Calcium in PDB 6jrf: Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium

The structure of Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium, PDB code: 6jrf 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)	63.50 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.850, 78.164, 64.033, 90.00, 97.39, 90.00
R / Rfree (%)	20.9 / 26.5

The binding sites of Calcium atom in the Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium (pdb code 6jrf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium, PDB code: 6jrf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:85.5 occ:1.00 O A:HOH1107 2.2 30.0 1.0 OD2 A:ASP115 2.4 63.2 1.0 OP1 D:DT26 2.4 84.7 1.0 OE1 A:GLU257 2.5 90.4 1.0 OD1 A:ASP117 2.7 94.5 1.0 OD2 A:ASP117 2.8 85.8 1.0 CG A:ASP117 2.9 84.5 1.0 CG A:ASP115 3.3 63.7 1.0 OD1 A:ASP115 3.5 65.9 1.0 CD A:GLU257 3.6 93.0 1.0 CA A:CA1002 3.7 0.2 1.0 P D:DT26 3.7 83.7 1.0 OE2 A:GLU257 4.0 96.9 1.0 CE1 A:HIS253 4.1 67.0 1.0 CB A:ASP117 4.2 58.2 1.0 ND1 A:HIS253 4.2 67.0 1.0 O A:HOH1101 4.2 56.0 1.0 O5' D:DT26 4.3 82.3 1.0 OP2 D:DT26 4.3 89.4 1.0 C5' D:DT26 4.5 77.9 1.0 CA A:GLY254 4.6 47.5 1.0 CB A:ASP115 4.7 49.1 1.0 CA A:GLY120 4.7 44.7 1.0 CG A:GLU257 4.8 74.3 1.0 O D:HOH101 4.9 30.0 1.0 N A:GLY120 4.9 45.5 1.0 O3' D:DC25 4.9 78.5 1.0 C A:GLY119 4.9 58.1 1.0 O A:GLY119 5.0 67.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:0.2 occ:1.00 OE2 A:GLU174 2.2 84.2 1.0 O D:HOH101 2.2 30.0 1.0 OP1 D:DT26 2.5 84.7 1.0 O A:HOH1101 2.7 56.0 1.0 OE1 A:GLU174 2.8 76.8 1.0 CD A:GLU174 2.8 77.9 1.0 OE1 A:GLU257 3.2 90.4 1.0 O3' D:DC25 3.3 78.5 1.0 P D:DT26 3.5 83.7 1.0 CA A:CA1001 3.7 85.5 1.0 OD1 A:ASP115 3.7 65.9 1.0 OD2 A:ASP117 3.8 85.8 1.0 OD2 A:ASP115 3.9 63.2 1.0 CG A:ASP115 4.1 63.7 1.0 CD A:GLU257 4.2 93.0 1.0 CG A:GLU174 4.3 68.9 1.0 OP2 D:DT26 4.5 89.4 1.0 O5' D:DT26 4.6 82.3 1.0 CG A:GLU257 4.6 74.3 1.0 C5' D:DT26 4.6 77.9 1.0 C3' D:DC25 4.6 70.8 1.0 CG A:ASP117 4.9 84.5 1.0 CB A:GLU174 5.0 65.5 1.0 C4' D:DC25 5.0 81.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:93.0 occ:1.00 OD2 B:ASP115 2.3 62.0 1.0 OP1 C:DC26 2.5 92.0 1.0 OE1 B:GLU257 2.7 0.9 1.0 OD2 B:ASP117 2.8 94.9 1.0 OD1 B:ASP117 3.0 93.5 1.0 CG B:ASP115 3.1 62.0 1.0 CG B:ASP117 3.3 83.3 1.0 OD1 B:ASP115 3.3 64.0 1.0 CD B:GLU257 3.7 0.2 1.0 P C:DC26 3.8 88.2 1.0 CA B:CA1002 3.8 0.7 1.0 OE2 B:GLU257 3.9 0.6 1.0 O B:HOH1102 4.1 56.7 1.0 CE1 B:HIS253 4.2 91.4 1.0 CA B:GLY120 4.3 49.7 1.0 ND1 B:HIS253 4.3 90.1 1.0 O5' C:DC26 4.3 87.9 1.0 OP2 C:DC26 4.4 93.6 1.0 N B:GLY120 4.4 49.0 1.0 C5' C:DC26 4.4 83.7 1.0 CA B:GLY254 4.4 53.8 1.0 CB B:ASP115 4.6 47.1 1.0 C B:GLY119 4.6 70.4 1.0 CB B:ASP117 4.7 59.1 1.0 O B:GLY119 4.8 71.2 1.0 NZ B:LYS229 4.8 83.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of ZMMOC1-Holliday Junction Complex in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:0.7 occ:1.00 OP1 C:DC26 2.3 92.0 1.0 OE1 B:GLU174 2.5 0.1 1.0 OE2 B:GLU174 2.6 82.1 1.0 O C:HOH101 2.7 30.0 1.0 O B:HOH1102 2.7 56.7 1.0 CD B:GLU174 2.9 89.2 1.0 O3' C:DC25 3.0 81.1 1.0 OE1 B:GLU257 3.1 0.9 1.0 P C:DC26 3.2 88.2 1.0 OD1 B:ASP115 3.6 64.0 1.0 CA B:CA1001 3.8 93.0 1.0 CD B:GLU257 4.0 0.2 1.0 CG B:ASP115 4.1 62.0 1.0 OD2 B:ASP115 4.2 62.0 1.0 OP2 C:DC26 4.2 93.6 1.0 OD1 B:ASP117 4.3 93.5 1.0 C3' C:DC25 4.3 78.9 1.0 NZ B:LYS229 4.4 83.9 1.0 CG B:GLU174 4.4 74.6 1.0 O5' C:DC26 4.4 87.9 1.0 CG B:GLU257 4.5 73.6 1.0 C5' C:DC26 4.5 83.7 1.0 C4' C:DC25 4.8 94.5 1.0 OE2 B:GLU257 4.8 0.6 1.0

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