Nickel in PDB 6m27: Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+

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

The structure of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+, PDB code: 6m27 was solved by T.Fujishiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.47 / 2.60
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	68.21, 68.21, 81.21, 90, 90, 90
R / Rfree (%)	19.2 / 23

The binding sites of Nickel atom in the Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ (pdb code 6m27). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+, PDB code: 6m27:
Jump to Nickel binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:82.4 occ:1.00 NE2 A:HIS9 2.0 88.6 1.0 NE2 A:HIS75 2.0 82.4 1.0 CE1 A:HIS9 2.6 80.8 1.0 CE1 A:HIS75 2.8 78.0 1.0 OE1 A:GLU42 2.9 91.6 1.0 CD2 A:HIS75 3.1 68.6 1.0 CD2 A:HIS9 3.3 79.6 1.0 ND1 A:HIS9 3.9 74.5 1.0 ND1 A:HIS75 4.0 71.5 1.0 CD A:GLU42 4.1 98.2 1.0 CG A:HIS75 4.2 65.3 1.0 CG A:HIS9 4.2 70.6 1.0 OE2 A:GLU42 4.8 109.2 1.0

Nickel binding site 2 out of 2 in the Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Sirohydrochlorin Nickelochelatase Cfba in Complex with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:85.9 occ:1.00 NE2 B:HIS9 2.0 86.0 1.0 NE2 B:HIS75 2.0 79.8 1.0 CE1 B:HIS9 2.7 78.4 1.0 CE1 B:HIS75 2.9 73.4 1.0 OE2 B:GLU42 2.9 103.2 1.0 CD2 B:HIS75 3.2 66.2 1.0 CD2 B:HIS9 3.3 74.4 1.0 ND1 B:HIS9 3.9 71.8 1.0 ND1 B:HIS75 4.0 66.8 1.0 CD B:GLU42 4.2 106.3 1.0 CG B:HIS75 4.2 62.9 1.0 CG B:HIS9 4.2 67.1 1.0 OE1 B:GLU42 4.8 116.4 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