Calcium in PDB 3jby: Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry)

The structure of Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry) (pdb code 3jby). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry), PDB code: 3jby:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:0.8 occ:1.00 ND2 A:ASN987 3.0 24.0 1.0 O A:GLY621 3.1 23.6 1.0 O3' G:DG15 3.1 15.6 1.0 OP1 G:DG15 3.1 12.9 1.0 OD2 A:ASP620 3.3 49.1 1.0 OP2 G:DT16 3.4 4.2 1.0 OE2 A:GLU984 3.7 77.3 1.0 P G:DT16 3.7 7.2 1.0 O5' G:DT16 3.8 12.1 1.0 CD A:GLU984 3.9 75.9 1.0 CG A:ASP620 3.9 38.2 1.0 C4' G:DG15 4.0 11.9 1.0 OE1 A:GLU984 4.1 70.4 1.0 C3' G:DG15 4.2 16.1 1.0 OD1 A:ASP620 4.2 43.5 1.0 C A:GLY621 4.3 18.8 1.0 CG A:ASN987 4.3 18.6 1.0 P G:DG15 4.4 8.4 1.0 CA A:MET622 4.6 16.5 1.0 CG A:GLU984 4.6 65.9 1.0 C5' G:DT16 4.6 24.9 1.0 O3' G:DT14 4.7 0.0 1.0 C5' G:DG15 4.7 12.3 1.0 CB A:MET622 4.7 30.4 1.0 CB A:ASN987 4.9 14.4 1.0 CG A:MET622 4.9 64.9 1.0 N A:MET622 4.9 12.0 1.0 C2' G:DG15 4.9 16.7 1.0 CB A:ASP620 5.0 21.1 1.0

Calcium binding site 2 out of 4 in the Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:24.8 occ:1.00 OD2 A:ASP730 2.2 50.1 1.0 O3' I:DA16 2.3 26.6 1.0 OE2 A:GLU684 2.9 0.2 1.0 OD1 A:ASP620 2.9 43.5 1.0 OP2 G:DT16 2.9 4.2 1.0 CG A:ASP730 3.4 50.2 1.0 C3' I:DA16 3.8 18.4 1.0 CD A:GLU684 3.8 91.7 1.0 OE1 A:GLU684 3.9 95.2 1.0 P G:DT16 3.9 7.2 1.0 CG A:ASP620 4.0 38.2 1.0 OD1 A:ASP730 4.1 57.0 1.0 O5' G:DT16 4.1 12.1 1.0 O A:GLY621 4.1 23.6 1.0 N A:GLY621 4.4 21.8 1.0 C4' I:DA16 4.4 11.1 1.0 OD2 A:ASP620 4.4 49.1 1.0 CB A:ASP730 4.5 35.2 1.0 OP1 G:DT16 4.5 1.5 1.0 C2' I:DA16 4.6 19.6 1.0 C A:GLY621 4.8 18.8 1.0 CA A:GLY621 4.8 20.6 1.0 C5' I:DA16 4.9 3.6 1.0

Calcium binding site 3 out of 4 in the Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:1.0 occ:1.00 O C:GLY621 3.0 21.6 1.0 OD2 C:ASP620 3.1 46.3 1.0 OE2 C:GLU984 3.1 60.1 1.0 OP2 F:DT16 3.1 4.8 1.0 O3' F:DG15 3.2 11.8 1.0 ND2 C:ASN987 3.2 15.8 1.0 OP1 F:DG15 3.4 9.5 1.0 P F:DT16 3.6 6.4 1.0 CD C:GLU984 3.6 60.4 1.0 CG C:ASP620 3.7 38.4 1.0 OE1 C:GLU984 3.9 56.3 1.0 OD1 C:ASP620 4.1 46.3 1.0 C4' F:DG15 4.1 8.8 1.0 C C:GLY621 4.2 8.9 1.0 C3' F:DG15 4.2 13.3 1.0 O5' F:DT16 4.3 18.8 1.0 CG C:ASN987 4.5 9.2 1.0 CG C:GLU984 4.5 53.9 1.0 CA C:MET622 4.6 15.8 1.0 P F:DG15 4.7 4.7 1.0 C5' F:DT16 4.7 31.7 1.0 CB C:MET622 4.7 26.9 1.0 CB C:ASP620 4.7 19.5 1.0 C5' F:DG15 4.8 11.4 1.0 OP1 F:DT16 4.9 4.4 1.0 CG C:MET622 4.9 49.0 1.0 N C:GLY621 4.9 10.8 1.0 N C:MET622 4.9 6.8 1.0 CA C:CA1103 4.9 15.7 1.0 O3' F:DT14 5.0 1.8 1.0

Calcium binding site 4 out of 4 in the Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Electron Microscopy Structure of Rag Paired Complex (C2 Symmetry) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1103 b:15.7 occ:1.00 O3' J:DA16 2.2 22.2 1.0 OD2 C:ASP730 2.5 39.4 1.0 OD1 C:ASP620 2.8 46.3 1.0 OP2 F:DT16 2.9 4.8 1.0 OE2 C:GLU684 3.5 93.5 1.0 C3' J:DA16 3.5 19.8 1.0 CG C:ASP730 3.7 35.9 1.0 CG C:ASP620 3.9 38.4 1.0 OE1 C:GLU684 4.0 91.6 1.0 C4' J:DA16 4.0 6.8 1.0 CD C:GLU684 4.2 84.2 1.0 P F:DT16 4.2 6.4 1.0 OD2 C:ASP620 4.2 46.3 1.0 O C:GLY621 4.3 21.6 1.0 C2' J:DA16 4.3 19.6 1.0 OD1 C:ASP730 4.4 42.1 1.0 OP1 F:DT16 4.5 4.4 1.0 N C:GLY621 4.5 10.8 1.0 C5' J:DA16 4.6 2.2 1.0 CB C:ASP730 4.7 27.2 1.0 CA C:CA1102 4.9 1.0 1.0 C C:GLY621 5.0 8.9 1.0

H.Ru, M.G.Chambers, T.M.Fu, A.B.Tong, M.Liao, H.Wu. Molecular Mechanism of V(D)J Recombination From Synaptic RAG1-RAG2 Complex Structures. Cell(Cambridge,Mass.) V. 163 1138 2015.
ISSN: ISSN 0092-8674
PubMed: 26548953
DOI: 10.1016/J.CELL.2015.10.055