Manganese in PDB 8kft: Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 15 Seconds

The structure of Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 15 Seconds, PDB code: 8kft 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)	43.46 / 2.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.28, 78.16, 63.31, 90, 98, 90
R / Rfree (%)	20.3 / 25.4

The binding sites of Manganese atom in the Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 15 Seconds (pdb code 8kft). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 15 Seconds, PDB code: 8kft:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 15 Seconds


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 15 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:71.4 occ:0.77 OD2 A:ASP115 2.2 58.2 1.0 OE1 A:GLU257 2.2 69.1 1.0 OP2 E:DC26 2.4 85.8 1.0 CG A:ASP115 2.9 45.0 1.0 OD1 A:ASP115 3.0 50.8 1.0 O A:HOH1105 3.1 54.1 1.0 OD2 A:ASP117 3.4 75.9 1.0 CD A:GLU257 3.4 64.4 1.0 P E:DC26 3.7 76.2 1.0 OE2 A:GLU257 4.1 64.7 1.0 CE1 A:HIS253 4.3 58.8 1.0 OP1 E:DC26 4.3 66.4 1.0 ND1 A:HIS253 4.3 57.2 1.0 C5' E:DC26 4.3 53.3 1.0 CG A:ASP117 4.3 64.3 1.0 CB A:ASP117 4.4 46.7 1.0 CB A:ASP115 4.4 42.9 1.0 CG A:GLU257 4.6 56.0 1.0 O3' D:DC25 4.6 70.7 1.0 O5' E:DC26 4.6 57.8 1.0 OP3 E:DC26 4.7 57.5 1.0 CA A:GLY254 4.7 32.9 1.0 CB A:GLU257 4.8 40.4 1.0 CA A:GLY120 4.8 39.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 15 Seconds


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 15 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:64.2 occ:0.71 OD2 B:ASP115 2.2 47.8 1.0 OE1 B:GLU257 2.2 81.3 1.0 OD1 B:ASP115 2.3 54.0 1.0 OP1 C:DC26 2.3 74.0 1.0 CG B:ASP115 2.5 37.1 1.0 CD B:GLU257 3.0 67.1 1.0 OE2 B:GLU257 3.3 73.7 1.0 OD2 B:ASP117 3.7 68.4 1.0 P C:DC26 3.7 68.6 1.0 CB B:ASP115 4.0 36.8 1.0 O3' C:DC25 4.1 62.5 1.0 CG B:GLU257 4.3 51.5 1.0 C5' C:DC26 4.3 54.8 1.0 O5' C:DC26 4.5 54.3 1.0 CB B:GLU257 4.5 43.0 1.0 CG B:ASP117 4.6 63.0 1.0 CB B:ASP117 4.6 48.3 1.0 CE1 B:HIS253 4.7 56.1 1.0 CA B:GLY254 4.8 36.3 1.0 ND1 B:HIS253 4.8 49.1 1.0 OP2 C:DC26 4.9 61.1 1.0 OE1 B:GLU174 4.9 70.8 1.0 CA B:ASP115 4.9 36.9 1.0 CA B:GLY120 5.0 37.7 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