Nickel in PDB 6m2h: A Reaction Intermediate of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ and Sirohydrochlorin

All present enzymatic activity of A Reaction Intermediate of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ and Sirohydrochlorin:
4.99.1.11; 4.99.1.3;

The structure of A Reaction Intermediate of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ and Sirohydrochlorin, PDB code: 6m2h was solved by T.Fujishiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.71 / 3.10
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	68.88, 68.88, 83, 90, 90, 90
R / Rfree (%)	17.1 / 21.9

The binding sites of Nickel atom in the A Reaction Intermediate of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ and Sirohydrochlorin (pdb code 6m2h). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the A Reaction Intermediate of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ and Sirohydrochlorin, PDB code: 6m2h:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the A Reaction Intermediate of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ and Sirohydrochlorin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of A Reaction Intermediate of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ and Sirohydrochlorin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:153.8 occ:1.00 NE2 A:HIS9 2.0 134.1 1.0 NE2 A:HIS75 2.0 138.3 1.0 CE1 A:HIS75 2.8 113.9 1.0 NA B:SHN202 2.8 217.4 1.0 CE1 A:HIS9 2.9 115.1 1.0 CD2 A:HIS75 3.0 119.4 1.0 C4A B:SHN202 3.1 238.6 1.0 CD2 A:HIS9 3.1 121.0 1.0 OE1 A:GLU42 3.2 140.0 1.0 NB B:SHN202 3.3 234.3 1.0 C1A B:SHN202 3.5 211.9 1.0 CAA B:SHN202 3.6 191.4 1.0 CHB B:SHN202 3.6 252.7 1.0 C1B B:SHN202 3.6 251.9 1.0 ND B:SHN202 3.7 181.9 1.0 ND1 A:HIS75 3.8 107.7 1.0 C3A B:SHN202 3.8 215.1 1.0 CG A:HIS75 3.9 118.3 1.0 ND1 A:HIS9 4.0 103.1 1.0 CHA B:SHN202 4.1 210.7 1.0 CG A:HIS9 4.2 101.2 1.0 C4D B:SHN202 4.2 205.1 1.0 C2A B:SHN202 4.3 208.9 1.0 CE A:MET41 4.3 98.1 1.0 NC B:SHN202 4.3 177.1 1.0 C4B B:SHN202 4.4 224.5 1.0 CD A:GLU42 4.5 148.2 1.0 O1A B:SHN202 4.5 148.6 1.0 C1D B:SHN202 4.7 192.8 1.0 CMA B:SHN202 4.8 183.8 1.0 CBA B:SHN202 4.9 148.6 1.0 C2B B:SHN202 4.9 244.7 1.0

Nickel binding site 2 out of 2 in the A Reaction Intermediate of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ and Sirohydrochlorin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of A Reaction Intermediate of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ and Sirohydrochlorin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:156.8 occ:1.00 NE2 B:HIS75 2.0 145.0 1.0 O3B B:SHN202 2.0 213.2 1.0 NE2 B:HIS9 2.1 143.5 1.0 CE1 B:HIS75 2.8 124.7 1.0 CD2 B:HIS75 3.0 131.2 1.0 CE1 B:HIS9 3.0 127.0 1.0 CD2 B:HIS9 3.1 132.2 1.0 CEB B:SHN202 3.3 214.7 1.0 O3A B:SHN202 3.4 222.4 1.0 NB B:SHN202 3.6 234.3 1.0 OE1 B:GLU42 3.7 159.9 1.0 C4B B:SHN202 3.7 224.5 1.0 NC B:SHN202 3.7 177.1 1.0 ND1 B:HIS75 3.9 110.6 1.0 C1B B:SHN202 3.9 251.9 1.0 CHC B:SHN202 4.0 212.0 1.0 O4B B:SHN202 4.0 180.8 1.0 CG B:HIS75 4.0 118.6 1.0 ND1 B:HIS9 4.1 106.9 1.0 NA B:SHN202 4.1 217.4 1.0 C1C B:SHN202 4.2 198.5 1.0 CG B:HIS9 4.2 104.8 1.0 CHB B:SHN202 4.3 252.7 1.0 C3B B:SHN202 4.4 235.5 1.0 ND B:SHN202 4.4 181.9 1.0 CDB B:SHN202 4.4 225.3 1.0 CEA B:SHN202 4.4 216.8 1.0 C4A B:SHN202 4.5 238.6 1.0 C2B B:SHN202 4.5 244.7 1.0 OE2 B:GLU42 4.6 129.5 1.0 CD B:GLU42 4.6 141.5 1.0 C4C B:SHN202 4.7 195.0 1.0 O4A B:SHN202 4.8 208.7 1.0 C1A B:SHN202 4.9 211.9 1.0 C4D B:SHN202 5.0 205.1 1.0 C1D B:SHN202 5.0 192.8 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