Cobalt in PDB 5req: Methylmalonyl-Coa Mutase, Y89F Mutant, Substrate Complex

All present enzymatic activity of Methylmalonyl-Coa Mutase, Y89F Mutant, Substrate Complex:
5.4.99.2;

The structure of Methylmalonyl-Coa Mutase, Y89F Mutant, Substrate Complex, PDB code: 5req was solved by P.R.Evans, N.H.Thomae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	120.200, 161.890, 88.700, 90.00, 104.88, 90.00
R / Rfree (%)	24.6 / 29.2

The binding sites of Cobalt atom in the Methylmalonyl-Coa Mutase, Y89F Mutant, Substrate Complex (pdb code 5req). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Methylmalonyl-Coa Mutase, Y89F Mutant, Substrate Complex, PDB code: 5req:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Methylmalonyl-Coa Mutase, Y89F Mutant, Substrate Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Methylmalonyl-Coa Mutase, Y89F Mutant, Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1800 b:31.7 occ:1.00 CO A:B121800 0.0 31.7 1.0 N21 A:B121800 1.7 16.3 1.0 N23 A:B121800 1.8 24.5 1.0 N24 A:B121800 1.9 27.1 1.0 N22 A:B121800 2.0 27.0 1.0 NE2 A:HIS610 2.4 32.1 1.0 C4 A:B121800 2.7 26.5 1.0 C1 A:B121800 2.8 26.6 1.0 C11 A:B121800 2.8 27.0 1.0 C19 A:B121800 2.9 24.5 1.0 C14 A:B121800 2.9 25.4 1.0 C16 A:B121800 2.9 23.0 1.0 C9 A:B121800 3.0 26.5 1.0 C6 A:B121800 3.0 24.5 1.0 CD2 A:HIS610 3.2 31.3 1.0 C10 A:B121800 3.3 26.1 1.0 C5 A:B121800 3.3 26.5 1.0 C15 A:B121800 3.4 25.7 1.0 CE1 A:HIS610 3.5 30.9 1.0 C20 A:B121800 3.5 30.2 1.0 C3 A:B121800 4.0 25.8 1.0 C2 A:B121800 4.0 25.1 1.0 C18 A:B121800 4.1 26.7 1.0 C12 A:B121800 4.1 26.6 1.0 C13 A:B121800 4.2 26.3 1.0 C17 A:B121800 4.2 27.5 1.0 C8 A:B121800 4.3 25.7 1.0 C7 A:B121800 4.3 27.6 1.0 C26 A:B121800 4.4 28.9 1.0 CG A:HIS610 4.4 33.5 1.0 ND1 A:HIS610 4.5 33.5 1.0 C42 A:B121800 4.6 27.9 1.0 C54 A:B121800 4.7 24.7 1.0 C46 A:B121800 4.7 27.0 1.0 C48 A:B121800 4.8 22.8 1.0 C35 A:B121800 4.8 29.2 1.0 C53 A:B121800 4.9 25.7 1.0

Cobalt binding site 2 out of 2 in the Methylmalonyl-Coa Mutase, Y89F Mutant, Substrate Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Methylmalonyl-Coa Mutase, Y89F Mutant, Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Co2800 b:25.1 occ:1.00 CO C:B122800 0.0 25.1 1.0 N21 C:B122800 1.7 18.1 1.0 N23 C:B122800 1.9 22.0 1.0 N24 C:B122800 1.9 21.9 1.0 N22 C:B122800 2.0 25.6 1.0 NE2 C:HIS610 2.4 28.9 1.0 C4 C:B122800 2.7 25.1 1.0 C1 C:B122800 2.8 26.1 1.0 C19 C:B122800 2.8 22.4 1.0 C11 C:B122800 2.9 26.7 1.0 C16 C:B122800 2.9 19.3 1.0 C14 C:B122800 2.9 24.6 1.0 C9 C:B122800 3.0 23.8 1.0 C6 C:B122800 3.0 24.0 1.0 CD2 C:HIS610 3.2 26.8 1.0 C5 C:B122800 3.3 23.7 1.0 C10 C:B122800 3.3 24.3 1.0 CE1 C:HIS610 3.4 27.3 1.0 C15 C:B122800 3.4 20.9 1.0 C20 C:B122800 3.5 29.1 1.0 C3 C:B122800 4.0 22.7 1.0 C2 C:B122800 4.0 24.2 1.0 C18 C:B122800 4.1 23.9 1.0 C13 C:B122800 4.2 23.8 1.0 C12 C:B122800 4.2 23.9 1.0 C17 C:B122800 4.2 25.6 1.0 C8 C:B122800 4.3 24.5 1.0 C7 C:B122800 4.4 27.2 1.0 CG C:HIS610 4.4 30.5 1.0 ND1 C:HIS610 4.4 31.7 1.0 C26 C:B122800 4.4 24.2 1.0 C42 C:B122800 4.6 26.7 1.0 C54 C:B122800 4.7 21.9 1.0 C48 C:B122800 4.8 21.6 1.0 C35 C:B122800 4.8 26.0 1.0 C46 C:B122800 4.8 22.6 1.0 C53 C:B122800 4.9 25.5 1.0 C30 C:B122800 5.0 25.5 1.0

N.H.Thoma, T.W.Meier, P.R.Evans, P.F.Leadlay. Stabilization of Radical Intermediates By An Active-Site Tyrosine Residue in Methylmalonyl-Coa Mutase. Biochemistry V. 37 14386 1998.
ISSN: ISSN 0006-2960
PubMed: 9772164
DOI: 10.1021/BI981375O