Zinc in PDB 6dbv: 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 6dbv). 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: 6dbv:
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:46.7 occ:1.00 NE2 A:HIS959 2.2 30.4 1.0 NE2 A:HIS964 2.2 43.9 1.0 CE1 A:HIS959 2.2 31.9 1.0 SG A:CYS749 2.4 45.8 1.0 CB A:CYS752 2.7 51.9 1.0 CB A:CYS749 2.9 47.2 1.0 CE1 A:HIS964 3.1 44.4 1.0 CD2 A:HIS964 3.2 43.5 1.0 SG A:CYS752 3.5 0.1 1.0 CD2 A:HIS959 3.5 30.7 1.0 ND1 A:HIS959 3.5 29.2 1.0 CA A:CYS752 3.7 49.3 1.0 N A:CYS752 3.7 51.6 1.0 CB A:HIS766 4.0 46.7 1.0 CG A:HIS959 4.2 26.6 1.0 ND1 A:HIS964 4.2 47.2 1.0 O A:CYS752 4.3 48.1 1.0 CA A:CYS749 4.3 41.2 1.0 C A:CYS752 4.3 46.5 1.0 CG A:HIS964 4.3 46.3 1.0 CG A:HIS766 4.3 49.7 1.0 ND1 A:HIS766 4.6 51.0 1.0 CB A:SER754 4.9 50.4 1.0 C A:LEU751 4.9 52.0 1.0 CB A:ALA963 4.9 44.5 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:0.3 occ:1.00 N C:SER767 2.2 78.6 1.0 C C:HIS766 2.3 77.4 1.0 O C:SER767 2.4 81.1 1.0 C C:SER767 2.4 81.0 1.0 CA C:SER767 2.8 81.1 1.0 CB C:HIS766 2.8 70.3 1.0 O C:HIS766 2.9 76.7 1.0 CA C:HIS766 3.0 75.0 1.0 N C:ILE768 3.2 73.5 1.0 NE2 C:HIS964 3.3 52.8 1.0 CD2 C:HIS964 3.5 57.1 1.0 CB C:CYS752 3.7 62.4 1.0 CA C:ILE768 3.9 65.1 1.0 SG C:CYS752 4.0 87.0 1.0 CB C:SER767 4.1 81.9 1.0 CG C:HIS766 4.2 68.6 1.0 CA C:CYS752 4.2 59.8 1.0 N C:HIS766 4.3 72.3 1.0 CE1 C:HIS964 4.3 45.9 1.0 OG C:SER767 4.4 79.8 1.0 ND1 C:HIS766 4.6 70.4 1.0 CG C:HIS964 4.7 51.0 1.0 N C:CYS752 4.7 54.0 1.0 CG1 C:ILE768 4.8 56.5 1.0 C C:ILE768 4.8 68.4 1.0 N C:THR769 4.9 72.5 1.0 CB C:ILE768 5.0 57.7 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