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

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

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

Protein crystallography data

The structure of Crystal Structure of Anaerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase, PDB code: 5xlg 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) 39.01 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.590, 98.960, 127.340, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 16.7

Other elements in 5xlg:

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

Nickel (Ni) 1 atom
Iron (Fe) 12 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 1 in 5xlg

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Anaerobically Purified and Aerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg602

b:10.3
occ:1.00
 O L:HOH740 2.1 8.7 1.0
O L:HOH726 2.1 9.6 1.0
O L:LEU498 2.1 10.1 1.0
O L:HOH743 2.1 10.6 1.0
NE2 L:HIS552 2.2 9.2 1.0
OE2 L:GLU62 2.2 9.4 1.0
CE1 L:HIS552 3.1 9.4 1.0
CD L:GLU62 3.1 9.4 1.0
CD2 L:HIS552 3.2 9.6 1.0
C L:LEU498 3.3 9.3 1.0
OE1 L:GLU62 3.4 9.5 1.0
N L:LEU498 3.7 12.4 1.0
CA L:LEU498 4.0 10.3 1.0
OE1 L:GLU337 4.1 12.0 1.0
OE1 L:GLN497 4.1 12.3 1.0
OE2 L:GLU337 4.1 11.0 1.0
NZ L:LYS374 4.2 9.6 1.0
CB L:LEU498 4.2 12.9 1.0
ND1 L:HIS552 4.2 10.4 1.0
O L:HOH963 4.3 9.4 1.0
O L:HOH768 4.3 11.7 1.0
CG L:HIS552 4.3 8.6 1.0
N L:VAL499 4.4 9.0 1.0
CG L:GLU62 4.5 8.5 1.0
CD L:GLU337 4.6 14.5 1.0
CD L:LYS374 4.6 11.9 1.0
CA L:VAL499 4.7 9.8 1.0
CE L:LYS374 4.7 10.4 1.0
C L:GLN497 4.8 9.1 1.0

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: Tue Aug 12 23:41:23 2025

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