Cobalt in PDB 6m29: Sirohydrochlorin Nickelochelatase Cfba in Complex with CO2+ and Formate

All present enzymatic activity of Sirohydrochlorin Nickelochelatase Cfba in Complex with CO2+ and Formate:
4.99.1.11; 4.99.1.3;

The structure of Sirohydrochlorin Nickelochelatase Cfba in Complex with CO2+ and Formate, PDB code: 6m29 was solved by T.Fujishiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.34 / 2.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	68.36, 68.36, 82.47, 90, 90, 90
R / Rfree (%)	19.8 / 24.3

The binding sites of Cobalt atom in the Sirohydrochlorin Nickelochelatase Cfba in Complex with CO2+ and Formate (pdb code 6m29). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Sirohydrochlorin Nickelochelatase Cfba in Complex with CO2+ and Formate, PDB code: 6m29:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Sirohydrochlorin Nickelochelatase Cfba in Complex with CO2+ and Formate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Sirohydrochlorin Nickelochelatase Cfba in Complex with CO2+ and Formate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co201 b:173.9 occ:1.00 NE2 A:HIS75 1.9 124.7 1.0 NE2 A:HIS9 1.9 163.2 1.0 O2 B:FMT202 1.9 153.3 1.0 CE1 A:HIS75 2.7 106.1 1.0 CE1 A:HIS9 2.8 136.8 1.0 CD2 A:HIS75 2.9 101.1 1.0 CD2 A:HIS9 3.0 135.3 1.0 C B:FMT202 3.3 142.2 1.0 ND1 A:HIS75 3.7 94.5 1.0 CG A:HIS75 3.9 94.3 1.0 ND1 A:HIS9 3.9 117.9 1.0 O B:HOH301 4.0 90.2 1.0 CG A:HIS9 4.0 110.3 1.0 O1 B:FMT202 4.2 167.1 1.0 OE2 A:GLU42 4.6 149.7 1.0

Cobalt binding site 2 out of 2 in the Sirohydrochlorin Nickelochelatase Cfba in Complex with CO2+ and Formate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Sirohydrochlorin Nickelochelatase Cfba in Complex with CO2+ and Formate within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:176.2 occ:1.00 NE2 B:HIS9 1.8 151.9 1.0 NE2 B:HIS75 1.9 118.6 1.0 O1 B:FMT202 1.9 167.1 1.0 CE1 B:HIS75 2.6 95.5 1.0 CE1 B:HIS9 2.7 124.0 1.0 CD2 B:HIS75 2.9 96.6 1.0 CD2 B:HIS9 3.0 126.5 1.0 C B:FMT202 3.1 142.2 1.0 ND1 B:HIS75 3.7 89.2 1.0 ND1 B:HIS9 3.8 102.5 1.0 O B:HOH301 3.9 90.2 1.0 CG B:HIS75 3.9 92.4 1.0 OE1 B:GLU42 4.0 132.4 1.0 CG B:HIS9 4.0 100.1 1.0 O2 B:FMT202 4.3 153.3 1.0 CE B:MET41 4.7 93.0 1.0

T.Fujishiro, S.Ogawa. The Nickel-Sirohydrochlorin Formation Mechanismof the Ancestral Class II Chelatase Cfba in COENZYMEF430 Biosynthesis Chem Sci 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC05439A