Zinc in PDB 6xny: Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-Form)

All present enzymatic activity of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-Form):
2.3.2.27;

The structure of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-Form) also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-Form) (pdb code 6xny). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-Form), PDB code: 6xny:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:45.3 occ:1.00 NE2 A:HIS942 2.0 35.5 1.0 NE2 A:HIS937 2.0 34.9 1.0 CB A:CYS727 2.1 36.4 1.0 SG A:CYS730 2.1 36.3 1.0 SG A:CYS727 2.2 36.4 1.0 CE1 A:HIS942 2.7 35.5 1.0 N A:CYS730 2.8 36.3 1.0 CB A:CYS730 2.9 36.3 1.0 CD2 A:HIS937 3.0 34.9 1.0 CE1 A:HIS937 3.1 34.9 1.0 CD2 A:HIS942 3.2 35.5 1.0 CA A:CYS730 3.3 36.3 1.0 CA A:CYS727 3.7 36.4 1.0 O A:CYS730 3.7 36.3 1.0 C A:LEU729 3.8 35.3 1.0 ND1 A:HIS942 3.9 35.5 1.0 C A:CYS730 3.9 36.3 1.0 CB A:LEU729 3.9 35.3 1.0 CG A:HIS942 4.1 35.5 1.0 N A:LEU729 4.1 35.3 1.0 ND1 A:HIS937 4.1 34.9 1.0 CG A:HIS937 4.2 34.9 1.0 CA A:LEU729 4.2 35.3 1.0 C A:CYS727 4.4 36.4 1.0 N A:CYS727 4.4 36.4 1.0 CG2 A:THR732 4.7 37.0 1.0 CD1 A:LEU729 4.8 35.3 1.0 O A:CYS727 4.9 36.4 1.0 O A:LEU729 4.9 35.3 1.0 CG A:LEU729 4.9 35.3 1.0 N A:THR728 4.9 34.9 1.0

Zinc binding site 2 out of 2 in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1103 b:46.4 occ:1.00 NE2 C:HIS942 2.0 34.5 1.0 CB C:CYS727 2.1 35.4 1.0 SG C:CYS730 2.1 35.0 1.0 SG C:CYS727 2.1 35.4 1.0 CE1 C:HIS942 2.6 34.5 1.0 NE2 C:HIS937 2.7 33.7 1.0 N C:CYS730 2.8 35.0 1.0 CB C:CYS730 3.0 35.0 1.0 CD2 C:HIS942 3.1 34.5 1.0 CA C:CYS730 3.3 35.0 1.0 CE1 C:HIS937 3.5 33.7 1.0 CA C:CYS727 3.6 35.4 1.0 CD2 C:HIS937 3.6 33.7 1.0 ND1 C:HIS942 3.7 34.5 1.0 O C:CYS730 3.7 35.0 1.0 C C:LEU729 3.8 34.5 1.0 C C:CYS730 3.9 35.0 1.0 CB C:LEU729 3.9 34.5 1.0 CG C:HIS942 4.0 34.5 1.0 N C:LEU729 4.1 34.5 1.0 CA C:LEU729 4.2 34.5 1.0 C C:CYS727 4.4 35.4 1.0 N C:CYS727 4.4 35.4 1.0 ND1 C:HIS937 4.6 33.7 1.0 CG2 C:THR732 4.6 35.9 1.0 CG C:HIS937 4.7 33.7 1.0 CD1 C:LEU729 4.7 34.5 1.0 N C:THR728 4.7 34.0 1.0 O C:LEU729 4.9 34.5 1.0 CB C:HIS744 4.9 37.0 1.0 CG C:LEU729 5.0 34.5 1.0

Y.Zhang, E.Corbett, S.Wu, D.G.Schatz. Structural Basis For the Activation and Suppression of Transposition During Evolution of the Rag Recombinase. Embo J. V. 39 05857 2020.
ISSN: ESSN 1460-2075
PubMed: 32945578
DOI: 10.15252/EMBJ.2020105857