Zinc in PDB 6dbi: 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 6dbi). 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: 6dbi:
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 C:Zn1101 b:44.2 occ:1.00 NE2 C:HIS959 2.0 28.2 1.0 SG C:CYS752 2.0 60.0 1.0 SG C:CYS749 2.2 39.7 1.0 NE2 C:HIS964 2.2 41.2 1.0 CB C:CYS752 2.6 44.7 1.0 CB C:CYS749 2.8 44.3 1.0 CE1 C:HIS959 2.9 33.0 1.0 CD2 C:HIS959 3.0 27.9 1.0 CD2 C:HIS964 3.1 45.3 1.0 CE1 C:HIS964 3.3 44.1 1.0 CA C:CYS752 3.7 46.7 1.0 N C:CYS752 3.8 49.2 1.0 ND1 C:HIS959 4.0 32.5 1.0 CG C:HIS959 4.1 22.4 1.0 CA C:CYS749 4.3 34.3 1.0 CG C:HIS964 4.3 43.0 1.0 ND1 C:HIS964 4.3 39.1 1.0 C C:CYS752 4.4 51.0 1.0 CB C:HIS766 4.5 47.1 1.0 CD1 C:ILE748 4.6 50.6 1.0 CG C:HIS766 4.6 45.9 1.0 OG C:SER754 4.6 50.7 1.0 C C:LEU751 4.7 51.0 1.0 O C:CYS752 4.8 52.5 1.0 CD2 C:HIS766 5.0 51.5 1.0 ND1 C:HIS766 5.0 46.7 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 A:Zn1101 b:7.1 occ:1.00 NE2 A:HIS959 2.1 21.0 1.0 SG A:CYS752 2.1 45.5 1.0 SG A:CYS749 2.2 19.7 1.0 CB A:CYS749 2.5 21.9 1.0 NE2 A:HIS964 2.6 23.0 1.0 CB A:CYS752 2.6 15.7 1.0 CE1 A:HIS959 3.0 22.9 1.0 CD2 A:HIS959 3.1 16.1 1.0 CE1 A:HIS964 3.5 26.0 1.0 CD2 A:HIS964 3.5 27.1 1.0 CA A:CYS752 3.6 18.0 1.0 N A:CYS752 3.7 20.3 1.0 CA A:CYS749 4.0 23.4 1.0 ND1 A:HIS959 4.2 14.5 1.0 CG A:HIS959 4.2 12.2 1.0 C A:CYS752 4.2 22.1 1.0 ND1 A:HIS964 4.6 19.8 1.0 O A:CYS752 4.6 24.9 1.0 CG A:HIS766 4.6 23.8 1.0 CB A:HIS766 4.7 24.2 1.0 N A:CYS749 4.7 20.9 1.0 CG A:HIS964 4.7 18.5 1.0 C A:LEU751 4.7 20.3 1.0 CD2 A:HIS766 4.8 27.4 1.0 CB A:SER754 4.8 31.6 1.0 C A:CYS749 4.8 22.5 1.0 N A:ASP753 4.9 21.4 1.0 N A:SER754 4.9 28.9 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