Manganese in PDB 8kfv: Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds

The structure of Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds, PDB code: 8kfv 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)	32.41 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.852, 78.044, 87.66, 90, 90, 90
R / Rfree (%)	20.7 / 24.1

The binding sites of Manganese atom in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds (pdb code 8kfv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds, PDB code: 8kfv:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 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 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:33.0 occ:0.78 OD2 A:ASP115 2.1 29.0 1.0 OE1 A:GLU257 2.2 44.9 1.0 O A:HOH1116 2.2 34.9 1.0 OD2 A:ASP117 2.2 36.9 1.0 OP3 E:DC26 2.3 48.1 1.0 OP2 E:DC26 2.7 50.1 1.0 CG A:ASP115 3.0 30.7 1.0 P E:DC26 3.1 45.4 1.0 OD1 A:ASP115 3.1 36.0 1.0 MN A:MN1002 3.2 39.5 0.6 CG A:ASP117 3.2 31.5 1.0 CD A:GLU257 3.3 42.8 1.0 OD1 A:ASP117 3.5 34.2 1.0 O A:HOH1103 3.6 31.8 1.0 OE2 A:GLU257 3.8 58.5 1.0 O E:HOH103 3.9 38.1 1.0 O5' E:DC26 4.0 43.4 1.0 CE1 A:HIS253 4.2 35.0 1.0 OP1 E:DC26 4.3 50.2 1.0 ND1 A:HIS253 4.3 37.3 1.0 CA A:GLY254 4.3 23.9 1.0 C5' E:DC26 4.4 36.3 1.0 CB A:ASP115 4.4 26.0 1.0 CG A:GLU257 4.5 34.2 1.0 CB A:ASP117 4.6 23.7 1.0 CB A:GLU257 4.7 24.4 1.0 CA A:GLY120 4.8 21.8 1.0 O3' D:DC25 4.8 42.8 1.0 N A:GLY254 5.0 24.8 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 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 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:39.5 occ:0.55 OE1 A:GLU174 2.1 38.4 1.0 OD1 A:ASP115 2.2 36.0 1.0 O E:HOH103 2.2 38.1 1.0 OP3 E:DC26 2.2 48.1 1.0 O A:HOH1103 2.3 31.8 1.0 O3' D:DC25 2.8 42.8 1.0 CD A:GLU174 3.0 33.5 1.0 MN A:MN1001 3.2 33.0 0.8 CG A:ASP115 3.3 30.7 1.0 OE2 A:GLU174 3.3 34.7 1.0 OD2 A:ASP117 3.5 36.9 1.0 P E:DC26 3.6 45.4 1.0 OD2 A:ASP115 3.7 29.0 1.0 OE1 A:GLU257 3.8 44.9 1.0 O A:HOH1123 3.8 36.8 1.0 O5' E:DC26 4.0 43.4 1.0 C3' D:DC25 4.2 40.7 1.0 CD A:GLU257 4.2 42.8 1.0 CG A:GLU174 4.3 28.4 1.0 OP1 E:DC26 4.3 50.2 1.0 CB A:GLU174 4.5 23.6 1.0 OP2 E:DC26 4.5 50.1 1.0 CB A:ASP115 4.5 26.0 1.0 OE2 A:GLU257 4.7 58.5 1.0 CG A:GLU257 4.8 34.2 1.0 CG A:ASP117 4.8 31.5 1.0 C4' D:DC25 4.8 42.5 1.0 CD A:PRO116 4.9 18.3 1.0 CA A:ASP115 4.9 21.4 1.0 CB A:GLU257 5.0 24.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:28.4 occ:0.71 OP1 C:DC26 1.9 49.1 1.0 OD2 B:ASP115 2.1 28.4 1.0 O B:HOH424 2.2 32.3 1.0 OD2 B:ASP117 2.2 36.2 1.0 OE1 B:GLU257 2.2 37.9 1.0 CG B:ASP115 3.0 28.8 1.0 OD1 B:ASP115 3.1 36.4 1.0 MN B:MN303 3.2 39.1 0.5 CG B:ASP117 3.2 31.3 1.0 P C:DC26 3.3 48.3 1.0 CD B:GLU257 3.3 36.5 1.0 OD1 B:ASP117 3.5 32.5 1.0 O B:HOH402 3.5 31.9 1.0 O5' C:DC26 3.7 45.2 1.0 OE2 B:GLU257 3.7 52.3 1.0 CE1 B:HIS253 4.0 35.6 1.0 O B:HOH418 4.1 37.4 1.0 ND1 B:HIS253 4.2 35.3 1.0 OP2 C:DC26 4.2 40.7 1.0 CA B:GLY254 4.3 21.7 1.0 O3' C:DC25 4.4 42.5 1.0 CB B:ASP115 4.4 23.7 1.0 CG B:GLU257 4.6 29.7 1.0 CB B:ASP117 4.6 23.7 1.0 C5' C:DC26 4.6 34.4 1.0 CA B:GLY120 4.7 19.6 1.0 O B:HOH405 4.7 43.0 1.0 CB B:GLU257 4.8 23.4 1.0 N B:GLY254 4.9 23.4 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:39.1 occ:0.53 OE1 B:GLU174 2.1 38.2 1.0 O B:HOH402 2.2 31.9 1.0 OD1 B:ASP115 2.2 36.4 1.0 O B:HOH418 2.3 37.4 1.0 OP1 C:DC26 2.4 49.1 1.0 O3' C:DC25 2.8 42.5 1.0 CD B:GLU174 3.0 35.2 1.0 P C:DC26 3.1 48.3 1.0 MN B:MN302 3.2 28.4 0.7 CG B:ASP115 3.3 28.8 1.0 OE2 B:GLU174 3.4 37.4 1.0 OD2 B:ASP117 3.5 36.2 1.0 OD2 B:ASP115 3.6 28.4 1.0 O5' C:DC26 3.8 45.2 1.0 OE1 B:GLU257 3.8 37.9 1.0 O B:HOH420 4.0 34.6 1.0 CD B:GLU257 4.0 36.5 1.0 C3' C:DC25 4.1 45.6 1.0 OE2 B:GLU257 4.2 52.3 1.0 CG B:GLU174 4.3 30.5 1.0 OP2 C:DC26 4.5 40.7 1.0 C4' C:DC25 4.5 45.2 1.0 CB B:ASP115 4.6 23.7 1.0 CB B:GLU174 4.6 24.9 1.0 C2' C:DC25 4.8 44.0 1.0 CG B:ASP117 4.8 31.3 1.0 CG B:GLU257 4.9 29.7 1.0 CB B:GLU257 5.0 23.4 1.0 C5' C:DC25 5.0 45.4 1.0 CA B:ASP115 5.0 19.9 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