Zinc in PDB 6dbw: Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna

All present enzymatic activity of Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna:
2.3.2.27;

The structure of Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna 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 Substrate Dna (pdb code 6dbw). 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 Substrate Dna, PDB code: 6dbw:
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 Substrate Dna


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 Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:0.5 occ:1.00 NE2 A:HIS964 1.9 0.0 1.0 SG A:CYS749 2.3 0.2 1.0 CB A:CYS752 2.4 0.2 1.0 N A:CYS752 2.4 0.5 1.0 NE2 A:HIS959 2.4 1.0 1.0 CD2 A:HIS964 2.6 0.1 1.0 CA A:CYS752 2.9 0.5 1.0 SG A:CYS752 2.9 0.1 1.0 CE1 A:HIS964 3.0 1.0 1.0 CE1 A:HIS959 3.0 97.7 1.0 CB A:CYS749 3.1 0.5 1.0 C A:LEU751 3.4 0.6 1.0 CD2 A:HIS959 3.6 89.6 1.0 CG A:HIS964 3.7 0.3 1.0 ND1 A:HIS964 3.9 0.6 1.0 C A:CYS752 3.9 0.5 1.0 O A:CYS752 4.0 0.7 1.0 CB A:LEU751 4.1 0.5 1.0 CA A:LEU751 4.1 0.3 1.0 O A:LEU751 4.2 0.8 1.0 N A:LEU751 4.2 0.8 1.0 ND1 A:HIS959 4.3 66.0 1.0 CA A:CYS749 4.6 0.2 1.0 CG A:HIS959 4.6 64.3 1.0 O A:SER767 4.8 0.1 1.0 N A:ASP753 5.0 0.9 1.0 CB A:HIS766 5.0 0.6 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna


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 Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1101 b:0.0 occ:1.00 NE2 C:HIS964 2.2 0.1 1.0 NE2 C:HIS959 2.3 0.1 1.0 SG C:CYS749 2.3 0.3 1.0 CE1 C:HIS959 2.4 0.3 1.0 CE1 C:HIS964 2.7 0.9 1.0 CB C:CYS749 3.1 0.4 1.0 CB C:CYS752 3.3 0.7 1.0 CD2 C:HIS964 3.3 0.8 1.0 ND1 C:HIS959 3.5 0.9 1.0 CB C:HIS766 3.6 0.6 1.0 CD2 C:HIS959 3.7 0.8 1.0 CD2 C:HIS766 3.8 0.4 1.0 CG C:HIS766 3.9 0.4 1.0 ND1 C:HIS964 3.9 0.9 1.0 N C:CYS752 4.0 0.7 1.0 CA C:CYS752 4.2 0.0 1.0 CG C:HIS964 4.2 0.0 1.0 CA C:CYS749 4.4 0.7 1.0 CG C:HIS959 4.4 0.2 1.0 SG C:CYS752 4.4 0.2 1.0 O C:SER767 4.5 0.5 1.0 NE2 C:HIS766 4.8 84.1 1.0 C C:CYS752 4.9 0.7 1.0 CB C:ALA963 4.9 0.1 1.0 ND1 C:HIS766 4.9 0.2 1.0 CA C:HIS766 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