Potassium 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
Zinc	(Zn)	2 atoms

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

Potassium 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 Potassium with other atoms in the K 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:K2005 b:49.3 occ:1.00 O L:HOH4104 2.6 34.9 1.0 OE1 A:GLU649 2.7 35.7 1.0 O2 L:DC19 2.9 40.0 1.0 O A:HOH2138 2.9 37.3 1.0 O4' L:DC19 2.9 47.6 1.0 OG A:SER963 3.4 44.5 1.0 N3 L:DA18 3.4 47.0 1.0 C2 L:DA18 3.5 43.1 1.0 CD A:GLU649 3.6 39.8 1.0 C1' L:DC19 3.6 48.6 1.0 C2 L:DC19 3.7 43.5 1.0 OE2 A:GLU649 3.7 38.7 1.0 C4' L:DC19 3.7 47.3 1.0 N2 F:DG28 3.9 42.6 1.0 CB A:SER963 4.0 40.1 1.0 N1 L:DC19 4.0 42.5 1.0 C5' L:DC19 4.5 48.2 1.0 C4 L:DA18 4.6 46.4 1.0 N1 L:DA18 4.6 45.1 1.0 N3 L:DC19 4.7 46.5 1.0 O4' L:DA20 4.7 44.4 1.0 N A:GLU649 4.8 42.2 1.0 C3' L:DC19 4.9 44.5 1.0 O3' L:DC19 4.9 47.8 1.0 CG A:GLU649 4.9 39.4 1.0 C2' L:DC19 5.0 45.1 1.0

Potassium 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 Potassium with other atoms in the K 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:K2003 b:42.4 occ:1.00 O G:HOH107 2.6 42.1 1.0 O C:HOH2104 2.6 38.9 1.0 O2 M:DC19 2.7 47.0 1.0 OE1 C:GLU649 2.7 44.0 1.0 O4' M:DC19 3.1 42.6 1.0 OG C:SER963 3.2 44.7 1.0 N2 G:DG39 3.5 41.5 1.0 N3 M:DA18 3.6 45.2 1.0 C2 M:DA18 3.6 44.1 1.0 CD C:GLU649 3.6 45.5 1.0 C2 M:DC19 3.6 46.7 1.0 C1' M:DC19 3.7 48.1 1.0 O G:HOH109 3.7 48.5 1.0 OE2 C:GLU649 3.8 45.5 1.0 C4' M:DC19 3.8 47.0 1.0 CB C:SER963 4.0 43.0 1.0 N1 M:DC19 4.1 46.2 1.0 O C:HOH2112 4.4 40.5 1.0 N1 M:DA18 4.6 41.1 1.0 C4 M:DA18 4.6 45.6 1.0 N3 M:DC19 4.6 49.0 1.0 C5' M:DC19 4.6 48.8 1.0 C2 G:DG39 4.7 45.4 1.0 O4' M:DA20 4.9 54.5 1.0 O2 G:DT40 4.9 44.2 1.0 C3' M:DC19 4.9 49.1 1.0 CG C:GLU649 5.0 38.1 1.0 N C:GLU649 5.0 44.3 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