Manganese in PDB 8kfw: Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 Seconds

The structure of Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 Seconds, PDB code: 8kfw 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)	49.07 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.644, 78.142, 63.621, 90, 97.72, 90
R / Rfree (%)	20.6 / 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 600 Seconds (pdb code 8kfw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 Seconds, PDB code: 8kfw:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 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 600 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:58.3 occ:1.00 OP3 E:DC26 2.0 66.6 1.0 O A:HOH1110 2.1 55.1 1.0 OE2 A:GLU257 2.2 76.8 1.0 OD2 A:ASP117 2.2 50.2 1.0 OD2 A:ASP115 2.4 48.9 1.0 OP2 E:DC26 2.5 63.5 1.0 P E:DC26 2.8 71.6 1.0 CD A:GLU257 3.1 75.9 1.0 CG A:ASP117 3.2 50.0 1.0 CG A:ASP115 3.2 53.7 1.0 MN A:MN1002 3.2 82.1 1.0 OD1 A:ASP115 3.4 68.2 1.0 OD1 A:ASP117 3.4 57.8 1.0 OE1 A:GLU257 3.6 62.8 1.0 O5' E:DC26 3.7 78.3 1.0 O A:HOH1105 3.9 53.6 1.0 OP1 E:DC26 4.0 69.7 1.0 CE1 A:HIS253 4.0 67.2 1.0 O A:HOH1101 4.1 59.5 1.0 CG A:GLU257 4.2 60.9 1.0 C5' E:DC26 4.2 66.0 1.0 ND1 A:HIS253 4.2 67.8 1.0 CB A:ASP117 4.6 48.5 1.0 CA A:GLY254 4.6 41.2 1.0 CB A:ASP115 4.6 50.2 1.0 CA A:GLY120 4.9 43.4 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 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 600 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:82.1 occ:1.00 OP3 E:DC26 2.0 66.6 1.0 O A:HOH1101 2.2 59.5 1.0 OE1 A:GLU174 2.2 58.7 1.0 OD1 A:ASP115 2.2 68.2 1.0 O A:HOH1105 2.4 53.6 1.0 O3' D:DC25 2.8 74.1 1.0 CD A:GLU174 3.0 63.7 1.0 MN A:MN1001 3.2 58.3 1.0 CG A:ASP115 3.3 53.7 1.0 OE2 A:GLU174 3.3 70.9 1.0 P E:DC26 3.3 71.6 1.0 OD2 A:ASP117 3.5 50.2 1.0 OE1 A:GLU257 3.7 62.8 1.0 OD2 A:ASP115 3.7 48.9 1.0 OP1 E:DC26 3.8 69.7 1.0 O5' E:DC26 3.8 78.3 1.0 CD A:GLU257 4.0 75.9 1.0 OE2 A:GLU257 4.1 76.8 1.0 C3' D:DC25 4.2 75.0 1.0 CG A:GLU174 4.3 57.4 1.0 OP2 E:DC26 4.4 63.5 1.0 CB A:GLU174 4.6 52.1 1.0 CB A:ASP115 4.6 50.2 1.0 CG A:ASP117 4.7 50.0 1.0 CG A:GLU257 4.8 60.9 1.0 C4' D:DC25 4.9 74.6 1.0 C5' E:DC26 5.0 66.0 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 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 600 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1003 b:110.0 occ:1.00 NE2 A:HIS253 2.1 79.4 1.0 CE1 A:HIS253 2.5 67.2 1.0 CD2 A:HIS253 3.4 67.5 1.0 ND1 A:HIS253 3.8 67.8 1.0 OP2 E:DC26 3.9 63.5 1.0 CG A:HIS253 4.2 60.1 1.0 O A:HOH1110 4.3 55.1 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 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 600 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:61.5 occ:1.00 O B:HOH1104 2.0 57.4 1.0 OP1 C:DC26 2.1 67.2 1.0 OD2 B:ASP115 2.1 51.4 1.0 OD2 B:ASP117 2.2 61.1 1.0 OE2 B:GLU257 2.2 79.8 1.0 CG B:ASP115 3.0 55.9 1.0 CG B:ASP117 3.1 55.7 1.0 CD B:GLU257 3.1 78.9 1.0 OD1 B:ASP115 3.2 67.4 1.0 MN B:MN1002 3.2 91.4 1.0 OD1 B:ASP117 3.3 55.6 1.0 P C:DC26 3.3 68.9 1.0 O5' C:DC26 3.7 69.1 1.0 O B:HOH1102 3.8 55.7 1.0 OE1 B:GLU257 3.8 65.8 1.0 OP2 C:DC26 4.0 61.8 1.0 CG B:GLU257 4.0 63.9 1.0 O B:HOH1101 4.0 61.1 1.0 CE1 B:HIS253 4.2 69.7 1.0 C5' C:DC26 4.4 63.2 1.0 ND1 B:HIS253 4.4 62.5 1.0 CB B:ASP115 4.4 51.3 1.0 CA B:GLY254 4.4 44.2 1.0 CB B:ASP117 4.5 49.5 1.0 CA B:GLY120 4.5 46.8 1.0 O3' C:DC25 4.6 71.4 1.0 N B:GLY120 4.8 45.9 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 Seconds


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:91.4 occ:1.00 OP1 C:DC26 1.9 67.2 1.0 OE1 B:GLU174 2.2 67.0 1.0 O B:HOH1102 2.2 55.7 1.0 O B:HOH1101 2.2 61.1 1.0 OD1 B:ASP115 2.2 67.4 1.0 O3' C:DC25 2.7 71.4 1.0 P C:DC26 2.8 68.9 1.0 CD B:GLU174 3.0 64.6 1.0 MN B:MN1001 3.2 61.5 1.0 CG B:ASP115 3.3 55.9 1.0 OE2 B:GLU174 3.3 64.1 1.0 OD2 B:ASP117 3.4 61.1 1.0 O5' C:DC26 3.4 69.1 1.0 OD2 B:ASP115 3.6 51.4 1.0 OE1 B:GLU257 3.9 65.8 1.0 C3' C:DC25 4.1 85.1 1.0 CD B:GLU257 4.1 78.9 1.0 OP2 C:DC26 4.1 61.8 1.0 OE2 B:GLU257 4.2 79.8 1.0 CG B:GLU174 4.4 63.1 1.0 CG B:ASP117 4.6 55.7 1.0 CB B:GLU174 4.6 52.0 1.0 C4' C:DC25 4.6 88.0 1.0 CB B:ASP115 4.6 51.3 1.0 C2' C:DC25 4.7 79.9 1.0 C5' C:DC26 4.8 63.2 1.0 CD B:PRO116 4.8 37.5 1.0 CG B:GLU257 4.9 63.9 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 Seconds


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of ZMMOC1 K229A in Complex with A Nicked Holliday Junction Soaked in MN2+ For 600 Seconds within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1003 b:107.4 occ:1.00 NE2 B:HIS253 2.1 80.2 1.0 CE1 B:HIS253 2.5 69.7 1.0 CD2 B:HIS253 3.3 65.8 1.0 ND1 B:HIS253 3.7 62.5 1.0 O B:HOH1104 3.9 57.4 1.0 CG B:HIS253 4.1 56.9 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