Zinc in PDB 6cik: Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+

All present enzymatic activity of Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+:
2.3.2.27;

The structure of Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+, PDB code: 6cik was solved by W.Chuenchor, X.Chen, M.S.Kim, M.Gellert, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.84 / 3.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.423, 123.149, 186.327, 90.00, 105.03, 90.00
R / Rfree (%)	20.9 / 24.9

The structure of Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+ also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+ (pdb code 6cik). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+, PDB code: 6cik:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:90.3 occ:1.00 NE2 A:HIS937 2.0 76.0 1.0 NE2 A:HIS942 2.0 86.4 1.0 SG A:CYS730 2.3 72.4 1.0 SG A:CYS727 2.3 69.8 1.0 CE1 A:HIS937 2.5 75.0 1.0 CD2 A:HIS942 2.9 97.3 1.0 CE1 A:HIS942 3.1 84.6 1.0 CB A:CYS727 3.1 70.8 1.0 CD2 A:HIS937 3.2 87.8 1.0 CB A:CYS730 3.3 72.9 1.0 ND1 A:HIS937 3.8 73.9 1.0 N A:CYS730 4.0 73.6 1.0 CG A:HIS942 4.0 80.4 1.0 ND1 A:HIS942 4.1 81.5 1.0 CG A:HIS937 4.1 84.2 1.0 CA A:CYS730 4.2 66.7 1.0 CB A:HIS744 4.4 79.3 1.0 CG2 A:THR732 4.4 82.6 1.0 CB A:LEU729 4.5 72.4 1.0 CA A:CYS727 4.5 81.9 1.0 C A:LEU729 4.7 79.8 1.0 CG A:HIS744 4.9 87.7 1.0 C A:CYS730 4.9 75.4 1.0 CB A:ALA941 4.9 85.7 1.0 ND1 A:HIS744 5.0 85.9 1.0

Zinc binding site 2 out of 2 in the Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pre-Reaction Complex, RAG1(E962Q)/2-Intact/Nicked 12/23RSS Complex in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1101 b:90.3 occ:1.00 NE2 C:HIS937 2.0 87.8 1.0 NE2 C:HIS942 2.0 90.8 1.0 SG C:CYS727 2.3 73.5 1.0 SG C:CYS730 2.3 78.6 1.0 CE1 C:HIS937 2.5 82.6 1.0 CD2 C:HIS942 2.7 86.3 1.0 CB C:CYS727 3.1 85.5 1.0 CE1 C:HIS942 3.2 89.7 1.0 CD2 C:HIS937 3.2 93.8 1.0 CB C:CYS730 3.4 85.8 1.0 ND1 C:HIS937 3.7 85.6 1.0 N C:CYS730 4.0 76.6 1.0 CG C:HIS942 4.0 77.6 1.0 CG C:HIS937 4.0 92.7 1.0 ND1 C:HIS942 4.1 84.9 1.0 CA C:CYS730 4.2 76.2 1.0 CB C:LEU729 4.4 68.2 1.0 C C:LEU729 4.5 84.7 1.0 CG2 C:THR732 4.6 88.1 1.0 CA C:CYS727 4.6 75.0 1.0 CB C:HIS744 4.7 81.3 1.0 CA C:LEU729 4.9 75.6 1.0 N C:LEU729 4.9 72.8 1.0

M.S.Kim, W.Chuenchor, X.Chen, Y.Cui, X.Zhang, Z.H.Zhou, M.Gellert, W.Yang. Cracking the Dna Code For V(D)J Recombination. Mol. Cell V. 70 358 2018.
ISSN: ISSN 1097-4164
PubMed: 29628308
DOI: 10.1016/J.MOLCEL.2018.03.008