Zinc in PDB 5zdz: Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+

All present enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+:
2.3.2.27;

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+, PDB code: 5zdz was solved by M.S.Kim, W.Chuenchor, X.Chen, M.Gellert, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.72 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	132.450, 109.000, 156.050, 90.00, 114.28, 90.00
R / Rfree (%)	20.2 / 24.2

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+ also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+ (pdb code 5zdz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+, PDB code: 5zdz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:57.5 occ:1.00 NE2 A:HIS942 2.0 56.8 1.0 SG A:CYS727 2.1 60.9 1.0 NE2 A:HIS937 2.4 58.7 1.0 SG A:CYS730 2.5 59.4 1.0 CB A:CYS727 2.6 47.7 1.0 CE1 A:HIS942 2.8 62.4 1.0 CD2 A:HIS937 3.0 57.2 1.0 CD2 A:HIS942 3.0 56.6 1.0 CB A:CYS730 3.3 59.2 1.0 CE1 A:HIS937 3.6 64.0 1.0 N A:CYS730 3.9 57.2 1.0 ND1 A:HIS942 3.9 59.1 1.0 CG A:HIS942 4.1 58.9 1.0 CA A:CYS727 4.1 58.0 1.0 CA A:CYS730 4.1 60.7 1.0 CG2 A:THR732 4.2 63.2 1.0 CG A:HIS937 4.3 55.9 1.0 C A:LEU729 4.5 59.3 1.0 ND1 A:HIS937 4.5 60.4 1.0 CB A:LEU729 4.6 51.9 1.0 C A:CYS730 4.8 59.5 1.0 CB A:HIS744 4.8 70.3 1.0 N A:LEU729 4.8 58.2 1.0 CA A:LEU729 4.9 54.3 1.0 O A:CYS730 4.9 62.1 1.0

Zinc binding site 2 out of 2 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2002 b:57.5 occ:1.00 NE2 C:HIS942 1.9 56.1 1.0 SG C:CYS730 2.1 65.2 1.0 NE2 C:HIS937 2.3 55.9 1.0 SG C:CYS727 2.3 62.9 1.0 CD2 C:HIS942 2.8 57.6 1.0 CD2 C:HIS937 2.8 54.4 1.0 CE1 C:HIS942 2.9 58.5 1.0 CB C:CYS730 3.0 52.2 1.0 CB C:CYS727 3.1 48.2 1.0 N C:CYS730 3.2 61.1 1.0 CE1 C:HIS937 3.5 62.4 1.0 CA C:CYS730 3.7 59.5 1.0 CG C:HIS942 4.0 53.9 1.0 ND1 C:HIS942 4.0 55.6 1.0 CG C:HIS937 4.1 49.1 1.0 C C:LEU729 4.2 59.7 1.0 CB C:LEU729 4.3 55.4 1.0 ND1 C:HIS937 4.4 64.7 1.0 C C:CYS730 4.5 59.2 1.0 CA C:LEU729 4.6 55.5 1.0 CA C:CYS727 4.6 50.8 1.0 N C:LEU729 4.6 57.0 1.0 O C:CYS730 4.7 61.4 1.0 CG2 C:THR732 4.7 56.1 1.0 CB C:ALA941 4.9 56.6 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