Calcium in PDB 6dbw: Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna

All present enzymatic activity of Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna:
2.3.2.27;

The structure of Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna (pdb code 6dbw). 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-Em Structure of Rag in Complex with 12-Rss Substrate Dna, PDB code: 6dbw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna


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 Rag in Complex with 12-Rss Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:0.3 occ:1.00 CA A:CA1103 2.1 0.6 1.0 OE2 A:GLU984 2.1 0.1 1.0 OD2 A:ASP620 2.3 0.9 1.0 OP1 E:DC17 2.4 0.4 1.0 OP2 E:DC17 2.6 0.8 1.0 CD A:GLU984 2.7 0.0 1.0 P E:DC17 2.8 0.3 1.0 OE1 A:GLU984 3.2 0.5 1.0 CG A:ASP620 3.4 0.6 1.0 CG A:GLU984 3.6 0.1 1.0 O3' E:DA16 3.7 0.6 1.0 OD1 A:ASP620 3.8 0.0 1.0 C3' E:DA16 4.1 0.1 1.0 O5' E:DC17 4.2 0.6 1.0 NE2 A:HIS817 4.6 0.7 1.0 CB A:ASP620 4.7 0.8 1.0 O A:GLY621 4.8 79.5 1.0 CB A:GLU984 5.0 0.1 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna


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 Rag in Complex with 12-Rss Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:0.6 occ:1.00 CA A:CA1102 2.1 0.3 1.0 OP1 E:DC17 2.5 0.4 1.0 O3' E:DA16 2.7 0.6 1.0 P E:DC17 2.8 0.3 1.0 C3' E:DA16 2.9 0.1 1.0 OD2 A:ASP620 2.9 0.9 1.0 OP2 E:DC17 3.2 0.8 1.0 NE2 A:HIS817 3.5 0.7 1.0 C4' E:DA16 3.6 0.2 1.0 CG A:ASP620 3.6 0.6 1.0 OD1 A:ASP620 3.7 0.0 1.0 CB A:ASP730 3.9 97.5 1.0 OE2 A:GLU984 4.2 0.1 1.0 C2' E:DA16 4.3 0.4 1.0 C5' E:DA16 4.3 0.9 1.0 O5' E:DC17 4.4 0.6 1.0 CE1 A:HIS817 4.4 0.0 1.0 CD A:GLU984 4.5 0.0 1.0 CD2 A:HIS817 4.5 0.4 1.0 CG A:ASP730 4.7 0.1 1.0 O4' E:DA16 4.8 0.7 1.0 OE1 A:GLU984 4.9 0.5 1.0 OD2 A:ASP730 4.9 0.8 1.0 CB A:ASP620 4.9 0.8 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:0.8 occ:1.00 CA C:CA1103 2.7 0.1 1.0 OE2 C:GLU984 4.1 0.1 1.0 NH1 C:ARG870 4.9 0.9 1.0 CD C:GLU984 4.9 0.1 1.0 OE1 C:GLU984 4.9 0.6 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1103 b:0.1 occ:1.00 CA C:CA1102 2.7 0.8 1.0 OD2 C:ASP730 4.0 0.5 1.0 NZ C:LYS732 4.5 0.2 1.0 CG C:ASP730 4.8 0.9 1.0 CE C:LYS732 4.9 96.3 1.0 CD C:LYS732 4.9 0.1 1.0 OE1 C:GLU684 5.0 0.0 1.0

H.Ru, W.Mi, P.Zhang, F.W.Alt, D.G.Schatz, M.Liao, H.Wu. Dna Melting Initiates the Rag Catalytic Pathway. Nat. Struct. Mol. Biol. V. 25 732 2018.
ISSN: ESSN 1545-9985
PubMed: 30061602
DOI: 10.1038/S41594-018-0098-5