Cobalt in PDB 2xiq: Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adenosylcobalamin and Malonyl-Coa

All present enzymatic activity of Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adenosylcobalamin and Malonyl-Coa:
5.4.99.2;

The structure of Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adenosylcobalamin and Malonyl-Coa, PDB code: 2xiq was solved by W.W.Yue, D.S.Froese, G.Kochan, A.Chaikuad, T.Krojer, J.Muniz, E.Ugochukwu, C.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	107.82 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.650, 143.620, 163.230, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 20.1

The binding sites of Cobalt atom in the Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adenosylcobalamin and Malonyl-Coa (pdb code 2xiq). 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 Human Methylmalonyl-Coa Mutase in Complex with Adenosylcobalamin and Malonyl-Coa, PDB code: 2xiq:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adenosylcobalamin and Malonyl-Coa


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 Human Methylmalonyl-Coa Mutase in Complex with Adenosylcobalamin and Malonyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Co3001 b:24.1 occ:1.00 CO A:B123001 0.0 24.1 1.0 N21 A:B123001 1.9 24.5 1.0 N23 A:B123001 1.9 27.8 1.0 N24 A:B123001 1.9 34.5 1.0 N22 A:B123001 1.9 35.6 1.0 NE2 A:HIS627 2.5 22.6 1.0 C19 A:B123001 2.7 22.4 1.0 C4 A:B123001 2.8 23.2 1.0 C11 A:B123001 2.8 21.1 1.0 C1 A:B123001 2.8 24.7 1.0 C9 A:B123001 2.9 17.6 1.0 C16 A:B123001 2.9 23.2 1.0 C14 A:B123001 2.9 25.2 1.0 C6 A:B123001 2.9 22.5 1.0 C10 A:B123001 3.3 22.1 1.0 CD2 A:HIS627 3.3 22.4 1.0 C15 A:B123001 3.3 22.2 1.0 C5 A:B123001 3.3 28.6 1.0 C5' A:5AD4001 3.4 48.6 0.5 CE1 A:HIS627 3.6 24.4 1.0 C5' A:5AD4001 3.7 76.9 0.5 C20 A:B123001 3.7 23.6 1.0 C2 A:B123001 4.0 23.0 1.0 C18 A:B123001 4.1 24.6 1.0 C3 A:B123001 4.1 22.4 1.0 C12 A:B123001 4.1 22.5 1.0 C8 A:B123001 4.2 24.5 1.0 C3' A:5AD4001 4.2 0.9 0.5 C17 A:B123001 4.2 25.3 1.0 C13 A:B123001 4.2 19.9 1.0 C7 A:B123001 4.3 27.8 1.0 C26 A:B123001 4.5 22.4 1.0 CG A:HIS627 4.5 23.4 1.0 C4' A:5AD4001 4.6 0.3 0.5 ND1 A:HIS627 4.6 24.5 1.0 C4' A:5AD4001 4.7 85.7 0.5 O3' A:5AD4001 4.7 89.0 0.5 C42 A:B123001 4.7 20.4 1.0 C53 A:B123001 4.8 20.2 1.0 C47 A:B123001 4.8 15.6 1.0 C35 A:B123001 4.8 25.6 1.0 C48 A:B123001 4.8 17.8 1.0 C3' A:5AD4001 4.9 87.5 0.5 C54 A:B123001 4.9 21.4 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adenosylcobalamin and Malonyl-Coa


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 Human Methylmalonyl-Coa Mutase in Complex with Adenosylcobalamin and Malonyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ B:Co3001 b:20.0 occ:1.00 CO B:B123001 0.0 20.0 1.0 N23 B:B123001 1.9 21.3 1.0 N21 B:B123001 1.9 23.9 1.0 N24 B:B123001 1.9 33.9 1.0 N22 B:B123001 1.9 32.0 1.0 NE2 B:HIS627 2.4 18.0 1.0 C19 B:B123001 2.7 18.1 1.0 C4 B:B123001 2.8 18.4 1.0 C11 B:B123001 2.8 17.3 1.0 C9 B:B123001 2.9 16.8 1.0 C16 B:B123001 2.9 18.2 1.0 C1 B:B123001 2.9 19.6 1.0 C14 B:B123001 2.9 19.4 1.0 C6 B:B123001 2.9 19.4 1.0 CD2 B:HIS627 3.2 16.8 1.0 C10 B:B123001 3.3 16.2 1.0 C15 B:B123001 3.3 20.6 1.0 C5 B:B123001 3.3 23.6 1.0 CE1 B:HIS627 3.4 16.9 1.0 C5' B:5AD4001 3.5 83.6 0.5 C5' B:5AD4001 3.7 51.1 0.5 C20 B:B123001 3.8 15.8 1.0 C2 B:B123001 4.0 18.9 1.0 C3 B:B123001 4.1 18.7 1.0 C18 B:B123001 4.1 16.5 1.0 C12 B:B123001 4.2 15.3 1.0 C17 B:B123001 4.2 19.3 1.0 C8 B:B123001 4.2 17.7 1.0 C13 B:B123001 4.2 16.2 1.0 C3' B:5AD4001 4.2 69.4 0.5 C7 B:B123001 4.2 23.0 1.0 CG B:HIS627 4.5 19.0 1.0 C26 B:B123001 4.5 19.8 1.0 O3' B:5AD4001 4.5 53.9 0.5 ND1 B:HIS627 4.5 15.2 1.0 C4' B:5AD4001 4.6 74.4 0.5 C42 B:B123001 4.7 18.1 1.0 C47 B:B123001 4.7 14.3 1.0 C4' B:5AD4001 4.7 0.4 0.5 C3' B:5AD4001 4.8 0.9 0.5 C53 B:B123001 4.8 14.3 1.0 C48 B:B123001 4.8 16.6 1.0 C35 B:B123001 4.8 24.9 1.0 C54 B:B123001 4.9 13.8 1.0

D.S.Froese, G.Kochan, J.Muniz, X.Wu, C.Gileadi, E.Ugochukwu, E.Krysztofinska, R.A.Gravel, U.Oppermann, W.W.Yue. Structures of the Human Gtpase Mmaa and Vitamin B12-Dependent Methylmalonyl-Coa Mutase and Insight Into Their Complex Formation. J.Biol.Chem. V. 285 38204 2010.
ISSN: ISSN 0021-9258
PubMed: 20876572
DOI: 10.1074/JBC.M110.177717