Calcium in PDB 6dbo: Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas

All present enzymatic activity of Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas:
2.3.2.27;

The structure of Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas 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 and 23-Rss Substrate Dnas (pdb code 6dbo). 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 and 23-Rss Substrate Dnas, PDB code: 6dbo:
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 and 23-Rss Substrate Dnas


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 and 23-Rss Substrate Dnas within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:0.9 occ:1.00 OE2 A:GLU984 2.0 1.0 1.0 OP2 E:DC17 2.3 0.9 1.0 OE1 A:GLU984 2.4 0.9 1.0 OP1 E:DC17 2.4 0.1 1.0 CD A:GLU984 2.5 0.5 1.0 P E:DC17 2.6 0.4 1.0 OD2 A:ASP620 3.2 0.1 1.0 O5' E:DC17 3.4 0.4 1.0 CG A:ASP620 3.9 0.3 1.0 OD1 A:ASP620 3.9 0.6 1.0 CG A:GLU984 4.0 0.3 1.0 O3' E:DA16 4.1 0.1 1.0 O A:GLY621 4.4 91.8 1.0 OP2 E:DA18 4.4 0.8 1.0 CA A:CA1103 4.5 0.2 1.0 C5' E:DC17 4.7 0.8 1.0 C3' E:DA16 4.7 0.9 1.0 CE1 A:HIS817 4.7 0.9 1.0 C3' E:DC17 4.9 0.5 1.0 CB A:GLU984 4.9 0.1 1.0 NE2 A:HIS817 5.0 0.2 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas


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 and 23-Rss Substrate Dnas within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:0.2 occ:1.00 O3' E:DA16 2.4 0.1 1.0 C4' E:DA16 2.6 0.2 1.0 OP1 E:DC17 2.7 0.1 1.0 C3' E:DA16 2.7 0.9 1.0 CG A:ASP730 2.8 0.8 1.0 OD2 A:ASP730 2.8 0.2 1.0 P E:DC17 3.1 0.4 1.0 OD1 A:ASP730 3.1 0.2 1.0 CB A:ASP730 3.5 0.2 1.0 C5' E:DA16 3.5 1.0 1.0 O4' E:DA16 3.8 0.8 1.0 OP2 E:DC17 3.9 0.9 1.0 O5' E:DA16 4.2 0.1 1.0 C2' E:DA16 4.2 0.4 1.0 OD1 A:ASP620 4.4 0.6 1.0 OE2 A:GLU684 4.4 0.9 1.0 O5' E:DC17 4.4 0.4 1.0 C1' E:DA16 4.5 0.1 1.0 CE1 A:HIS817 4.5 0.9 1.0 CA A:CA1102 4.5 0.9 1.0 OD2 A:ASP620 4.7 0.1 1.0 OE1 A:GLU684 4.7 0.1 1.0 CG A:ASP620 4.9 0.3 1.0 CA A:ASP730 4.9 91.2 1.0 CB A:LYS732 4.9 90.6 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas


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 and 23-Rss Substrate Dnas within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:0.8 occ:1.00 OE2 C:GLU984 2.0 0.5 1.0 OP2 G:DC17 2.2 0.7 1.0 OE1 C:GLU984 2.4 0.6 1.0 OP1 G:DC17 2.5 0.7 1.0 CD C:GLU984 2.5 0.5 1.0 P G:DC17 2.6 0.6 1.0 OD2 C:ASP620 3.3 0.3 1.0 O5' G:DC17 3.5 0.3 1.0 CG C:GLU984 4.0 0.8 1.0 O3' G:DA16 4.0 0.1 1.0 CG C:ASP620 4.4 96.1 1.0 OP2 G:DA18 4.4 0.8 1.0 CA C:CA1103 4.5 0.7 1.0 CE1 C:HIS817 4.6 0.9 1.0 C3' G:DA16 4.6 0.4 1.0 C5' G:DC17 4.7 0.6 1.0 OD1 C:ASP620 4.7 0.4 1.0 NE2 C:HIS817 4.7 0.3 1.0 C3' G:DC17 4.8 0.2 1.0 O C:GLY621 4.8 83.0 1.0 CB C:GLU984 4.9 0.1 1.0 NH1 C:ARG870 5.0 0.1 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas


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 and 23-Rss Substrate Dnas within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1103 b:0.7 occ:1.00 O3' G:DA16 2.4 0.1 1.0 OP1 G:DC17 2.7 0.7 1.0 C4' G:DA16 2.7 0.1 1.0 C3' G:DA16 2.7 0.4 1.0 CG C:ASP730 2.9 1.0 1.0 OD2 C:ASP730 3.0 0.6 1.0 P G:DC17 3.1 0.6 1.0 OD1 C:ASP730 3.3 0.0 1.0 CB C:ASP730 3.5 0.5 1.0 C5' G:DA16 3.7 0.8 1.0 O4' G:DA16 3.8 0.1 1.0 OD1 C:ASP620 4.0 0.4 1.0 OP2 G:DC17 4.0 0.7 1.0 O5' G:DA16 4.1 0.1 1.0 C2' G:DA16 4.2 0.7 1.0 CE1 C:HIS817 4.3 0.9 1.0 O5' G:DC17 4.4 0.3 1.0 OE2 C:GLU684 4.5 0.7 1.0 C1' G:DA16 4.5 0.8 1.0 CA C:CA1102 4.5 0.8 1.0 CG C:ASP620 4.8 96.1 1.0 OD2 C:ASP620 4.8 0.3 1.0 CB C:LYS732 4.8 88.4 1.0 OE1 C:GLU684 4.9 99.0 1.0 ND1 C:HIS817 5.0 0.6 1.0 CA C:ASP730 5.0 90.9 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