Magnesium in PDB 6is8: Crystal Structure of ZMMOC1 D115N Mutant in Complex with Holliday Junction

The structure of Crystal Structure of ZMMOC1 D115N Mutant in Complex with Holliday Junction, PDB code: 6is8 was solved by Z.Lin, H.Lin, D.Zhang, C.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.699, 77.907, 63.577, 90.00, 97.55, 90.00
R / Rfree (%)	15.7 / 20.4

The binding sites of Magnesium atom in the Crystal Structure of ZMMOC1 D115N Mutant in Complex with Holliday Junction (pdb code 6is8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of ZMMOC1 D115N Mutant in Complex with Holliday Junction, PDB code: 6is8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of ZMMOC1 D115N Mutant in Complex with Holliday Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of ZMMOC1 D115N Mutant in Complex with Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:40.3 occ:1.00 OD2 A:ASP117 2.0 15.1 0.4 O A:HOH1127 2.0 25.0 1.0 OD1 A:ASN115 2.1 12.8 1.0 O A:HOH1112 2.3 46.9 1.0 OP1 D:DT26 2.3 28.8 1.0 O A:HOH1194 2.5 22.4 1.0 CG A:ASN115 2.9 10.8 1.0 CG A:ASP117 3.0 12.0 0.4 ND2 A:ASN115 3.2 11.3 1.0 OD1 A:ASP117 3.3 12.8 0.4 O A:HOH1106 3.7 30.7 1.0 OD2 A:ASP117 3.7 13.0 0.6 P D:DT26 3.8 26.8 1.0 OE1 A:GLU257 3.9 13.8 1.0 O A:HOH1191 4.1 35.8 1.0 C5' D:DT26 4.1 20.9 1.0 OE2 A:GLU174 4.1 24.1 1.0 CB A:ASN115 4.3 5.8 1.0 CB A:ASP117 4.3 9.5 0.6 CB A:ASP117 4.3 10.1 0.4 O5' D:DT26 4.3 22.8 1.0 O A:HOH1108 4.4 33.6 1.0 CG A:ASP117 4.5 10.1 0.6 O3' D:DC25 4.6 23.2 1.0 N A:ASP117 4.7 4.2 0.6 N A:ASP117 4.7 4.5 0.4 O A:HOH1104 4.8 32.5 1.0 CA A:ASN115 4.8 2.4 1.0 C A:ASN115 4.8 3.0 1.0 OP2 D:DT26 4.8 28.1 1.0 CD A:GLU174 4.9 20.1 1.0 N A:PRO116 5.0 1.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of ZMMOC1 D115N Mutant in Complex with Holliday Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of ZMMOC1 D115N Mutant in Complex with Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:42.0 occ:1.00 OD1 B:ASP117 1.9 12.1 0.4 O B:HOH1102 2.0 19.6 1.0 OD1 B:ASN115 2.0 18.1 1.0 O B:HOH1134 2.4 23.6 1.0 OP1 C:DC26 2.4 28.7 1.0 O B:HOH1141 2.4 36.4 1.0 CG B:ASN115 2.9 13.8 1.0 CG B:ASP117 3.0 10.2 0.4 ND2 B:ASN115 3.3 13.9 1.0 OD2 B:ASP117 3.5 11.9 0.4 OD2 B:ASP117 3.7 17.7 0.6 P C:DC26 3.8 26.4 1.0 OE1 B:GLU174 4.0 24.6 1.0 C5' C:DC26 4.1 19.6 1.0 O B:HOH1114 4.1 33.1 1.0 OE1 B:GLU257 4.2 14.6 1.0 CB B:ASP117 4.2 8.1 0.4 CB B:ASN115 4.2 8.1 1.0 CB B:ASP117 4.3 11.3 0.6 O B:HOH1103 4.4 29.6 1.0 O5' C:DC26 4.4 21.4 1.0 O3' C:DC25 4.4 24.3 1.0 CG B:ASP117 4.5 13.0 0.6 N B:ASP117 4.5 5.5 0.6 N B:ASP117 4.5 5.4 0.4 C B:ASN115 4.6 4.3 1.0 CA B:ASN115 4.7 2.9 1.0 CD B:PRO116 4.7 4.5 1.0 N B:PRO116 4.7 2.3 1.0 CD B:GLU174 4.8 20.8 1.0 OP2 C:DC26 4.9 26.8 1.0 CA B:ASP117 5.0 6.8 0.4

H.Lin, D.Zhang, K.Zuo, C.Yuan, J.Li, M.Huang, Z.Lin. Structural Basis of Sequence-Specific Holliday Junction Cleavage By MOC1. Nat.Chem.Biol. V. 15 1241 2019.
ISSN: ESSN 1552-4469
PubMed: 31611704
DOI: 10.1038/S41589-019-0377-4