Zinc 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:

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 Nicked Dna Intermediates (pdb code 6dbj). 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 Nicked Dna Intermediates, PDB code: 6dbj:
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 Nicked Dna Intermediates


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 Nicked Dna Intermediates within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:15.0 occ:1.00 NE2 A:HIS964 2.0 49.1 1.0 NE2 A:HIS959 2.0 12.7 1.0 SG A:CYS752 2.5 60.1 1.0 SG A:CYS749 2.6 19.5 1.0 CE1 A:HIS959 2.9 18.1 1.0 CB A:CYS752 2.9 34.0 1.0 CD2 A:HIS964 2.9 50.5 1.0 CE1 A:HIS964 3.0 36.7 1.0 CD2 A:HIS959 3.1 15.2 1.0 CB A:CYS749 3.2 15.7 1.0 N A:CYS752 4.0 42.2 1.0 CA A:CYS752 4.0 45.7 1.0 ND1 A:HIS959 4.0 7.7 1.0 CG A:HIS964 4.1 38.6 1.0 ND1 A:HIS964 4.1 26.5 1.0 CB A:HIS766 4.1 55.7 1.0 CG A:HIS959 4.2 11.3 1.0 CG A:HIS766 4.5 63.0 1.0 CA A:CYS749 4.7 38.1 1.0 C A:CYS752 4.8 56.4 1.0 C A:LEU751 4.8 32.6 1.0 CD2 A:HIS766 4.8 54.7 1.0 CB A:ALA963 4.9 36.2 1.0

Zinc binding site 2 out of 2 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 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 Nicked Dna Intermediates within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1101 b:10.2 occ:1.00 NE2 C:HIS959 2.1 11.5 1.0 NE2 C:HIS964 2.1 43.3 1.0 SG C:CYS749 2.5 24.7 1.0 SG C:CYS752 2.5 52.5 1.0 CD2 C:HIS964 3.0 49.5 1.0 CB C:CYS749 3.0 17.9 1.0 CE1 C:HIS959 3.0 16.5 1.0 CD2 C:HIS959 3.0 13.7 1.0 CB C:CYS752 3.2 29.7 1.0 CE1 C:HIS964 3.2 35.3 1.0 N C:CYS752 4.0 38.4 1.0 ND1 C:HIS959 4.1 8.3 1.0 CA C:CYS752 4.2 37.7 1.0 CG C:HIS959 4.2 11.0 1.0 CG C:HIS964 4.2 38.0 1.0 ND1 C:HIS964 4.3 25.6 1.0 CB C:HIS766 4.4 56.6 1.0 CA C:CYS749 4.5 39.7 1.0 CG C:HIS766 4.7 65.4 1.0 C C:CYS752 4.9 50.5 1.0 C C:LEU751 4.9 29.4 1.0 CD2 C:HIS766 5.0 54.2 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