Magnesium in PDB 6xm8: Crystal Structure of Lignostilbene Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6

Protein crystallography data

The structure of Crystal Structure of Lignostilbene Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6, PDB code: 6xm8 was solved by E.Kuatsjah, A.C.Chan, R.Katahira, G.T.Beckham, M.E.Murphy, L.D.Eltis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.31 / 1.85
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.7, 112.54, 115.52, 90, 90, 90
R / Rfree (%) 14.7 / 17.3

Other elements in 6xm8:

The structure of Crystal Structure of Lignostilbene Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 also contains other interesting chemical elements:

Cobalt (Co) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Lignostilbene Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 (pdb code 6xm8). 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 Lignostilbene Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6, PDB code: 6xm8:

Magnesium binding site 1 out of 1 in 6xm8

Go back to Magnesium Binding Sites List in 6xm8
Magnesium binding site 1 out of 1 in the Crystal Structure of Lignostilbene Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6


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 Lignostilbene Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:46.5
occ:0.51
O A:HOH854 1.9 42.6 1.0
O A:HOH1061 2.0 52.9 1.0
O A:HOH1121 2.1 48.3 1.0
O A:HOH983 2.1 42.8 1.0
O A:HOH879 3.5 32.9 1.0
HA A:PHE155 3.8 19.8 1.0
OE2 A:GLU153 4.2 20.0 1.0
OE1 A:GLU153 4.3 24.9 1.0
H A:GLY156 4.3 29.3 1.0
O A:GLY201 4.4 21.3 1.0
N A:GLY156 4.7 24.5 1.0
CD A:GLU153 4.7 19.4 1.0
OE2 A:GLU202 4.7 58.4 1.0
CA A:PHE155 4.7 16.5 1.0
HD1 A:PHE155 4.8 16.5 1.0
O A:HOH887 4.9 23.8 1.0
HA A:GLU202 4.9 21.1 1.0
HZ1 A:LYS158 4.9 60.7 1.0
C A:PHE155 5.0 22.5 1.0

Reference:

E.Kuatsjah, A.C.K.Chan, R.Katahira, S.J.Haugen, G.T.Beckham, M.E.Murphy, L.D.Eltis. Structural and Functional Analysis of Lignostilbene Dioxygenases From Sphingobium Sp. Syk-6 J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Sun Jul 11 15:02:38 2021

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