Cobalt in PDB 2zdp: Crystal Structure of Isdi in Complex with Cobalt Protoporphyrin IX

All present enzymatic activity of Crystal Structure of Isdi in Complex with Cobalt Protoporphyrin IX:
1.14.99.3;

The structure of Crystal Structure of Isdi in Complex with Cobalt Protoporphyrin IX, PDB code: 2zdp was solved by W.C.Lee, M.L.Reniere, E.P.Skaar, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.81 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.320, 65.668, 58.660, 90.00, 107.81, 90.00
R / Rfree (%)	18.1 / 20.1

The structure of Crystal Structure of Isdi in Complex with Cobalt Protoporphyrin IX also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cobalt atom in the Crystal Structure of Isdi in Complex with Cobalt Protoporphyrin IX (pdb code 2zdp). 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 Isdi in Complex with Cobalt Protoporphyrin IX, PDB code: 2zdp:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Isdi in Complex with Cobalt Protoporphyrin IX


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 Isdi in Complex with Cobalt Protoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Co200 b:10.9 occ:1.00 CO A:COH200 0.0 10.9 1.0 NA A:COH200 1.9 13.4 1.0 ND A:COH200 2.0 9.6 1.0 NC A:COH200 2.0 11.7 1.0 NB A:COH200 2.0 11.4 1.0 NE2 A:HIS76 2.1 11.4 1.0 CL A:CL201 2.6 14.2 1.0 C4A A:COH200 3.0 13.6 1.0 C4D A:COH200 3.0 10.5 1.0 C1D A:COH200 3.0 11.7 1.0 C4C A:COH200 3.0 11.7 1.0 C1A A:COH200 3.0 13.8 1.0 C4B A:COH200 3.0 13.9 1.0 C1B A:COH200 3.0 13.6 1.0 C1C A:COH200 3.0 12.2 1.0 CD2 A:HIS76 3.1 11.7 1.0 CE1 A:HIS76 3.2 11.6 1.0 CHD A:COH200 3.3 12.1 1.0 CHA A:COH200 3.3 13.1 1.0 CHC A:COH200 3.3 12.6 1.0 CHB A:COH200 3.3 14.6 1.0 ND2 A:ASN6 4.1 10.8 1.0 C2D A:COH200 4.2 10.8 1.0 C3A A:COH200 4.2 13.9 1.0 C2A A:COH200 4.2 15.2 1.0 C3B A:COH200 4.2 14.7 1.0 C3D A:COH200 4.2 10.0 1.0 C2C A:COH200 4.2 12.0 1.0 C2B A:COH200 4.2 15.2 1.0 C3C A:COH200 4.2 12.5 1.0 CG A:HIS76 4.2 13.1 1.0 ND1 A:HIS76 4.3 12.5 1.0 CE1 A:PHE22 4.5 11.1 1.0 CZ A:PHE22 4.8 11.7 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Isdi in Complex with Cobalt Protoporphyrin IX


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 Isdi in Complex with Cobalt Protoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ B:Co200 b:10.9 occ:1.00 CO B:COH200 0.0 10.9 1.0 NC B:COH200 1.9 11.4 1.0 NA B:COH200 1.9 11.4 1.0 ND B:COH200 2.0 10.2 1.0 NB B:COH200 2.0 11.5 1.0 NE2 B:HIS76 2.1 10.7 1.0 CL B:CL202 2.5 14.3 1.0 C4C B:COH200 2.9 10.3 1.0 C1C B:COH200 3.0 10.3 1.0 C1A B:COH200 3.0 13.0 1.0 C4A B:COH200 3.0 14.0 1.0 C4D B:COH200 3.0 10.4 1.0 C1D B:COH200 3.0 9.9 1.0 C4B B:COH200 3.0 13.5 1.0 C1B B:COH200 3.0 14.0 1.0 CD2 B:HIS76 3.1 12.3 1.0 CE1 B:HIS76 3.2 10.1 1.0 CHA B:COH200 3.3 12.7 1.0 CHC B:COH200 3.3 13.2 1.0 CHD B:COH200 3.3 11.2 1.0 CHB B:COH200 3.3 14.5 1.0 ND2 B:ASN6 4.1 9.8 1.0 C3C B:COH200 4.2 10.9 1.0 C2C B:COH200 4.2 10.1 1.0 C3A B:COH200 4.2 13.9 1.0 C2A B:COH200 4.2 14.6 1.0 C2D B:COH200 4.2 10.0 1.0 C3B B:COH200 4.2 15.7 1.0 C3D B:COH200 4.2 10.8 1.0 C2B B:COH200 4.2 14.5 1.0 CG B:HIS76 4.2 11.9 1.0 ND1 B:HIS76 4.2 11.9 1.0 CE1 B:PHE22 4.5 11.2 1.0 CZ B:PHE22 4.8 11.7 1.0

W.C.Lee, M.L.Reniere, E.P.Skaar, M.E.P.Murphy. Ruffling of Metalloporphyrins Bound to Isdg and Isdi, Two Heme-Degrading Enzymes in Staphylococcus Aureus J.Biol.Chem. V. 283 30957 2008.
ISSN: ISSN 0021-9258
PubMed: 18713745
DOI: 10.1074/JBC.M709486200