Zinc in PDB 6dbt: 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 6dbt). 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: 6dbt:
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:0.1 occ:1.00 CE1 A:HIS964 2.2 89.9 1.0 NE2 A:HIS964 2.3 95.4 1.0 SG A:CYS749 2.5 0.7 1.0 NE2 A:HIS959 2.5 94.8 1.0 CE1 A:HIS959 2.7 97.3 1.0 N A:CYS752 2.7 98.2 1.0 SG A:CYS752 2.9 0.4 1.0 CB A:CYS752 3.0 98.7 1.0 CA A:CYS752 3.4 89.6 1.0 ND1 A:HIS964 3.4 85.8 1.0 CB A:LEU751 3.5 84.7 1.0 CD2 A:HIS964 3.6 93.1 1.0 C A:LEU751 3.7 93.9 1.0 CD2 A:HIS959 3.9 89.5 1.0 CB A:CYS749 3.9 0.9 1.0 CA A:LEU751 4.0 69.4 1.0 ND1 A:HIS959 4.0 91.9 1.0 CG A:HIS964 4.2 92.2 1.0 N A:LEU751 4.3 43.2 1.0 C A:CYS752 4.4 86.0 1.0 CG A:HIS959 4.6 82.1 1.0 CB A:HIS766 4.6 58.0 1.0 O A:LEU751 4.6 89.5 1.0 CB A:ALA963 4.7 90.8 1.0 CG A:LEU751 4.7 73.7 1.0 O A:CYS752 4.7 84.2 1.0 CG A:HIS766 4.9 68.8 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:0.7 occ:1.00 NE2 C:HIS964 1.9 69.0 1.0 NE2 C:HIS959 2.1 69.9 1.0 CE1 C:HIS964 2.2 72.0 1.0 CB C:CYS752 2.3 91.2 1.0 SG C:CYS749 2.5 60.4 1.0 CE1 C:HIS959 2.5 80.2 1.0 N C:CYS752 2.9 81.9 1.0 CA C:CYS752 3.1 90.5 1.0 CD2 C:HIS964 3.2 62.4 1.0 CD2 C:HIS959 3.4 56.9 1.0 CB C:CYS749 3.5 86.5 1.0 ND1 C:HIS964 3.5 76.0 1.0 SG C:CYS752 3.8 0.3 1.0 ND1 C:HIS959 3.8 68.8 1.0 CG C:HIS964 4.0 76.3 1.0 C C:CYS752 4.1 98.8 1.0 C C:LEU751 4.1 79.2 1.0 CG C:HIS959 4.3 55.0 1.0 O C:CYS752 4.4 88.2 1.0 CB C:HIS766 4.5 54.8 1.0 N C:LEU751 4.6 35.5 1.0 CB C:ALA963 4.7 68.0 1.0 CA C:LEU751 4.7 59.1 1.0 CA C:CYS749 4.8 52.7 1.0 CB C:LEU751 4.8 62.8 1.0 CG C:HIS766 4.9 65.9 1.0 N C:ASP753 5.0 0.4 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