crystal Structure of Aerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Crystal Structure of Aerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase, PDB code: 5xlf was solved by K.Nishikawa, S.Mochida, T.Hiromoto, N.Shibata, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.05 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.570, 98.970, 127.120, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 17.5

Other elements in 5xlf:

The structure of Crystal Structure of Aerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 12 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Aerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase (pdb code 5xlf). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Aerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase, PDB code: 5xlf:

Nickel binding site 1 out of 1 in 5xlf

Go back to Nickel Binding Sites List in 5xlf
Nickel binding site 1 out of 1 in the Crystal Structure of Aerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Aerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni601

b:13.4
occ:0.84
 NI L:NFV601 0.0 13.4 0.8
SG L:CYS81 1.7 9.7 0.2
O4 L:NFV601 1.7 9.0 0.9
SG L:CSO546 2.1 14.8 1.0
SG L:CYS84 2.2 9.4 0.2
SG L:CYS81 2.3 13.5 0.8
OD L:CSO546 2.6 10.2 0.5
SG L:CYS549 2.7 11.2 1.0
SG L:CYS84 2.7 7.4 0.8
FE L:NFV601 2.9 10.4 1.0
CB L:CYS81 3.1 13.0 0.8
CB L:CYS81 3.2 10.1 0.2
CB L:CSO546 3.2 11.1 1.0
CB L:CYS84 3.4 7.8 0.2
CB L:CYS84 3.6 7.7 0.8
CB L:CYS549 3.7 8.6 1.0
N L:CYS84 3.7 7.3 0.8
N L:CYS84 3.8 7.3 0.2
C3 L:NFV601 4.0 7.6 1.0
C2 L:NFV601 4.2 5.6 1.0
CA L:CYS84 4.2 7.5 0.2
CA L:CYS84 4.3 7.4 0.8
CA L:CYS81 4.4 9.1 0.2
CB L:VAL83 4.5 5.0 1.0
CA L:CYS81 4.5 9.1 0.8
N L:CYS549 4.5 9.2 1.0
CA L:CSO546 4.5 7.1 1.0
CA L:CYS549 4.6 7.8 1.0
C1 L:NFV601 4.6 8.6 1.0
NH1 L:ARG479 4.6 8.5 1.0
CD L:ARG479 4.8 8.1 1.0
CZ L:ARG479 4.8 9.9 1.0
C L:VAL83 4.8 6.9 1.0
N3 L:NFV601 4.8 11.3 1.0
NE L:ARG479 4.8 8.1 1.0
N L:VAL83 4.9 8.0 1.0
CG L:GLU34 4.9 8.2 1.0
CA L:VAL83 5.0 6.2 1.0
C L:CYS81 5.0 9.6 0.8
C L:CYS81 5.0 9.5 0.2

Reference:

K.Nishikawa, S.Mochida, T.Hiromoto, N.Shibata, Y.Higuchi. Ni-Elimination From the Active Site of the Standard [Nife]‐Hydrogenase Upon Oxidation By O2. J. Inorg. Biochem. V. 177 435 2017.
ISSN: ISSN 1873-3344
PubMed: 28967475
DOI: 10.1016/J.JINORGBIO.2017.09.011
Page generated: Thu Oct 10 08:15:37 2024

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