Zinc in PDB 6dbq: 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:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas (pdb code 6dbq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas, PDB code: 6dbq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn1101 b:0.4 occ:1.00 N A:CYS752 1.9 85.1 1.0 CE1 A:HIS964 2.1 93.0 1.0 NE2 A:HIS964 2.1 0.1 1.0 SG A:CYS749 2.3 75.0 1.0 CB A:LEU751 2.7 0.5 1.0 C A:LEU751 2.8 69.1 1.0 CA A:CYS752 2.9 87.2 1.0 CB A:CYS752 2.9 82.4 1.0 CA A:LEU751 3.1 59.7 1.0 ND1 A:HIS964 3.2 89.3 1.0 NE2 A:HIS959 3.2 44.9 1.0 CD2 A:HIS964 3.3 0.3 1.0 N A:LEU751 3.4 49.5 1.0 CG A:LEU751 3.7 0.1 1.0 CG A:HIS964 3.8 0.9 1.0 O A:LEU751 3.8 79.0 1.0 CB A:CYS749 3.9 73.9 1.0 CE1 A:HIS959 3.9 47.2 1.0 C A:CYS752 4.0 0.5 1.0 O A:CYS752 4.1 0.9 1.0 CD1 A:LEU751 4.2 0.5 1.0 CD2 A:HIS959 4.3 51.2 1.0 C A:THR750 4.7 37.6 1.0 SG A:CYS752 4.7 0.2 1.0 C A:CYS749 5.0 66.4 1.0 N A:THR750 5.0 47.8 1.0 CA A:CYS749 5.0 60.4 1.0

Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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 C:Zn1101 b:42.6 occ:1.00 NE2 C:HIS959 2.0 40.8 1.0 NE2 C:HIS964 2.2 61.3 1.0 SG C:CYS749 2.3 62.0 1.0 CE1 C:HIS959 2.4 44.5 1.0 CB C:CYS752 2.4 91.1 1.0 CB C:CYS749 2.8 71.9 1.0 N C:CYS752 2.9 61.2 1.0 CA C:CYS752 3.1 72.3 1.0 CD2 C:HIS964 3.1 56.8 1.0 CE1 C:HIS964 3.2 65.6 1.0 CD2 C:HIS959 3.3 38.4 1.0 O C:CYS752 3.4 71.1 1.0 ND1 C:HIS959 3.7 49.5 1.0 C C:CYS752 3.7 69.7 1.0 SG C:CYS752 3.9 0.1 1.0 CG C:HIS959 4.1 51.6 1.0 C C:LEU751 4.2 51.2 1.0 ND1 C:HIS964 4.3 68.9 1.0 CG C:HIS964 4.3 67.1 1.0 CA C:CYS749 4.3 57.9 1.0 CB C:LEU751 4.6 67.0 1.0 CB C:ALA963 4.7 57.9 1.0 CA C:LEU751 4.7 46.6 1.0 N C:LEU751 4.7 38.0 1.0 N C:ASP753 5.0 84.0 1.0 C C:CYS749 5.0 35.8 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