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

The structure of Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds, PDB code: 8kfu 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)	43.66 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.573, 77.838, 63.548, 90, 97.98, 90
R / Rfree (%)	21.2 / 24.1

The binding sites of Manganese atom in the Crystal Structure of ZMMOC1 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds (pdb code 8kfu). 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 in Complex with A Nicked Holliday Junction Soaked in MN2+ For 180 Seconds, PDB code: 8kfu:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of ZMMOC1 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 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:23.1 occ:0.73 OP3 E:DC26 2.0 36.4 1.0 O A:HOH1105 2.1 27.4 1.0 OD2 A:ASP115 2.1 23.2 1.0 OD2 A:ASP117 2.1 28.1 1.0 OE1 A:GLU257 2.6 41.6 1.0 OP2 E:DC26 2.6 42.2 1.0 P E:DC26 2.8 47.4 1.0 CG A:ASP115 2.9 26.3 1.0 OD1 A:ASP115 3.0 34.3 1.0 MN A:MN1002 3.1 29.8 0.6 CG A:ASP117 3.1 27.1 1.0 OD1 A:ASP117 3.4 28.9 1.0 O A:HOH1113 3.6 29.2 1.0 CD A:GLU257 3.7 37.6 1.0 O5' E:DC26 3.7 40.7 1.0 O A:HOH1120 4.0 33.0 1.0 OP1 E:DC26 4.0 42.0 1.0 OE2 A:GLU257 4.1 41.1 1.0 CE1 A:HIS253 4.2 29.0 1.0 ND1 A:HIS253 4.3 31.3 1.0 CB A:ASP115 4.4 25.5 1.0 CA A:GLY254 4.4 22.1 1.0 C5' E:DC26 4.5 32.7 1.0 CB A:ASP117 4.5 25.1 1.0 CA A:GLY120 4.6 22.2 1.0 O3' D:DC25 4.7 32.7 1.0 CG A:GLU257 4.9 32.3 1.0 N A:GLY120 5.0 23.6 1.0 O E:HOH112 5.0 30.6 1.0 CB A:GLU257 5.0 26.0 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of ZMMOC1 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 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:29.8 occ:0.56 O A:HOH1120 2.1 33.0 1.0 OE1 A:GLU174 2.2 37.0 1.0 O A:HOH1113 2.2 29.2 1.0 OD1 A:ASP115 2.2 34.3 1.0 OP3 E:DC26 2.3 36.4 1.0 O3' D:DC25 2.7 32.7 1.0 CD A:GLU174 3.1 33.6 1.0 MN A:MN1001 3.1 23.1 0.7 CG A:ASP115 3.3 26.3 1.0 OE2 A:GLU174 3.4 37.2 1.0 OD2 A:ASP117 3.5 28.1 1.0 P E:DC26 3.6 47.4 1.0 OD2 A:ASP115 3.8 23.2 1.0 OE1 A:GLU257 3.8 41.6 1.0 O5' E:DC26 4.0 40.7 1.0 O A:HOH1131 4.0 29.1 1.0 C3' D:DC25 4.1 33.2 1.0 CG A:GLU174 4.3 29.5 1.0 OP1 E:DC26 4.3 42.0 1.0 CD A:GLU257 4.4 37.6 1.0 CB A:GLU174 4.5 24.3 1.0 CB A:ASP115 4.5 25.5 1.0 CD A:PRO116 4.6 21.2 1.0 OP2 E:DC26 4.6 42.2 1.0 CG A:ASP117 4.7 27.1 1.0 CA A:ASP115 4.8 22.0 1.0 C4' D:DC25 4.9 32.3 1.0 C2' D:DC25 5.0 32.3 1.0 CB A:GLU257 5.0 26.0 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of ZMMOC1 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 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:Mn1001 b:23.1 occ:0.72 OP1 C:DC26 1.8 32.4 1.0 OD2 B:ASP115 2.1 20.7 1.0 OD2 B:ASP117 2.1 24.3 1.0 O B:HOH1122 2.2 26.4 1.0 OE1 B:GLU257 2.2 33.5 1.0 O C:HOH225 2.7 36.0 1.0 CG B:ASP115 2.9 23.4 1.0 OD1 B:ASP115 3.0 32.4 1.0 MN B:MN1002 3.0 24.9 0.5 P C:DC26 3.1 36.8 1.0 CG B:ASP117 3.2 24.4 1.0 CD B:GLU257 3.2 33.9 1.0 O B:HOH1115 3.5 26.4 1.0 OD1 B:ASP117 3.5 25.2 1.0 O5' C:DC26 3.6 34.1 1.0 OE2 B:GLU257 3.6 41.5 1.0 OP2 C:DC26 3.9 28.1 1.0 O B:HOH1112 4.0 27.9 1.0 O3' C:DC25 4.2 31.4 1.0 CA B:GLY254 4.3 23.5 1.0 CB B:ASP115 4.3 22.3 1.0 ND1 B:HIS253 4.3 28.6 1.0 CE1 B:HIS253 4.4 29.6 1.0 C5' C:DC26 4.5 29.1 1.0 CG B:GLU257 4.5 28.4 1.0 CB B:ASP117 4.5 23.2 1.0 CA B:GLY120 4.6 23.6 1.0 CB B:GLU257 4.6 24.9 1.0 O B:HOH1134 4.9 31.9 1.0 NZ B:LYS229 4.9 37.8 1.0 N B:GLY254 4.9 22.6 1.0 N B:GLY120 4.9 22.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of ZMMOC1 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 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:Mn1002 b:24.9 occ:0.53 OP1 C:DC26 2.1 32.4 1.0 OE1 B:GLU174 2.1 31.9 1.0 O B:HOH1112 2.1 27.9 1.0 O B:HOH1115 2.2 26.4 1.0 OD1 B:ASP115 2.2 32.4 1.0 O3' C:DC25 2.5 31.4 1.0 P C:DC26 2.8 36.8 1.0 MN B:MN1001 3.0 23.1 0.7 CD B:GLU174 3.1 29.7 1.0 CG B:ASP115 3.3 23.4 1.0 O5' C:DC26 3.5 34.1 1.0 OE2 B:GLU174 3.5 33.1 1.0 OD2 B:ASP117 3.5 24.3 1.0 OD2 B:ASP115 3.7 20.7 1.0 OE1 B:GLU257 3.8 33.5 1.0 C3' C:DC25 3.9 30.9 1.0 O B:HOH1151 4.1 29.8 1.0 CD B:GLU257 4.1 33.9 1.0 OP2 C:DC26 4.1 28.1 1.0 CG B:GLU174 4.4 28.0 1.0 C4' C:DC25 4.4 33.2 1.0 OE2 B:GLU257 4.4 41.5 1.0 CB B:ASP115 4.6 22.3 1.0 C2' C:DC25 4.6 33.0 1.0 CB B:GLU174 4.6 25.3 1.0 CD B:PRO116 4.7 20.3 1.0 O C:HOH226 4.7 26.2 1.0 CG B:ASP117 4.7 24.4 1.0 CG B:GLU257 4.8 28.4 1.0 C5' C:DC26 4.9 29.1 1.0 CB B:GLU257 4.9 24.9 1.0 CA B:ASP115 4.9 21.1 1.0 O C:HOH225 5.0 36.0 1.0 C5' C:DC25 5.0 34.7 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