Calcium in PDB 8kfr: Crystal Structure of ZMMOC1/Nicked Holliday Junction/CA2+ Complex

The structure of Crystal Structure of ZMMOC1/Nicked Holliday Junction/CA2+ Complex, PDB code: 8kfr was solved by D.Zhang, Z.Luo, Z.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.81 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.98, 77.6, 63.28, 90, 98.05, 90
R / Rfree (%)	20.1 / 24

The binding sites of Calcium atom in the Crystal Structure of ZMMOC1/Nicked Holliday Junction/CA2+ Complex (pdb code 8kfr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of ZMMOC1/Nicked Holliday Junction/CA2+ Complex, PDB code: 8kfr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of ZMMOC1/Nicked Holliday Junction/CA2+ Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of ZMMOC1/Nicked Holliday Junction/CA2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:37.6 occ:1.00 O A:HOH1110 2.1 29.3 1.0 OD2 A:ASP117 2.3 33.7 1.0 OD2 A:ASP115 2.3 30.7 1.0 OP1 E:DC26 2.5 54.0 1.0 OD1 A:ASP115 2.6 33.1 1.0 OE1 A:GLU257 2.6 43.2 1.0 CG A:ASP115 2.8 30.7 1.0 O A:HOH1104 2.8 37.1 1.0 CG A:ASP117 3.2 34.4 1.0 OD1 A:ASP117 3.4 45.2 1.0 P E:DC26 3.7 60.4 1.0 CD A:GLU257 3.7 40.5 1.0 OP2 E:DC26 4.0 56.7 1.0 C5' E:DC26 4.2 45.3 1.0 CB A:ASP115 4.3 27.2 1.0 OE2 A:GLU257 4.3 44.2 1.0 O5' E:DC26 4.4 54.0 1.0 CB A:ASP117 4.6 26.6 1.0 CE1 A:HIS253 4.6 29.6 1.0 ND1 A:HIS253 4.8 34.5 1.0 CG A:GLU257 4.8 36.0 1.0 CA A:GLY254 4.8 28.4 1.0 OP3 E:DC26 4.8 57.0 1.0 OE2 A:GLU174 4.8 34.0 1.0 CB A:GLU257 4.8 28.7 1.0 CA A:GLY120 4.9 29.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of ZMMOC1/Nicked Holliday Junction/CA2+ Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of ZMMOC1/Nicked Holliday Junction/CA2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:33.1 occ:1.00 O B:HOH1105 2.2 29.9 1.0 OP1 C:DC26 2.3 41.3 1.0 OE1 B:GLU257 2.3 36.9 1.0 OD2 B:ASP115 2.4 31.6 1.0 OD2 B:ASP117 2.4 32.5 1.0 O B:HOH1101 2.6 40.9 1.0 OD1 B:ASP115 2.7 32.9 1.0 CG B:ASP115 2.9 31.0 1.0 CG B:ASP117 3.3 37.4 1.0 OD1 B:ASP117 3.4 33.5 1.0 CD B:GLU257 3.5 34.6 1.0 P C:DC26 3.7 48.7 1.0 O3' C:DC25 4.1 44.4 1.0 OE2 B:GLU257 4.1 45.6 1.0 CE1 B:HIS253 4.2 30.8 1.0 C5' C:DC26 4.3 41.1 1.0 CB B:ASP115 4.3 28.0 1.0 O5' C:DC26 4.4 43.7 1.0 CA B:GLY254 4.5 30.0 1.0 ND1 B:HIS253 4.5 33.0 1.0 CG B:GLU257 4.5 30.8 1.0 CB B:GLU257 4.6 27.3 1.0 CB B:ASP117 4.7 30.1 1.0 OP2 C:DC26 4.8 42.3 1.0 OE2 B:GLU174 4.8 40.8 1.0 CA B:GLY120 4.9 27.2 1.0

D.Zhang, S.Xu, Z.Luo, Z.Lin. MOC1 Cleaves Holliday Junctions Through A Cooperative Nick and Counter-Nick Mechanism Mediated By Metal Ions Nat Commun V. 15 5140 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-49490-9