Sodium in PDB 4lvk: Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (22NT+3'Phosphate). Mn-Bound Crystal Structure at pH 4.6

The structure of Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (22NT+3'Phosphate). Mn-Bound Crystal Structure at pH 4.6, PDB code: 4lvk was solved by R.Pluta, D.R.Boer, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.93 / 2.37
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	112.743, 112.743, 91.660, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 25

The structure of Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (22NT+3'Phosphate). Mn-Bound Crystal Structure at pH 4.6 also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Sodium atom in the Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (22NT+3'Phosphate). Mn-Bound Crystal Structure at pH 4.6 (pdb code 4lvk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (22NT+3'Phosphate). Mn-Bound Crystal Structure at pH 4.6, PDB code: 4lvk:

Sodium binding site 1 out of 1 in the Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (22NT+3'Phosphate). Mn-Bound Crystal Structure at pH 4.6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (22NT+3'Phosphate). Mn-Bound Crystal Structure at pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:64.5 occ:1.00 OP2 B:DT3 2.4 0.6 1.0 C5' B:DT3 2.8 92.6 1.0 O5' B:DT3 3.4 0.3 1.0 P B:DT3 3.5 0.9 1.0 C6 B:DT3 3.6 79.4 1.0 C4' B:DT3 4.0 86.5 1.0 C2' B:DC2 4.0 96.7 1.0 C7 B:DT3 4.0 84.3 1.0 C3' B:DT3 4.1 86.4 1.0 C2' B:DT3 4.1 81.4 1.0 O3' B:DC2 4.2 0.8 1.0 C5 B:DT3 4.3 79.7 1.0 C3' B:DC2 4.4 0.5 1.0 O4' B:DT3 4.6 80.5 1.0 N1 B:DT3 4.6 75.5 1.0 C1' B:DT3 4.7 77.2 1.0 OP1 B:DT3 4.8 0.8 1.0 C7 B:DT4 4.9 78.9 1.0

R.Pluta, D.R.Boer, S.Russi, C.Fernandez-Lopez, F.Lorenzo-Diaz, R.Perez-Luque, M.Espinosa, M.Coll. Structures of Dna-Mobm Relaxase Complexes Reveal A Histidine/Metal Catalysis For Dna Cleavage and Ligation To Be Published.