Cobalt in PDB 5hi0: The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase

All present enzymatic activity of The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase:
4.1.1.2;

The structure of The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase, PDB code: 5hi0 was solved by W.Zhu, L.M.Easthon, L.A.Reinhardt, C.Tu, S.E.Cohen, D.N.Silverman, K.N.Allen, N.G.J.Richards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.78 / 2.60
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	154.619, 154.619, 121.954, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 22.4

The structure of The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase (pdb code 5hi0). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase, PDB code: 5hi0:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:34.5 occ:1.00 O2 A:OXL403 1.7 38.3 1.0 OE1 A:GLU101 2.0 33.1 1.0 NE2 A:HIS140 2.1 35.2 1.0 CE1 A:HIS97 2.1 37.9 1.0 NE2 A:HIS97 2.2 40.9 1.0 NE2 A:HIS95 2.3 35.4 1.0 O A:HOH516 2.4 32.0 1.0 C2 A:OXL403 2.8 41.5 1.0 CE1 A:HIS140 2.9 32.8 1.0 CD2 A:HIS95 3.1 35.3 1.0 CD A:GLU101 3.2 35.5 1.0 CD2 A:HIS140 3.2 32.3 1.0 CE1 A:HIS95 3.3 35.1 1.0 O4 A:OXL403 3.4 32.9 1.0 ND1 A:HIS97 3.4 39.6 1.0 CD2 A:HIS97 3.5 41.6 1.0 OE2 A:GLU101 3.8 35.9 1.0 C1 A:OXL403 4.1 46.1 1.0 ND1 A:HIS140 4.1 32.4 1.0 CG A:HIS97 4.1 34.0 1.0 CG A:HIS140 4.3 32.2 1.0 CE2 A:PHE155 4.3 37.3 1.0 CG A:HIS95 4.3 34.4 1.0 O1 A:OXL403 4.3 50.3 1.0 ND1 A:HIS95 4.3 34.9 1.0 CG A:GLU101 4.4 31.5 1.0 CB A:GLU101 4.6 29.8 1.0 CZ A:PHE155 4.8 36.7 1.0

Cobalt binding site 2 out of 2 in the The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Substrate Binding Mode and Chemical Basis of A Reaction Specificity Switch in Oxalate Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:40.0 occ:1.00 O A:HOH503 1.5 35.8 1.0 O A:HOH524 1.9 30.8 1.0 OE1 A:GLU279 1.9 36.5 1.0 NE2 A:HIS318 1.9 35.5 1.0 NE2 A:HIS274 2.1 30.8 1.0 NE2 A:HIS272 2.4 28.9 1.0 CE1 A:HIS318 2.7 31.3 1.0 CD2 A:HIS274 2.9 29.6 1.0 CD A:GLU279 3.0 35.1 1.0 CD2 A:HIS318 3.1 30.8 1.0 CE1 A:HIS272 3.2 31.6 1.0 CE1 A:HIS274 3.2 30.5 1.0 CD2 A:HIS272 3.4 31.1 1.0 OE2 A:GLU332 3.5 35.9 1.0 OE2 A:GLU279 3.5 30.5 1.0 ND1 A:HIS318 3.9 29.0 1.0 CD A:GLU332 4.1 36.0 1.0 CG A:HIS274 4.1 29.4 1.0 CG A:HIS318 4.1 28.3 1.0 ND1 A:HIS274 4.2 30.5 1.0 CG A:GLU279 4.3 29.1 1.0 ND1 A:HIS272 4.4 32.4 1.0 CG A:HIS272 4.5 32.4 1.0 CB A:GLU279 4.6 31.7 1.0 CZ A:PHE334 4.6 31.2 1.0 CG A:GLU332 4.7 28.5 1.0 OE1 A:GLU332 4.7 37.5 1.0 NH2 A:ARG269 4.9 28.5 1.0

W.Zhu, L.M.Easthon, L.A.Reinhardt, C.Tu, S.E.Cohen, D.N.Silverman, K.N.Allen, N.G.Richards. Substrate Binding Mode and Molecular Basis of A Specificity Switch in Oxalate Decarboxylase. Biochemistry V. 55 2163 2016.
ISSN: ISSN 0006-2960
PubMed: 27014926
DOI: 10.1021/ACS.BIOCHEM.6B00043