Calcium in PDB 6dbj: 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 6dbj). 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: 6dbj:
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 A:Ca1102 b:0.3 occ:1.00 OD2 A:ASP620 2.4 0.1 1.0 O A:GLY621 2.7 43.6 1.0 OE1 A:GLU984 3.2 82.4 1.0 OP1 G:DG15 3.2 58.3 1.0 O3' G:DG15 3.3 67.6 1.0 CG A:ASP620 3.3 0.3 1.0 ND2 A:ASN987 3.4 33.3 1.0 O5' G:DT16 3.7 70.4 1.0 OD1 A:ASP620 3.8 97.3 1.0 C A:GLY621 3.8 28.4 1.0 OP2 G:DT16 3.9 1.0 1.0 P G:DT16 3.9 70.0 1.0 OE2 A:GLU984 4.0 0.2 1.0 CD A:GLU984 4.0 98.6 1.0 CA A:CA1103 4.1 54.9 1.0 C5' G:DT16 4.2 79.7 1.0 CA A:MET622 4.3 21.1 1.0 C3' G:DG15 4.4 57.5 1.0 C4' G:DG15 4.5 44.9 1.0 CB A:ASP620 4.5 68.3 1.0 N A:MET622 4.5 24.2 1.0 P G:DG15 4.6 61.6 1.0 CB A:MET622 4.6 19.1 1.0 CG A:ASN987 4.8 33.5 1.0 N A:GLY621 4.9 58.8 1.0 O3' G:DT14 5.0 46.2 1.0 CA A:GLY621 5.0 42.0 1.0 CG A:MET622 5.0 39.0 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 A:Ca1103 b:54.9 occ:1.00 OD2 A:ASP730 2.5 1.0 1.0 OD1 A:ASP620 2.5 97.3 1.0 O3' I:DA16 2.9 64.8 1.0 OE2 A:GLU684 3.1 0.5 1.0 OP2 G:DT16 3.3 1.0 1.0 CG A:ASP730 3.5 64.1 1.0 CG A:ASP620 3.6 0.3 1.0 OD2 A:ASP620 3.9 0.1 1.0 C3' I:DA16 3.9 51.4 1.0 OD1 A:ASP730 4.0 70.7 1.0 O5' G:DT16 4.0 70.4 1.0 CD A:GLU684 4.1 0.8 1.0 CA A:CA1102 4.1 0.3 1.0 OE1 A:GLU684 4.3 0.4 1.0 P G:DT16 4.3 70.0 1.0 O A:GLY621 4.3 43.6 1.0 N A:GLY621 4.4 58.8 1.0 CB A:ASP730 4.7 36.5 1.0 C4' I:DA16 4.7 32.9 1.0 C5' I:DA16 4.8 38.7 1.0 C A:GLY621 4.9 28.4 1.0 CB A:ASP620 4.9 68.3 1.0 CA A:GLY621 4.9 42.0 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 C:Ca1102 b:0.7 occ:1.00 OD2 C:ASP620 2.5 0.8 1.0 O C:GLY621 2.9 41.4 1.0 OP1 F:DG15 2.9 62.1 1.0 OE2 C:GLU984 3.1 0.7 1.0 O3' F:DG15 3.1 65.5 1.0 ND2 C:ASN987 3.3 30.6 1.0 CG C:ASP620 3.5 0.5 1.0 O5' F:DT16 3.7 72.0 1.0 P F:DT16 3.9 67.3 1.0 OP2 F:DT16 3.9 0.5 1.0 CD C:GLU984 3.9 0.0 1.0 OD1 C:ASP620 4.0 95.8 1.0 OE1 C:GLU984 4.0 83.4 1.0 C5' F:DT16 4.0 79.8 1.0 C C:GLY621 4.1 30.7 1.0 C3' F:DG15 4.3 58.3 1.0 CA C:CA1103 4.3 57.6 1.0 C4' F:DG15 4.3 43.1 1.0 P F:DG15 4.3 61.2 1.0 CA C:MET622 4.5 22.4 1.0 O3' F:DT14 4.6 48.0 1.0 CG C:ASN987 4.6 29.1 1.0 CB C:ASP620 4.7 68.7 1.0 N C:MET622 4.8 26.7 1.0 CB C:MET622 4.8 21.6 1.0 CG C:MET622 4.8 39.8 1.0 C2' F:DG15 5.0 43.6 1.0 C5' F:DG15 5.0 45.8 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 C:Ca1103 b:57.6 occ:1.00 OD2 C:ASP730 2.5 0.9 1.0 OD1 C:ASP620 2.5 95.8 1.0 O3' J:DA16 2.7 67.7 1.0 OE2 C:GLU684 3.0 0.6 1.0 OP2 F:DT16 3.4 0.5 1.0 CG C:ASP620 3.5 0.5 1.0 CG C:ASP730 3.6 66.1 1.0 O5' F:DT16 3.8 72.0 1.0 OD2 C:ASP620 3.8 0.8 1.0 C3' J:DA16 4.0 51.3 1.0 CD C:GLU684 4.0 0.0 1.0 OD1 C:ASP730 4.1 70.5 1.0 O C:GLY621 4.2 41.4 1.0 OE1 C:GLU684 4.3 0.3 1.0 CA C:CA1102 4.3 0.7 1.0 P F:DT16 4.3 67.3 1.0 N C:GLY621 4.4 58.0 1.0 C4' J:DA16 4.7 36.0 1.0 CB C:ASP730 4.7 36.8 1.0 C C:GLY621 4.8 30.7 1.0 CB C:ASP620 4.8 68.7 1.0 C5' J:DA16 4.9 42.4 1.0 CA C:GLY621 4.9 43.6 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