Calcium in PDB 6b40: Bbragl-3'Tir Synaptic Complex with Nicked Dna Refined with C2 Symmetry

The structure of Bbragl-3'Tir Synaptic Complex with Nicked Dna Refined with C2 Symmetry also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Bbragl-3'Tir Synaptic Complex with Nicked Dna Refined with C2 Symmetry (pdb code 6b40). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Bbragl-3'Tir Synaptic Complex with Nicked Dna Refined with C2 Symmetry, PDB code: 6b40:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Bbragl-3'Tir Synaptic Complex with Nicked Dna Refined with C2 Symmetry


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bbragl-3'Tir Synaptic Complex with Nicked Dna Refined with C2 Symmetry within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1201 b:50.0 occ:1.00 OP2 B:DC46 2.5 50.0 1.0 O3' B:DG45 2.5 50.0 1.0 OD2 A:ASP701 2.6 50.0 1.0 OD1 A:ASP701 2.7 50.0 1.0 CG A:ASP701 2.8 50.0 1.0 P B:DC46 2.9 50.0 1.0 O A:GLY702 3.0 50.0 1.0 O5' B:DC46 3.3 50.0 1.0 C A:GLY702 3.7 50.0 1.0 N A:GLY702 3.8 50.0 1.0 C3' B:DG45 3.9 50.0 1.0 CB A:ASP701 4.0 50.0 1.0 CA A:GLY702 4.2 50.0 1.0 C4' B:DG45 4.3 50.0 1.0 OP1 B:DC46 4.3 50.0 1.0 C A:ASP701 4.4 50.0 1.0 C5' B:DC46 4.5 50.0 1.0 N A:MET703 4.5 50.0 1.0 C2' B:DG45 4.5 50.0 1.0 OE1 A:GLU1063 4.5 50.0 1.0 CA A:ASP701 4.8 50.0 1.0 OE2 A:GLU1063 4.8 50.0 1.0 CA A:MET703 4.9 50.0 1.0

Calcium binding site 2 out of 2 in the Bbragl-3'Tir Synaptic Complex with Nicked Dna Refined with C2 Symmetry


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bbragl-3'Tir Synaptic Complex with Nicked Dna Refined with C2 Symmetry within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1201 b:50.0 occ:1.00 OP2 F:DC46 2.5 50.0 1.0 O3' F:DG45 2.5 50.0 1.0 OD2 E:ASP701 2.6 50.0 1.0 OD1 E:ASP701 2.7 50.0 1.0 CG E:ASP701 2.8 50.0 1.0 P F:DC46 2.9 50.0 1.0 O E:GLY702 3.0 50.0 1.0 O5' F:DC46 3.3 50.0 1.0 C E:GLY702 3.7 50.0 1.0 N E:GLY702 3.8 50.0 1.0 C3' F:DG45 3.9 50.0 1.0 CB E:ASP701 4.0 50.0 1.0 CA E:GLY702 4.2 50.0 1.0 C4' F:DG45 4.3 50.0 1.0 OP1 F:DC46 4.3 50.0 1.0 C E:ASP701 4.4 50.0 1.0 C5' F:DC46 4.5 50.0 1.0 N E:MET703 4.5 50.0 1.0 C2' F:DG45 4.5 50.0 1.0 OE1 E:GLU1063 4.5 50.0 1.0 CA E:ASP701 4.8 50.0 1.0 OE2 E:GLU1063 4.8 50.0 1.0 CA E:MET703 4.9 50.0 1.0

Y.Zhang, T.C.Cheng, G.Huang, Q.Lu, M.D.Surleac, J.D.Mandell, P.Pontarotti, A.J.Petrescu, A.Xu, Y.Xiong, D.G.Schatz. Transposon Molecular Domestication and the Evolution of the Rag Recombinase. Nature V. 569 79 2019.
ISSN: ESSN 1476-4687
PubMed: 30971819
DOI: 10.1038/S41586-019-1093-7