Zinc in PDB 5ze0: Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS Complex in MG2+

All present enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS Complex in MG2+:
2.3.2.27;

The structure of Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS Complex in MG2+, PDB code: 5ze0 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)	34.80 / 2.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	132.440, 109.030, 156.850, 90.00, 114.43, 90.00
R / Rfree (%)	19.9 / 23.4

The structure of Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS Complex in MG2+ also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	2 atoms

The binding sites of Zinc atom in the Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS Complex in MG2+ (pdb code 5ze0). 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(with Dideoxy) 12RSS/23RSS Complex in MG2+, PDB code: 5ze0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS Complex in MG2+


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(with Dideoxy) 12RSS/23RSS Complex in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:49.9 occ:1.00 NE2 A:HIS942 1.9 47.8 1.0 SG A:CYS727 2.2 46.2 1.0 SG A:CYS730 2.2 52.1 1.0 NE2 A:HIS937 2.3 46.0 1.0 CE1 A:HIS942 2.9 52.0 1.0 CD2 A:HIS942 2.9 47.1 1.0 CB A:CYS727 3.0 40.8 1.0 CD2 A:HIS937 3.0 42.5 1.0 CB A:CYS730 3.2 47.5 1.0 CE1 A:HIS937 3.4 52.7 1.0 N A:CYS730 3.7 50.1 1.0 ND1 A:HIS942 4.0 50.9 1.0 CA A:CYS730 4.0 51.6 1.0 CG A:HIS942 4.0 48.9 1.0 CG A:HIS937 4.3 43.3 1.0 CG2 A:THR732 4.4 52.0 1.0 ND1 A:HIS937 4.4 48.5 1.0 CA A:CYS727 4.5 46.0 1.0 CB A:LEU729 4.5 42.4 1.0 C A:LEU729 4.6 51.2 1.0 C A:CYS730 4.7 51.2 1.0 CB A:HIS744 4.7 63.5 1.0 CA A:LEU729 4.9 45.2 1.0 N A:LEU729 4.9 48.4 1.0

Zinc binding site 2 out of 2 in the Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS Complex in MG2+


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(with Dideoxy) 12RSS/23RSS Complex in MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2002 b:54.0 occ:1.00 NE2 C:HIS942 1.9 46.6 1.0 NE2 C:HIS937 2.1 52.1 1.0 SG C:CYS730 2.2 53.0 1.0 SG C:CYS727 2.2 53.3 1.0 CD2 C:HIS937 2.9 48.8 1.0 CE1 C:HIS942 2.9 54.7 1.0 CD2 C:HIS942 2.9 50.3 1.0 CB C:CYS727 3.0 42.9 1.0 CE1 C:HIS937 3.1 55.8 1.0 CB C:CYS730 3.4 56.0 1.0 N C:CYS730 3.7 53.4 1.0 ND1 C:HIS942 4.0 54.8 1.0 CG C:HIS937 4.0 46.1 1.0 CG C:HIS942 4.1 50.2 1.0 CA C:CYS730 4.1 56.3 1.0 ND1 C:HIS937 4.1 57.9 1.0 CA C:CYS727 4.5 42.4 1.0 CB C:LEU729 4.5 50.4 1.0 C C:LEU729 4.5 56.9 1.0 CG2 C:THR732 4.6 56.2 1.0 C C:CYS730 4.7 52.4 1.0 O C:CYS730 4.8 53.9 1.0 CA C:LEU729 4.9 52.3 1.0 CB C:HIS744 4.9 64.6 1.0 N C:LEU729 4.9 50.2 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