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

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

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

Magnesium

(Mg)

1 atom

The binding sites of Cobalt 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 Cobalt atom.
In total only one binding site of Cobalt was determined in the Crystal Structure of Lignostilbene Bound to Co-LSD4 From Sphingobium Sp. Strain Syk-6, PDB code: 6xm8:

Cobalt 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 Cobalt with other atoms in the Co 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:Co501 b:12.5 occ:1.00 NE2 A:HIS476 2.0 8.1 1.0 NE2 A:HIS284 2.0 13.8 1.0 NE2 A:HIS167 2.1 11.7 1.0 NE2 A:HIS218 2.1 12.7 1.0 O A:HOH749 2.2 32.0 1.0 CE1 A:HIS167 2.9 12.8 1.0 CD2 A:HIS284 2.9 12.3 1.0 CE1 A:HIS476 2.9 9.3 1.0 CD2 A:HIS218 3.0 11.5 1.0 HE1 A:HIS167 3.0 15.4 1.0 CD2 A:HIS476 3.0 10.2 1.0 HD2 A:HIS284 3.0 14.8 1.0 CE1 A:HIS218 3.1 16.2 1.0 HE1 A:HIS476 3.1 11.2 1.0 CE1 A:HIS284 3.1 12.2 1.0 HD2 A:HIS218 3.1 13.8 1.0 CD2 A:HIS167 3.2 15.0 1.0 HD2 A:HIS476 3.2 12.2 1.0 HE1 A:HIS218 3.3 19.4 1.0 HE1 A:HIS284 3.4 14.6 1.0 HD2 A:HIS167 3.4 17.9 1.0 H081 A:V5P502 4.0 39.7 1.0 ND1 A:HIS476 4.0 9.9 1.0 ND1 A:HIS167 4.1 9.2 1.0 CG A:HIS476 4.1 8.1 1.0 CG A:HIS284 4.1 10.7 1.0 CG A:HIS218 4.1 12.6 1.0 ND1 A:HIS218 4.1 13.1 1.0 ND1 A:HIS284 4.2 11.6 1.0 CG A:HIS167 4.2 8.4 1.0 HG23 A:THR121 4.4 12.4 1.0 C08 A:V5P502 4.4 33.1 1.0 HG22 A:THR121 4.4 12.4 1.0 HG21 A:THR121 4.5 12.4 1.0 CG2 A:THR121 4.7 10.4 1.0 HD12 A:LEU475 4.7 18.0 1.0 HB2 A:ASP219 4.7 12.8 1.0 C09 A:V5P502 4.8 41.5 1.0 HD1 A:HIS476 4.8 11.9 1.0 HE1 A:PHE354 4.8 25.9 1.0 C10 A:V5P502 4.8 48.8 1.0 HD1 A:HIS167 4.8 11.0 1.0 HD1 A:HIS218 4.9 15.8 1.0 HD1 A:HIS284 5.0 13.9 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