Cobalt in PDB 5azr: Crystal Structure of Aqua-Cobalt(III) Tetradehydrocorrin in the Heme Pocket of Horse Heart Myoglobin

The structure of Crystal Structure of Aqua-Cobalt(III) Tetradehydrocorrin in the Heme Pocket of Horse Heart Myoglobin, PDB code: 5azr was solved by E.Mizohata, Y.Morita, K.Oohora, T.Inoue, T.Hayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.786, 28.837, 63.324, 90.00, 106.17, 90.00
R / Rfree (%)	12.1 / 16.8

The binding sites of Cobalt atom in the Crystal Structure of Aqua-Cobalt(III) Tetradehydrocorrin in the Heme Pocket of Horse Heart Myoglobin (pdb code 5azr). 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 Aqua-Cobalt(III) Tetradehydrocorrin in the Heme Pocket of Horse Heart Myoglobin, PDB code: 5azr:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Aqua-Cobalt(III) Tetradehydrocorrin in the Heme Pocket of Horse Heart Myoglobin


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 Aqua-Cobalt(III) Tetradehydrocorrin in the Heme Pocket of Horse Heart Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1001 b:11.1 occ:0.65 CO A:J1R1001 0.0 11.1 0.7 CO A:J1S1002 0.0 10.5 0.3 NA A:J1R1001 1.8 13.6 0.7 O A:HOH1105 1.8 13.8 0.5 NC A:J1S1002 1.9 12.3 0.3 NC A:J1R1001 1.9 11.3 0.7 ND A:J1R1001 1.9 15.3 0.7 NB A:J1S1002 1.9 13.4 0.3 ND A:J1S1002 1.9 10.1 0.3 NA A:J1S1002 1.9 9.8 0.3 NB A:J1R1001 1.9 10.4 0.7 NE2 A:HIS93 2.1 11.2 1.0 C4D A:J1R1001 2.9 15.7 0.7 C4C A:J1S1002 2.9 12.1 0.3 C1A A:J1R1001 2.9 13.7 0.7 C1B A:J1S1002 2.9 13.2 0.3 C1D A:J1S1002 2.9 9.9 0.3 C1C A:J1R1001 2.9 10.9 0.7 C1D A:J1R1001 2.9 11.9 0.7 C1C A:J1S1002 2.9 13.0 0.3 C4C A:J1R1001 2.9 11.9 0.7 C4A A:J1R1001 2.9 10.9 0.7 C1B A:J1R1001 2.9 9.8 0.7 C1A A:J1S1002 2.9 8.9 0.3 C4A A:J1S1002 2.9 9.8 0.3 C4B A:J1R1001 2.9 11.6 0.7 C4D A:J1S1002 2.9 8.8 0.3 C4B A:J1S1002 3.0 13.7 0.3 O A:HOH1105 3.0 17.0 0.5 CE1 A:HIS93 3.0 13.0 1.0 CD2 A:HIS93 3.1 11.7 1.0 CHC A:J1S1002 3.3 10.2 0.3 CHA A:J1S1002 3.3 11.1 0.3 CHB A:J1R1001 3.3 12.6 0.7 CHC A:J1R1001 3.3 12.8 0.7 CHA A:J1R1001 3.3 11.0 0.7 CHB A:J1S1002 3.3 14.0 0.3 CAA A:J1S1002 3.5 10.2 0.3 CAA A:J1R1001 3.5 13.6 0.7 CAD A:J1R1001 3.6 13.8 0.7 CAD A:J1S1002 3.7 9.5 0.3 C2A A:J1R1001 4.1 11.7 0.7 C2A A:J1S1002 4.1 9.6 0.3 C2D A:J1R1001 4.1 12.8 0.7 C2D A:J1S1002 4.1 10.0 0.3 C3D A:J1R1001 4.1 12.9 0.7 C2C A:J1R1001 4.1 11.8 0.7 C2C A:J1S1002 4.1 13.9 0.3 C3A A:J1S1002 4.1 9.4 0.3 C3A A:J1R1001 4.1 11.8 0.7 C3C A:J1S1002 4.1 13.3 0.3 C3D A:J1S1002 4.1 9.8 0.3 C3B A:J1R1001 4.1 12.0 0.7 C3B A:J1S1002 4.1 13.5 0.3 C2B A:J1S1002 4.1 13.5 0.3 C3C A:J1R1001 4.1 12.3 0.7 C2B A:J1R1001 4.1 11.3 0.7 ND1 A:HIS93 4.2 13.1 1.0 CG A:HIS93 4.3 11.7 1.0 CG2 A:VAL68 4.8 14.0 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Aqua-Cobalt(III) Tetradehydrocorrin in the Heme Pocket of Horse Heart Myoglobin


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 Aqua-Cobalt(III) Tetradehydrocorrin in the Heme Pocket of Horse Heart Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1002 b:10.5 occ:0.35 CO A:J1S1002 0.0 10.5 0.3 CO A:J1R1001 0.0 11.1 0.7 NA A:J1R1001 1.8 13.6 0.7 O A:HOH1105 1.9 13.8 0.5 NA A:J1S1002 1.9 9.8 0.3 ND A:J1R1001 1.9 15.3 0.7 NC A:J1S1002 1.9 12.3 0.3 ND A:J1S1002 1.9 10.1 0.3 NC A:J1R1001 1.9 11.3 0.7 NB A:J1S1002 1.9 13.4 0.3 NB A:J1R1001 1.9 10.4 0.7 NE2 A:HIS93 2.1 11.2 1.0 C4D A:J1R1001 2.8 15.7 0.7 C1A A:J1R1001 2.9 13.7 0.7 C4C A:J1S1002 2.9 12.1 0.3 C1D A:J1S1002 2.9 9.9 0.3 C1B A:J1S1002 2.9 13.2 0.3 C1D A:J1R1001 2.9 11.9 0.7 C1A A:J1S1002 2.9 8.9 0.3 C4A A:J1R1001 2.9 10.9 0.7 C4A A:J1S1002 2.9 9.8 0.3 C1C A:J1R1001 2.9 10.9 0.7 C4D A:J1S1002 2.9 8.8 0.3 C1B A:J1R1001 2.9 9.8 0.7 C4C A:J1R1001 2.9 11.9 0.7 C1C A:J1S1002 2.9 13.0 0.3 C4B A:J1R1001 3.0 11.6 0.7 C4B A:J1S1002 3.0 13.7 0.3 O A:HOH1105 3.0 17.0 0.5 CE1 A:HIS93 3.0 13.0 1.0 CD2 A:HIS93 3.1 11.7 1.0 CHC A:J1S1002 3.3 10.2 0.3 CHA A:J1S1002 3.3 11.1 0.3 CHA A:J1R1001 3.3 11.0 0.7 CHC A:J1R1001 3.3 12.8 0.7 CHB A:J1R1001 3.3 12.6 0.7 CHB A:J1S1002 3.4 14.0 0.3 CAA A:J1R1001 3.5 13.6 0.7 CAA A:J1S1002 3.5 10.2 0.3 CAD A:J1R1001 3.6 13.8 0.7 CAD A:J1S1002 3.6 9.5 0.3 C2A A:J1R1001 4.0 11.7 0.7 C2A A:J1S1002 4.1 9.6 0.3 C3D A:J1R1001 4.1 12.9 0.7 C2D A:J1R1001 4.1 12.8 0.7 C2D A:J1S1002 4.1 10.0 0.3 C3A A:J1S1002 4.1 9.4 0.3 C3A A:J1R1001 4.1 11.8 0.7 C3D A:J1S1002 4.1 9.8 0.3 C2C A:J1R1001 4.1 11.8 0.7 C2C A:J1S1002 4.1 13.9 0.3 C2B A:J1S1002 4.1 13.5 0.3 C3C A:J1S1002 4.1 13.3 0.3 C3B A:J1R1001 4.1 12.0 0.7 C3B A:J1S1002 4.1 13.5 0.3 C2B A:J1R1001 4.2 11.3 0.7 ND1 A:HIS93 4.2 13.1 1.0 C3C A:J1R1001 4.2 12.3 0.7 CG A:HIS93 4.2 11.7 1.0 CG2 A:VAL68 4.8 14.0 1.0

Y.Morita, K.Oohora, E.Mizohata, A.Sawada, T.Kamachi, K.Yoshizawa, T.Inoue, T.Hayashi. Crystal Structures and Coordination Behavior of Aqua- and Cyano-Co(III) Tetradehydrocorrins in the Heme Pocket of Myoglobin Inorg.Chem. V. 55 1287 2016.
ISSN: ISSN 0020-1669
PubMed: 26760442
DOI: 10.1021/ACS.INORGCHEM.5B02598