Cobalt in PDB 8phm: Oxalate-Bound Cobalt(II) Human Carbonic Anhydrase II

All present enzymatic activity of Oxalate-Bound Cobalt(II) Human Carbonic Anhydrase II:
4.2.1.1; 4.2.1.69;

The structure of Oxalate-Bound Cobalt(II) Human Carbonic Anhydrase II, PDB code: 8phm was solved by L.Gigli, J.Malanho Silva, L.Cerofolini, A.L.Macedo, C.F.G.C.Geraldes, E.A.Suturina, V.Calderone, M.Fragai, G.Parigi, E.Ravera, C.Luchinat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.56 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.91, 41.21, 71.71, 90, 104.29, 90
R / Rfree (%)	16.4 / 19.8

The structure of Oxalate-Bound Cobalt(II) Human Carbonic Anhydrase II also contains other interesting chemical elements:

Mercury

(Hg)

1 atom

The binding sites of Cobalt atom in the Oxalate-Bound Cobalt(II) Human Carbonic Anhydrase II (pdb code 8phm). 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 Oxalate-Bound Cobalt(II) Human Carbonic Anhydrase II, PDB code: 8phm:

Cobalt binding site 1 out of 1 in the Oxalate-Bound Cobalt(II) Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Oxalate-Bound Cobalt(II) Human Carbonic Anhydrase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:10.8 occ:1.00 O6 A:OXD303 1.9 19.2 1.0 NE2 A:HIS93 2.0 9.0 1.0 O5 A:OXD303 2.1 14.7 1.0 ND1 A:HIS118 2.1 7.4 1.0 NE2 A:HIS95 2.1 6.8 1.0 C2 A:OXD303 2.6 19.3 1.0 C1 A:OXD303 2.7 19.1 1.0 CE1 A:HIS93 3.0 8.8 1.0 CE1 A:HIS118 3.0 7.5 1.0 CD2 A:HIS93 3.0 8.6 1.0 CE1 A:HIS95 3.1 7.4 1.0 CD2 A:HIS95 3.1 7.5 1.0 CG A:HIS118 3.2 6.9 1.0 CB A:HIS118 3.6 6.2 1.0 OG1 A:THR197 3.7 7.8 1.0 O4 A:OXD303 3.8 19.4 1.0 O3 A:OXD303 3.9 21.4 1.0 OE1 A:GLU105 4.0 7.7 1.0 O A:HOH432 4.0 26.3 1.0 ND1 A:HIS93 4.1 8.8 1.0 NE2 A:HIS118 4.1 6.5 1.0 CG A:HIS93 4.2 8.5 1.0 ND1 A:HIS95 4.2 7.3 1.0 CD2 A:HIS118 4.2 7.7 1.0 CG A:HIS95 4.3 5.8 1.0 O A:HOH679 4.5 31.9 0.9 CD A:GLU105 5.0 8.0 1.0

L.Gigli, J.M.Silva, L.Cerofolini, A.L.Macedo, C.F.G.C.Geraldes, E.A.Suturina, V.Calderone, M.Fragai, G.Parigi, E.Ravera, C.Luchinat. Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins. Inorg.Chem. V. 63 10713 2024.
ISSN: ISSN 0020-1669
PubMed: 38805564
DOI: 10.1021/ACS.INORGCHEM.4C01274