Manganese in PDB 8amu: Repb PMV158 Obd Domain Bound to Ddr Region

The structure of Repb PMV158 Obd Domain Bound to Ddr Region, PDB code: 8amu was solved by J.Amodio, C.Machon, R.D.Boer, J.A.Ruiz-Maso, G.Del Solar, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.69 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.234, 33.619, 289.672, 90, 93.51, 90
R / Rfree (%)	22.7 / 28.2

The binding sites of Manganese atom in the Repb PMV158 Obd Domain Bound to Ddr Region (pdb code 8amu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Repb PMV158 Obd Domain Bound to Ddr Region, PDB code: 8amu:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Repb PMV158 Obd Domain Bound to Ddr Region


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Repb PMV158 Obd Domain Bound to Ddr Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:55.3 occ:1.00 NE2 A:HIS57 2.4 35.1 1.0 NE2 A:HIS55 2.5 37.3 1.0 ND1 A:HIS39 2.7 37.2 1.0 OD2 A:ASP42 2.7 34.7 1.0 CE1 A:HIS57 3.1 38.8 1.0 CE1 A:HIS39 3.2 30.6 1.0 CD2 A:HIS55 3.3 38.3 1.0 CD2 A:HIS57 3.5 28.0 1.0 CE1 A:HIS55 3.6 37.9 1.0 CG A:ASP42 3.7 37.0 1.0 NE2 A:HIS102 3.9 33.9 1.0 CG A:HIS39 3.9 38.1 1.0 OD1 A:ASP42 3.9 37.9 1.0 CE1 A:HIS102 4.3 36.7 1.0 ND1 A:HIS57 4.3 32.1 1.0 NE2 A:HIS39 4.4 27.8 1.0 CB A:HIS39 4.4 36.9 1.0 CG A:HIS57 4.5 29.5 1.0 CG A:HIS55 4.5 39.4 1.0 OH A:TYR99 4.6 19.6 1.0 ND1 A:HIS55 4.6 38.6 1.0 CD2 A:HIS39 4.8 35.5 1.0 CB A:ASP42 4.9 39.1 1.0

Manganese binding site 2 out of 3 in the Repb PMV158 Obd Domain Bound to Ddr Region


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Repb PMV158 Obd Domain Bound to Ddr Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:225.6 occ:1.00 OD2 B:ASP42 2.6 133.7 1.0 NE2 B:HIS55 2.6 107.8 1.0 NE2 B:HIS57 2.9 86.4 1.0 ND1 B:HIS39 2.9 103.2 1.0 CE1 B:HIS55 3.3 110.7 1.0 CE1 B:HIS39 3.5 105.2 1.0 CG B:ASP42 3.7 129.3 1.0 CE1 B:HIS57 3.8 87.6 1.0 CD2 B:HIS55 3.8 93.4 1.0 CD2 B:HIS57 3.9 85.1 1.0 CG B:HIS39 4.0 97.7 1.0 NE2 B:HIS102 4.1 121.3 1.0 CE1 B:HIS102 4.4 122.1 1.0 CB B:ASP42 4.4 125.5 1.0 CB B:HIS39 4.5 104.6 1.0 ND1 B:HIS55 4.5 103.1 1.0 OD1 B:ASP42 4.7 124.9 1.0 NE2 B:HIS39 4.8 97.7 1.0 CG B:HIS55 4.8 89.2 1.0 ND1 B:HIS57 5.0 74.0 1.0

Manganese binding site 3 out of 3 in the Repb PMV158 Obd Domain Bound to Ddr Region


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Repb PMV158 Obd Domain Bound to Ddr Region within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn201 b:61.7 occ:1.00 NE2 E:HIS57 2.5 52.4 1.0 NE2 E:HIS55 2.7 40.7 1.0 OD2 E:ASP42 2.7 40.4 1.0 ND1 E:HIS39 2.8 45.3 1.0 CE1 E:HIS39 3.1 45.5 1.0 CD2 E:HIS57 3.3 45.9 1.0 CD2 E:HIS55 3.5 44.9 1.0 CG E:ASP42 3.5 37.0 1.0 CE1 E:HIS57 3.6 45.5 1.0 CE1 E:HIS55 3.7 40.0 1.0 OD1 E:ASP42 3.7 41.4 1.0 NE2 E:HIS102 3.9 49.6 1.0 CG E:HIS39 4.0 45.6 1.0 CE1 E:HIS102 4.4 46.5 1.0 NE2 E:HIS39 4.4 40.6 1.0 CG E:HIS57 4.5 45.7 1.0 OH E:TYR99 4.6 52.9 1.0 ND1 E:HIS57 4.6 45.7 1.0 CB E:HIS39 4.7 45.9 1.0 CG E:HIS55 4.7 43.5 1.0 ND1 E:HIS55 4.7 42.2 1.0 CB E:ASP42 4.8 39.7 1.0 CE1 E:TYR99 4.9 42.8 1.0 CD2 E:HIS39 4.9 43.0 1.0

C.Machon, J.A.Ruiz-Maso, J.Amodio, D.R.Boer, L.Bordanaba-Ruiseco, K.Bury, I.Konieczny, G.Del Solar, M.Coll. Structures of PMV158 Replication Initiator Repb with and Without Dna Reveal A Flexible Dual-Function Protein. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36688326
DOI: 10.1093/NAR/GKAC1271