Calcium in PDB 6dbi: Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Nicked Dna Intermediates

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

The structure of Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Nicked Dna Intermediates 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 Nicked Dna Intermediates (pdb code 6dbi). 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 Nicked Dna Intermediates, PDB code: 6dbi:
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 Nicked Dna Intermediates


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 Nicked Dna Intermediates within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:43.9 occ:1.00 OD2 C:ASP730 2.6 93.6 1.0 CA C:CA1103 2.6 66.7 1.0 O3' J:DA16 2.8 34.3 1.0 OE2 C:GLU684 3.6 0.9 1.0 OP2 G:DT46 3.7 63.3 1.0 O5' G:DT46 3.8 52.4 1.0 CG C:ASP730 3.8 67.4 1.0 OE1 C:GLU684 4.2 73.8 1.0 OD1 C:ASP620 4.2 53.4 1.0 C3' J:DA16 4.2 23.0 1.0 CD C:GLU684 4.2 75.5 1.0 OD1 C:ASP730 4.3 59.6 1.0 P G:DT46 4.4 48.1 1.0 N C:GLY621 4.6 26.0 1.0 O C:GLY621 4.7 42.5 1.0 C4' J:DA16 4.8 27.1 1.0 C5' G:DT46 4.9 44.3 1.0 CB C:ASP730 4.9 57.5 1.0 C2' J:DA16 5.0 31.6 1.0

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


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 Nicked Dna Intermediates within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1103 b:66.7 occ:1.00 O5' G:DT46 2.5 52.4 1.0 CA C:CA1102 2.6 43.9 1.0 O C:GLY621 3.0 42.5 1.0 OP2 G:DT46 3.2 63.3 1.0 OD1 C:ASP620 3.3 53.4 1.0 P G:DT46 3.3 48.1 1.0 C5' G:DT46 3.4 44.3 1.0 O3' G:DG45 3.5 53.3 1.0 C C:GLY621 3.9 29.9 1.0 OD2 C:ASP620 4.0 76.6 1.0 CG C:ASP620 4.0 50.9 1.0 O3' J:DA16 4.1 34.3 1.0 OE2 C:GLU684 4.3 0.9 1.0 N C:GLY621 4.3 26.0 1.0 OE2 C:GLU984 4.5 87.8 1.0 OD2 C:ASP730 4.5 93.6 1.0 CA C:GLY621 4.6 26.0 1.0 C4' G:DT46 4.7 45.0 1.0 N C:MET622 4.7 21.5 1.0 OP1 G:DT46 4.7 62.4 1.0 OE1 C:GLU984 4.8 50.1 1.0 C3' G:DG45 4.8 42.2 1.0 CA C:MET622 4.9 22.2 1.0

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


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 Nicked Dna Intermediates within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:73.0 occ:1.00 CA A:CA1103 2.1 53.6 1.0 O3' I:DA16 2.4 27.7 1.0 OE1 A:GLU684 2.9 70.3 1.0 CD A:GLU684 3.7 72.3 1.0 C3' I:DA16 3.7 19.1 1.0 OE2 A:GLU684 3.8 98.6 1.0 OP2 F:DT35 3.9 61.8 1.0 OD2 A:ASP730 4.0 70.5 1.0 OP1 F:DA36 4.1 50.2 1.0 O5' F:DT35 4.4 59.0 1.0 C4' I:DA16 4.7 16.4 1.0 CD A:LYS732 4.7 14.0 1.0 OD1 A:ASP620 4.7 42.1 1.0 C2' I:DA16 4.7 24.5 1.0 P F:DT35 4.7 39.5 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Nicked Dna Intermediates


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 Nicked Dna Intermediates within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:53.6 occ:1.00 CA A:CA1102 2.1 73.0 1.0 OP2 F:DT35 2.6 61.8 1.0 OD2 A:ASP730 2.7 70.5 1.0 OD1 A:ASP620 3.3 42.1 1.0 O3' I:DA16 3.3 27.7 1.0 CG A:ASP730 3.7 41.4 1.0 P F:DT35 3.9 39.5 1.0 OD1 A:ASP730 4.0 34.7 1.0 C3' I:DA16 4.0 19.1 1.0 OE2 A:GLU684 4.1 98.6 1.0 OE1 A:GLU684 4.1 70.3 1.0 O5' F:DT35 4.1 59.0 1.0 CG A:ASP620 4.3 47.4 1.0 CD A:GLU684 4.6 72.3 1.0 N A:GLY621 4.7 29.9 1.0 OD2 A:ASP620 4.8 90.0 1.0 O A:GLY621 4.9 26.8 1.0 CB A:ASP730 4.9 40.4 1.0 OP1 F:DT35 4.9 41.6 1.0 O3' F:DG34 4.9 35.0 1.0 C4' I:DA16 5.0 16.4 1.0 C5' I:DA16 5.0 21.3 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