Manganese in PDB 4lvm: Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (23NT). Mn-Bound Crystal Structure at pH 6.5

The structure of Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (23NT). Mn-Bound Crystal Structure at pH 6.5, PDB code: 4lvm 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)	28.40 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.340, 130.120, 87.380, 90.00, 90.00, 90.00
R / Rfree (%)	25.5 / 29.4

The structure of Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (23NT). Mn-Bound Crystal Structure at pH 6.5 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	5 atoms
Sodium	(Na)	1 atom

The binding sites of Manganese atom in the Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (23NT). Mn-Bound Crystal Structure at pH 6.5 (pdb code 4lvm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (23NT). Mn-Bound Crystal Structure at pH 6.5, PDB code: 4lvm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (23NT). Mn-Bound Crystal Structure at pH 6.5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (23NT). Mn-Bound Crystal Structure at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:88.5 occ:1.00 NE2 A:HIS135 2.2 0.3 1.0 ND1 A:HIS126 2.2 0.2 1.0 NE2 A:HIS22 2.2 0.2 1.0 NE2 A:HIS133 2.2 0.4 1.0 OE2 A:GLU129 2.4 0.9 1.0 CE1 A:HIS126 2.9 0.0 1.0 CE1 A:HIS135 2.9 0.8 1.0 CE1 A:HIS22 3.0 0.5 1.0 CE1 A:HIS133 3.0 0.1 1.0 CD A:GLU129 3.2 0.2 1.0 CG A:HIS126 3.3 1.0 1.0 CD2 A:HIS133 3.3 0.8 1.0 CD2 A:HIS135 3.4 0.0 1.0 CD2 A:HIS22 3.4 0.0 1.0 O3' E:DG26 3.6 0.9 1.0 O5' E:DT27 3.8 0.5 1.0 CB A:HIS126 3.9 1.0 1.0 OE1 A:GLU129 3.9 0.7 1.0 NE2 A:HIS126 4.0 0.1 1.0 CG A:GLU129 4.1 0.5 1.0 ND1 A:HIS135 4.1 0.9 1.0 P E:DT27 4.2 0.4 1.0 OP1 E:DT27 4.2 0.1 1.0 ND1 A:HIS22 4.2 0.3 1.0 ND1 A:HIS133 4.2 0.6 1.0 CD2 A:HIS126 4.2 0.2 1.0 CG A:HIS135 4.3 0.4 1.0 CG A:HIS133 4.4 0.8 1.0 CG A:HIS22 4.4 0.5 1.0 C3' E:DG26 4.7 0.0 1.0 C2' E:DG26 4.9 0.9 1.0

Manganese binding site 2 out of 2 in the Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (23NT). Mn-Bound Crystal Structure at pH 6.5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mobm Relaxase Domain (Mobv; MOB_PRE) Bound to Plasmid PMV158 Orit Dna (23NT). Mn-Bound Crystal Structure at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn201 b:35.1 occ:1.00 O C:HOH308 1.9 80.5 1.0 NE2 C:HIS133 2.1 24.8 1.0 NE2 C:HIS135 2.1 12.5 1.0 CE1 C:HIS135 2.5 12.4 1.0 NE2 C:HIS22 2.5 38.6 1.0 OE2 C:GLU129 2.6 42.8 1.0 CE1 C:HIS133 2.7 25.9 1.0 ND1 C:HIS126 2.8 25.8 1.0 OE1 C:GLU129 3.0 40.0 1.0 CD C:GLU129 3.1 40.8 1.0 CD2 C:HIS133 3.2 25.3 1.0 CE1 C:HIS126 3.3 24.7 1.0 CE1 C:HIS22 3.4 40.0 1.0 CD2 C:HIS135 3.4 12.7 1.0 CD2 C:HIS22 3.5 39.4 1.0 CG C:HIS126 3.7 26.9 1.0 ND1 C:HIS135 3.8 12.6 1.0 ND1 C:HIS133 3.9 27.2 1.0 O C:HOH309 4.1 34.6 1.0 CG C:HIS133 4.2 26.6 1.0 CB C:HIS126 4.2 28.8 1.0 NH2 C:ARG25 4.3 55.0 1.0 NE2 C:HIS126 4.3 26.0 1.0 CG C:HIS135 4.3 19.2 1.0 ND1 C:HIS22 4.5 41.2 1.0 CD2 C:HIS126 4.5 26.1 1.0 CG C:HIS22 4.6 41.2 1.0 CG C:GLU129 4.6 37.1 1.0 NH1 C:ARG25 4.8 56.1 1.0 CD1 C:ILE84 4.9 39.4 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.