Cobalt 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:

Magnesium

(Mg)

2 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Vanillin Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6, PDB code: 6xm9:
Jump to Cobalt binding site number: 1; 2;

Cobalt 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 Cobalt with other atoms in the Co 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:Co511 b:14.4 occ:1.00 NE2 A:HIS284 2.0 8.8 1.0 NE2 A:HIS476 2.0 8.5 1.0 NE2 A:HIS218 2.1 10.2 1.0 NE2 A:HIS167 2.1 8.7 1.0 O A:HOH612 2.2 17.2 1.0 CE1 A:HIS476 3.0 10.2 1.0 CE1 A:HIS167 3.0 7.7 1.0 CD2 A:HIS284 3.0 10.0 1.0 CE1 A:HIS218 3.0 10.7 1.0 CD2 A:HIS476 3.0 8.8 1.0 CE1 A:HIS284 3.0 8.8 1.0 HE1 A:HIS167 3.1 9.2 1.0 CD2 A:HIS218 3.1 9.3 1.0 HD2 A:HIS284 3.1 12.1 1.0 HE1 A:HIS476 3.1 12.3 1.0 HE1 A:HIS218 3.2 12.9 1.0 CD2 A:HIS167 3.2 9.5 1.0 HD2 A:HIS476 3.2 10.5 1.0 HE1 A:HIS284 3.2 10.6 1.0 HD2 A:HIS218 3.3 11.1 1.0 HD2 A:HIS167 3.5 11.4 1.0 OAB A:V55501 4.0 21.8 1.0 ND1 A:HIS476 4.1 8.1 1.0 ND1 A:HIS284 4.1 10.5 1.0 CG A:HIS284 4.1 8.2 1.0 ND1 A:HIS218 4.1 8.8 1.0 CG A:HIS476 4.1 6.8 1.0 ND1 A:HIS167 4.1 8.9 1.0 CG A:HIS218 4.2 10.2 1.0 HG23 A:THR121 4.2 11.7 1.0 CAD A:V55501 4.3 18.5 1.0 CG A:HIS167 4.3 8.9 1.0 HG22 A:THR121 4.3 11.7 1.0 HG21 A:THR121 4.4 11.7 1.0 CG2 A:THR121 4.6 9.7 1.0 HD12 A:LEU475 4.6 15.3 1.0 O A:HOH817 4.7 20.1 1.0 HB2 A:ASP219 4.8 10.8 1.0 HD1 A:HIS476 4.8 9.8 1.0 HE1 A:PHE354 4.9 25.3 1.0 HD1 A:HIS218 4.9 10.6 1.0 HD1 A:HIS167 4.9 10.7 1.0 HD1 A:HIS284 4.9 12.6 1.0

Cobalt 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 Cobalt with other atoms in the Co 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:Co512 b:37.7 occ:0.56 HZ1 A:LYS158 2.8 37.5 1.0 NZ A:LYS158 3.6 31.2 1.0 HZ2 A:LYS158 3.7 37.5 1.0 O A:ILE204 3.7 15.3 1.0 HZ3 A:LYS158 3.8 37.5 1.0 O A:HOH876 3.9 23.4 1.0 HG23 A:ILE204 4.3 17.9 1.0 HA A:ILE204 4.4 18.6 1.0 CE A:LYS158 4.7 30.4 1.0 HE3 A:LYS158 4.8 36.5 1.0 C A:ILE204 4.8 16.6 1.0 HE2 A:LYS158 4.8 36.5 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