Calcium 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
Zinc	(Zn)	2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+, PDB code: 5zdz:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca2001 b:84.0 occ:1.00 O F:HOH102 2.4 57.2 1.0 OD1 A:ASP600 2.5 69.0 1.0 O A:HOH2103 2.5 54.1 1.0 OP2 F:DT31 2.5 57.1 1.0 OE1 A:GLU962 3.2 61.0 1.0 CG A:ASP600 3.3 67.1 1.0 OD2 A:ASP708 3.3 52.5 1.0 OD2 A:ASP600 3.4 66.9 1.0 P F:DT31 3.5 52.8 1.0 O3' F:DG30 3.6 52.8 1.0 O A:GLY601 3.6 53.8 1.0 O3' I:DA16 3.9 61.5 1.0 C3' I:DA16 4.0 56.1 1.0 OP1 F:DT31 4.1 56.2 1.0 CD A:GLU962 4.1 58.9 1.0 OE2 A:GLU962 4.2 59.7 1.0 NE2 A:HIS795 4.4 50.1 1.0 CG A:ASP708 4.5 56.2 1.0 CE1 A:HIS795 4.6 52.9 1.0 N A:GLY601 4.7 56.7 1.0 CB A:ASP600 4.7 57.1 1.0 C A:GLY601 4.7 55.5 1.0 C3' F:DG30 4.9 51.0 1.0 O5' F:DT31 4.9 69.5 1.0 C2' I:DA16 4.9 57.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca2001 b:69.6 occ:1.00 O C:HOH2103 2.5 42.9 1.0 O C:HOH2108 2.5 54.5 1.0 OD1 C:ASP600 2.7 66.2 1.0 O C:HOH2111 2.7 46.9 1.0 OE1 C:GLU962 2.8 54.7 1.0 O C:GLY601 2.9 49.6 1.0 OP2 G:DT42 3.0 49.2 1.0 O C:HOH2110 3.2 56.7 1.0 CD C:GLU962 3.7 51.1 1.0 CG C:ASP600 3.7 60.7 1.0 OE2 C:GLU962 3.7 53.8 1.0 O3' G:DG41 3.7 53.5 1.0 CB C:ASP600 3.9 51.6 1.0 P G:DT42 4.0 53.9 1.0 N C:GLY601 4.0 48.8 1.0 C C:GLY601 4.0 50.4 1.0 OD2 C:ASP708 4.1 52.9 1.0 CA C:GLY601 4.7 50.5 1.0 CA C:ASP600 4.7 51.1 1.0 O3' J:DA16 4.7 57.7 1.0 C C:ASP600 4.7 50.8 1.0 OP1 G:DT42 4.8 53.9 1.0 OD2 C:ASP600 4.9 56.4 1.0 C3' G:DG41 5.0 46.5 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