Manganese in PDB 6cim: Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+

All present enzymatic activity of Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+:
2.3.2.27;

The structure of Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+, PDB code: 6cim was solved by W.Chuenchor, X.Chen, M.S.Kim, M.Gellert, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.69 / 3.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.678, 123.562, 186.286, 90.00, 105.60, 90.00
R / Rfree (%)	21.4 / 25.4

The structure of Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+ also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+ (pdb code 6cim). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+, PDB code: 6cim:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1102 b:84.8 occ:1.00 OD2 A:ASP708 2.2 0.7 1.0 OD1 A:ASP600 2.2 0.7 1.0 CG A:ASP600 3.3 95.9 1.0 CG A:ASP708 3.3 0.7 1.0 OD2 A:ASP600 3.6 0.5 1.0 OD1 A:ASP708 3.8 0.8 1.0 OE1 A:GLU662 3.8 1.0 1.0 OE2 A:GLU662 4.0 99.9 1.0 CD A:GLU662 4.4 97.3 1.0 N A:GLY601 4.4 97.7 1.0 OP2 F:DA32 4.4 0.8 1.0 O A:GLY601 4.5 94.9 1.0 CB A:ASP708 4.5 99.9 1.0 CB A:ASP600 4.6 81.6 1.0 OP1 F:DA32 4.9 0.8 1.0 CA A:ASP600 4.9 80.0 1.0

Manganese binding site 2 out of 2 in the Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pre-Reaction Complex, RAG1(E962Q)/2-Nicked/Intact 12/23RSS Complex in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1102 b:86.3 occ:1.00 OD2 C:ASP708 2.1 0.6 1.0 OD1 C:ASP600 2.2 89.9 1.0 CG C:ASP708 3.2 0.9 1.0 CG C:ASP600 3.3 95.7 1.0 OD1 C:ASP708 3.5 0.1 1.0 OE2 C:GLU662 3.6 0.5 1.0 OD2 C:ASP600 3.6 0.3 1.0 OE1 C:GLU662 3.8 0.3 1.0 CD C:GLU662 4.1 0.2 1.0 N C:GLY601 4.3 93.3 1.0 CB C:ASP708 4.5 0.9 1.0 O C:GLY601 4.5 98.4 1.0 CB C:ASP600 4.6 95.0 1.0 CA C:ASP600 4.7 84.8 1.0 OP2 G:DA43 5.0 87.7 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