Magnesium 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:

Potassium	(K)	2 atoms
Zinc	(Zn)	2 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2001 b:61.5 occ:1.00 O A:GLY601 2.7 51.0 1.0 O3' F:DG30 3.0 42.3 1.0 OP2 F:DT31 3.0 42.6 1.0 OD1 A:ASP600 3.0 64.0 1.0 OP1 F:DG30 3.2 46.0 1.0 OE2 A:GLU962 3.2 48.7 1.0 O F:HOH102 3.2 50.9 1.0 OD2 A:ASP600 3.3 62.2 1.0 CG A:ASP600 3.5 62.0 1.0 OE1 A:GLU962 3.6 54.2 1.0 ND2 A:ASN965 3.6 45.2 1.0 O F:HOH104 3.7 54.9 1.0 P F:DT31 3.7 43.6 1.0 CD A:GLU962 3.8 51.8 1.0 C A:GLY601 3.8 50.4 1.0 C3' F:DG30 4.1 41.5 1.0 C4' F:DG30 4.2 43.3 1.0 CA A:MET602 4.3 43.7 1.0 CG A:MET602 4.4 45.8 1.0 N A:MET602 4.5 45.6 1.0 P F:DG30 4.5 43.2 1.0 C5' F:DT31 4.6 56.3 1.0 O5' F:DT31 4.7 57.8 1.0 O A:HOH2113 4.7 52.8 1.0 N A:GLY601 4.7 51.4 1.0 CG A:ASN965 4.8 44.1 1.0 C5' F:DG30 4.8 44.4 1.0 O3' F:DT29 4.9 45.5 1.0 CB A:ASP600 4.9 54.9 1.0 CA A:GLY601 4.9 49.5 1.0 OP1 F:DT31 4.9 42.4 1.0 CB A:MET602 4.9 41.1 1.0 C2' F:DG30 4.9 41.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2001 b:54.5 occ:1.00 OD1 C:ASP600 2.6 61.4 1.0 OP2 G:DT42 2.8 40.7 1.0 O C:GLY601 2.9 47.1 1.0 O3' G:DG41 2.9 48.3 1.0 OE1 C:GLU962 3.0 48.6 1.0 OE2 C:GLU962 3.0 47.4 1.0 O G:HOH102 3.1 52.9 1.0 CD C:GLU962 3.4 46.8 1.0 P G:DT42 3.5 45.0 1.0 ND2 C:ASN965 3.7 47.9 1.0 OP1 G:DG41 3.8 46.2 1.0 O G:HOH105 3.8 47.5 1.0 CG C:ASP600 3.8 54.6 1.0 C C:GLY601 4.0 43.4 1.0 C3' G:DG41 4.2 39.6 1.0 C4' G:DG41 4.4 43.4 1.0 CG C:MET602 4.5 47.5 1.0 OP1 G:DT42 4.5 46.8 1.0 OD2 C:ASP600 4.6 50.8 1.0 N C:GLY601 4.6 45.1 1.0 O5' G:DG41 4.6 51.0 1.0 CA C:MET602 4.6 39.7 1.0 O5' G:DT42 4.6 57.2 1.0 N C:MET602 4.7 38.0 1.0 CB C:ASP600 4.7 47.7 1.0 C5' G:DT42 4.8 52.6 1.0 C2' G:DG41 4.8 34.0 1.0 P G:DG41 4.8 43.0 1.0 CG C:ASN965 4.8 46.1 1.0 CA C:GLY601 4.9 43.3 1.0 CG C:GLU962 4.9 45.1 1.0 CB C:MET602 5.0 38.3 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