Calcium in PDB 6cij: Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A)

All present enzymatic activity of Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A):
2.3.2.27;

The structure of Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A) (pdb code 6cij). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A), PDB code: 6cij:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:78.7 occ:1.00 OD2 A:ASP600 2.3 65.0 1.0 O A:GLY601 2.7 66.1 1.0 OP2 F:DT31 2.8 79.5 1.0 OD1 A:ASP600 2.9 65.0 1.0 CG A:ASP600 2.9 65.0 1.0 C A:GLY601 3.6 66.1 1.0 P F:DT31 3.9 79.5 1.0 O3' F:DG30 4.0 70.5 1.0 N A:GLY601 4.1 66.1 1.0 C5' F:DT31 4.1 79.5 1.0 NE2 A:GLN962 4.1 66.9 1.0 O5' F:DT31 4.3 79.5 1.0 CB A:ASP600 4.4 65.0 1.0 N A:MET602 4.4 66.9 1.0 CA A:GLY601 4.4 66.1 1.0 CA A:MET602 4.5 66.9 1.0 OP1 F:DG30 4.5 70.5 1.0 OE1 A:GLN962 4.6 66.9 1.0 CD A:GLN962 4.8 66.9 1.0 C A:ASP600 4.9 65.0 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:80.2 occ:1.00 OP2 G:DT42 2.1 77.8 1.0 O C:GLY601 2.5 67.6 1.0 OD1 C:ASP600 2.6 67.6 1.0 OD2 C:ASP600 2.7 67.6 1.0 CG C:ASP600 2.9 67.6 1.0 P G:DT42 3.3 77.8 1.0 O3' G:DG41 3.4 67.4 1.0 C C:GLY601 3.7 67.6 1.0 C5' G:DT42 4.0 77.8 1.0 O5' G:DT42 4.1 77.8 1.0 N C:GLY601 4.1 67.6 1.0 O3' J:DA16 4.2 81.2 1.0 CB C:ASP600 4.3 67.6 1.0 OP1 G:DT42 4.4 77.8 1.0 CA C:GLY601 4.5 67.6 1.0 N C:MET602 4.7 68.0 1.0 C3' G:DG41 4.7 67.4 1.0 NE2 C:GLN962 4.8 67.8 1.0 OE1 C:GLN962 4.8 67.8 1.0 CA C:MET602 4.8 68.0 1.0 C C:ASP600 4.9 67.6 1.0

M.S.Kim, W.Chuenchor, X.Chen, Y.Cui, X.Zhang, Z.H.Zhou, M.Gellert, W.Yang. Cracking the Dna Code For V(D)J Recombination. Mol. Cell V. 70 358 2018.
ISSN: ISSN 1097-4164
PubMed: 29628308
DOI: 10.1016/J.MOLCEL.2018.03.008