Cobalt in PDB 8j2y: Acidimicrobiaceae Bacterium Photocobilins Protein, Dark State

The structure of Acidimicrobiaceae Bacterium Photocobilins Protein, Dark State, PDB code: 8j2y was solved by S.Zhang, H.Poddar, W.C.Levy, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.31 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	108.773, 125.836, 124.63, 90, 90, 90
R / Rfree (%)	20.9 / 23.7

The binding sites of Cobalt atom in the Acidimicrobiaceae Bacterium Photocobilins Protein, Dark State (pdb code 8j2y). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Acidimicrobiaceae Bacterium Photocobilins Protein, Dark State, PDB code: 8j2y:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Acidimicrobiaceae Bacterium Photocobilins Protein, Dark State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Acidimicrobiaceae Bacterium Photocobilins Protein, Dark State within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:34.9 occ:1.00 CO A:B12401 0.0 34.9 1.0 N23 A:B12401 1.9 34.8 1.0 N24 A:B12401 1.9 34.5 1.0 N21 A:B12401 1.9 36.4 1.0 N22 A:B12401 1.9 34.8 1.0 CE1 A:HIS103 2.2 34.9 1.0 C5' A:5AD402 2.5 48.3 1.0 C19 A:B12401 2.8 36.2 1.0 C14 A:B12401 2.8 34.5 1.0 C16 A:B12401 2.8 34.6 1.0 C4 A:B12401 2.9 37.4 1.0 C6 A:B12401 2.9 37.4 1.0 C9 A:B12401 2.9 36.1 1.0 C1 A:B12401 2.9 36.0 1.0 C11 A:B12401 2.9 35.1 1.0 NE2 A:HIS103 3.2 34.4 1.0 ND1 A:HIS103 3.2 34.4 1.0 C15 A:B12401 3.2 34.4 1.0 C4' A:5AD402 3.2 53.1 1.0 C5 A:B12401 3.3 38.6 1.0 C10 A:B12401 3.3 35.4 1.0 C20 A:B12401 3.6 34.8 1.0 O4' A:5AD402 3.7 55.6 1.0 C17 A:B12401 4.1 34.9 1.0 C2 A:B12401 4.1 37.7 1.0 C18 A:B12401 4.1 36.0 1.0 C3 A:B12401 4.2 39.1 1.0 C13 A:B12401 4.2 35.7 1.0 C7 A:B12401 4.2 38.4 1.0 C8 A:B12401 4.2 36.9 1.0 C12 A:B12401 4.2 36.0 1.0 CD2 A:HIS103 4.3 33.5 1.0 CG A:HIS103 4.4 33.7 1.0 C26 A:B12401 4.5 39.0 1.0 C3' A:5AD402 4.7 55.0 1.0 C53 A:B12401 4.7 34.0 1.0 C55 A:B12401 4.7 35.7 1.0 C41 A:B12401 4.7 36.1 1.0 C35 A:B12401 4.8 40.3 1.0 C37 A:B12401 4.8 39.9 1.0 C48 A:B12401 5.0 35.8 1.0 C54 A:B12401 5.0 35.1 1.0

Cobalt binding site 2 out of 2 in the Acidimicrobiaceae Bacterium Photocobilins Protein, Dark State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Acidimicrobiaceae Bacterium Photocobilins Protein, Dark State within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:35.4 occ:1.00 CO B:B12401 0.0 35.4 1.0 N23 B:B12401 1.8 36.4 1.0 N21 B:B12401 1.8 36.4 1.0 N24 B:B12401 1.9 36.1 1.0 N22 B:B12401 1.9 36.9 1.0 NE2 B:HIS103 2.3 33.5 1.0 C5' B:5AD402 2.3 39.3 1.0 C19 B:B12401 2.7 35.1 1.0 C14 B:B12401 2.8 36.1 1.0 C4 B:B12401 2.8 37.1 1.0 C16 B:B12401 2.9 35.8 1.0 C11 B:B12401 2.9 35.5 1.0 C1 B:B12401 2.9 35.7 1.0 C9 B:B12401 2.9 35.6 1.0 C6 B:B12401 3.0 37.3 1.0 CD2 B:HIS103 3.1 33.4 1.0 C15 B:B12401 3.2 34.9 1.0 C4' B:5AD402 3.2 40.6 1.0 C10 B:B12401 3.3 35.2 1.0 C5 B:B12401 3.3 37.5 1.0 CE1 B:HIS103 3.4 35.0 1.0 C20 B:B12401 3.5 34.9 1.0 O4' B:5AD402 3.7 41.0 1.0 C18 B:B12401 4.0 35.3 1.0 C17 B:B12401 4.1 35.5 1.0 C2 B:B12401 4.1 36.5 1.0 C13 B:B12401 4.1 35.7 1.0 C3 B:B12401 4.1 37.7 1.0 C12 B:B12401 4.2 35.8 1.0 C8 B:B12401 4.2 36.6 1.0 C7 B:B12401 4.2 37.1 1.0 CG B:HIS103 4.3 34.2 1.0 ND1 B:HIS103 4.5 35.1 1.0 C26 B:B12401 4.6 36.3 1.0 C3' B:5AD402 4.6 41.3 1.0 C53 B:B12401 4.7 35.2 1.0 C37 B:B12401 4.8 37.1 1.0 C41 B:B12401 4.8 37.2 1.0 C35 B:B12401 4.8 38.5 1.0 C55 B:B12401 4.9 37.0 1.0 C46 B:B12401 5.0 36.2 1.0 C54 B:B12401 5.0 35.9 1.0

S.Zhang, L.N.Jeffreys, H.Poddar, Y.Yu, C.Liu, K.Patel, L.O.Johannissen, L.Zhu, M.J.Cliff, C.Yan, G.Schiro, M.Weik, M.Sakuma, C.W.Levy, D.Leys, D.J.Heyes, N.S.Scrutton. Photocobilins Integrate B12 and Bilin Photochemistry For Enzyme Control. Nat Commun V. 15 2740 2024.
ISSN: ESSN 2041-1723
PubMed: 38548733
DOI: 10.1038/S41467-024-46995-1