Calcium in PDB 6dbr: Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss

All present enzymatic activity of Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss:
2.3.2.27;

The structure of Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss 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 One Melted Rss and One Unmelted Rss (pdb code 6dbr). 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 One Melted Rss and One Unmelted Rss, PDB code: 6dbr:
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 One Melted Rss and One Unmelted Rss


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 One Melted Rss and One Unmelted Rss within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:75.4 occ:1.00 OD2 A:ASP620 2.4 0.7 1.0 CG A:ASP620 3.2 67.6 1.0 OD1 A:ASP620 3.2 62.9 1.0 CA A:CA1103 3.4 0.3 1.0 OP1 F:DA20 3.4 0.0 1.0 OD2 A:ASP730 4.0 0.5 1.0 O A:GLY621 4.5 33.6 1.0 OE1 A:GLU984 4.5 99.2 1.0 CB A:ASP620 4.7 43.4 1.0 ND2 A:ASN987 4.8 37.5 1.0 P F:DA20 4.8 0.4 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss


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 One Melted Rss and One Unmelted Rss within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:0.3 occ:1.00 OE2 A:GLU684 2.7 0.8 1.0 OD1 A:ASP620 3.0 62.9 1.0 OE1 A:GLU684 3.1 73.8 1.0 OD2 A:ASP730 3.2 0.5 1.0 CD A:GLU684 3.2 85.2 1.0 CA A:CA1102 3.4 75.4 1.0 CG A:ASP620 4.0 67.6 1.0 O A:GLY621 4.2 33.6 1.0 OP1 F:DA20 4.3 0.0 1.0 OD2 A:ASP620 4.4 0.7 1.0 CG A:ASP730 4.4 93.4 1.0 N A:GLY621 4.6 24.2 1.0 CG A:GLU684 4.6 64.2 1.0 C A:GLY621 5.0 24.5 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss


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 One Melted Rss and One Unmelted Rss within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:0.3 occ:1.00 OP2 G:DC17 2.3 0.4 1.0 OE2 C:GLU984 2.4 0.6 1.0 OP1 G:DC17 2.4 87.8 1.0 OE1 C:GLU984 2.4 78.6 1.0 CD C:GLU984 2.6 85.7 1.0 P G:DC17 2.7 100.0 1.0 OD2 C:ASP620 3.1 1.0 1.0 OD1 C:ASP620 3.5 70.7 1.0 CG C:ASP620 3.7 63.6 1.0 O5' G:DC17 3.7 91.4 1.0 CA C:CA1103 3.9 0.4 1.0 CG C:GLU984 3.9 71.0 1.0 O3' G:DA16 4.0 89.6 1.0 OP2 G:DA18 4.3 88.8 1.0 O C:GLY621 4.5 23.8 1.0 C3' G:DA16 4.6 88.8 1.0 CE1 C:HIS817 4.6 40.9 1.0 NE2 C:HIS817 4.8 36.1 1.0 CB C:GLU984 4.8 51.0 1.0 C5' G:DC17 4.8 84.7 1.0 C3' G:DC17 4.9 84.4 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss


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 One Melted Rss and One Unmelted Rss within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1103 b:0.4 occ:1.00 OD2 C:ASP730 2.2 0.3 1.0 OP1 G:DC17 2.3 87.8 1.0 CG C:ASP730 2.6 57.8 1.0 O3' G:DA16 2.9 89.6 1.0 CB C:ASP730 3.1 44.1 1.0 P G:DC17 3.1 100.0 1.0 OD2 C:ASP620 3.4 1.0 1.0 OD1 C:ASP730 3.4 38.2 1.0 C3' G:DA16 3.6 88.8 1.0 C4' G:DA16 3.8 74.6 1.0 OD1 C:ASP620 3.8 70.7 1.0 CG C:ASP620 3.9 63.6 1.0 CA C:CA1102 3.9 0.3 1.0 OP2 G:DC17 4.0 0.4 1.0 OE2 C:GLU684 4.1 85.2 1.0 CE1 C:HIS817 4.4 40.9 1.0 O5' G:DC17 4.4 91.4 1.0 CA C:ASP730 4.5 29.3 1.0 C5' G:DA16 4.7 91.6 1.0 NE2 C:HIS817 4.7 36.1 1.0 O4' G:DA16 4.8 61.1 1.0 N C:ASP730 4.9 22.0 1.0 O5' G:DA16 5.0 61.6 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