Potassium 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:

Zinc	(Zn)	2 atoms
Calcium	(Ca)	2 atoms

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

Potassium 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 Potassium with other atoms in the K 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:K2005 b:49.2 occ:1.00 O A:HOH2102 2.6 35.7 1.0 OE1 A:GLU649 2.7 40.2 1.0 O2 L:DC19 2.8 48.9 1.0 O4' L:DC19 2.9 54.8 1.0 O A:HOH2123 2.9 39.0 1.0 OG A:SER963 3.2 52.3 1.0 N3 L:DA18 3.4 53.2 1.0 C2 L:DA18 3.5 52.2 1.0 CD A:GLU649 3.5 42.4 1.0 C2 L:DC19 3.7 53.5 1.0 OE2 A:GLU649 3.7 40.1 1.0 C1' L:DC19 3.8 55.7 1.0 C4' L:DC19 3.8 53.8 1.0 N2 F:DG28 3.9 52.8 1.0 CB A:SER963 3.9 44.3 1.0 N1 L:DC19 4.1 54.9 1.0 C5' L:DC19 4.5 54.3 1.0 C4 L:DA18 4.6 53.0 1.0 N1 L:DA18 4.6 54.2 1.0 N3 L:DC19 4.6 56.1 1.0 N A:GLU649 4.8 47.3 1.0 O4' L:DA20 4.8 52.6 1.0 CG A:GLU649 4.9 45.0 1.0 O A:ASN647 4.9 61.6 1.0 C3' L:DC19 4.9 52.0 1.0 C2 F:DG28 5.0 47.9 1.0

Potassium 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 Potassium with other atoms in the K 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:K2003 b:51.2 occ:1.00 O G:HOH102 2.7 50.9 1.0 OE1 C:GLU649 2.7 49.7 1.0 O2 M:DC19 2.8 54.7 1.0 O4' M:DC19 2.9 49.4 1.0 OG C:SER963 3.1 51.1 1.0 N3 M:DA18 3.6 51.7 1.0 C4' M:DC19 3.6 55.3 1.0 CD C:GLU649 3.6 52.0 1.0 C2 M:DA18 3.6 51.0 1.0 C1' M:DC19 3.7 57.3 1.0 C2 M:DC19 3.7 54.5 1.0 N2 G:DG39 3.7 53.3 1.0 OE2 C:GLU649 3.8 48.4 1.0 CB C:SER963 3.9 50.2 1.0 O C:HOH2126 4.1 51.1 1.0 N1 M:DC19 4.1 53.9 1.0 C5' M:DC19 4.4 57.0 1.0 C4 M:DA18 4.6 52.6 1.0 N1 M:DA18 4.7 53.1 1.0 O C:HOH2116 4.7 47.0 1.0 N3 M:DC19 4.7 57.5 1.0 N C:GLU649 4.7 48.8 1.0 O C:ASN647 4.8 55.3 1.0 C3' M:DC19 4.8 58.1 1.0 O4' M:DA20 4.8 58.2 1.0 O3' M:DC19 4.9 63.1 1.0 C2 G:DG39 4.9 53.2 1.0 CG C:GLU649 5.0 48.6 1.0 C2' M:DC19 5.0 57.6 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