Magnesium in PDB 6xm9: Crystal Structure of Vanillin Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6

The structure of Crystal Structure of Vanillin Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6, PDB code: 6xm9 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)	29.71 / 1.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	85.16, 112.157, 115.311, 90, 90, 90
R / Rfree (%)	15.9 / 18.7

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

Cobalt

(Co)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Vanillin Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 (pdb code 6xm9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Vanillin Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6, PDB code: 6xm9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Vanillin 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 Vanillin Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg513 b:30.1 occ:0.85 O A:HOH1039 1.9 33.5 1.0 O A:HOH672 2.0 29.9 1.0 O A:HOH691 2.0 28.9 1.0 O A:HOH646 2.2 25.3 1.0 O A:HOH713 3.0 32.1 1.0 OE1 A:GLU202 4.0 54.7 1.0 O A:ACT506 4.1 32.3 1.0 HA A:PHE155 4.1 15.9 1.0 O A:GLY201 4.4 17.5 1.0 OE1 A:GLU153 4.4 19.5 1.0 OXT A:ACT506 4.4 26.8 1.0 OE2 A:GLU153 4.6 15.8 1.0 O A:HOH1058 4.6 36.9 1.0 C A:ACT506 4.6 30.8 1.0 HZ1 A:LYS129 4.6 61.5 1.0 HA A:GLU202 4.7 23.4 1.0 CD A:GLU202 4.8 50.6 1.0 H A:GLY156 4.8 24.1 1.0 CD A:GLU153 4.9 16.4 1.0 HD1 A:PHE155 4.9 16.7 1.0 O A:HOH858 5.0 18.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Vanillin 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 2 of Crystal Structure of Vanillin Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg514 b:36.1 occ:0.49 O A:HOH603 2.0 39.4 1.0 O A:HOH1130 2.1 38.2 1.0 O A:HOH1046 2.4 44.4 1.0 O A:HOH709 2.5 25.0 1.0 O A:HOH1123 3.4 44.2 1.0 HG3 A:GLU303 3.5 32.3 1.0 HG2 A:GLU303 3.7 32.3 1.0 O A:HOH727 3.9 20.2 1.0 OE2 A:GLU303 4.0 35.7 1.0 CG A:GLU303 4.0 26.9 1.0 O A:ASN279 4.2 13.0 1.0 O A:GLU303 4.3 14.9 1.0 O A:HOH1194 4.4 42.1 1.0 CD A:GLU303 4.5 33.6 1.0 O A:HOH608 4.6 44.6 1.0 HB3 A:ASN279 4.6 19.6 1.0

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