Manganese in PDB 6lrd: Structure of Recj Complexed with A 5'-P-Dspacer-Modified Ssdna

The structure of Structure of Recj Complexed with A 5'-P-Dspacer-Modified Ssdna, PDB code: 6lrd was solved by K.Cheng, Y.Hua, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.35 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.140, 106.140, 164.560, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 23.4

The binding sites of Manganese atom in the Structure of Recj Complexed with A 5'-P-Dspacer-Modified Ssdna (pdb code 6lrd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Recj Complexed with A 5'-P-Dspacer-Modified Ssdna, PDB code: 6lrd:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of Recj Complexed with A 5'-P-Dspacer-Modified Ssdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Recj Complexed with A 5'-P-Dspacer-Modified Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:37.4 occ:1.00 O A:HOH928 2.0 36.8 1.0 NE2 A:HIS159 2.2 28.6 1.0 OD2 A:ASP223 2.4 28.4 1.0 OD1 A:ASP135 2.4 24.1 1.0 OD2 A:ASP83 2.4 28.2 1.0 OP2 C:DT3 2.4 44.9 1.0 CE1 A:HIS159 3.1 28.1 1.0 CG A:ASP223 3.1 31.2 1.0 CG A:ASP135 3.1 26.9 1.0 CD2 A:HIS159 3.3 27.6 1.0 OD2 A:ASP135 3.3 31.0 1.0 OD1 A:ASP223 3.3 31.4 1.0 CG A:ASP83 3.4 26.4 1.0 P C:DT3 3.5 37.7 1.0 MN A:MN802 3.8 41.5 1.0 CB A:ASP83 3.8 27.4 1.0 O5' C:DT3 3.9 43.6 1.0 OP1 C:DT3 3.9 41.3 1.0 O A:HOH1161 3.9 38.5 1.0 N A:GLY189 4.2 25.6 1.0 ND1 A:HIS159 4.2 26.4 1.0 CG A:HIS159 4.4 29.5 1.0 CB A:ASP223 4.4 28.7 1.0 CB A:ASP135 4.5 21.3 1.0 OD1 A:ASP83 4.5 25.5 1.0 C5' C:DT3 4.5 35.5 1.0 NE2 A:HIS397 4.6 41.2 1.0 CB A:THR188 4.7 25.8 1.0 CA A:GLY189 4.8 23.9 1.0 O3' C:DT2 4.9 38.2 1.0 CE1 A:HIS397 5.0 41.4 1.0

Manganese binding site 2 out of 2 in the Structure of Recj Complexed with A 5'-P-Dspacer-Modified Ssdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Recj Complexed with A 5'-P-Dspacer-Modified Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:41.5 occ:1.00 OD2 A:ASP135 2.1 31.0 1.0 OP1 C:DT3 2.2 41.3 1.0 OD2 A:ASP79 2.2 31.7 1.0 OD2 A:ASP81 2.2 34.7 1.0 OD1 A:ASP81 2.3 28.7 1.0 O A:HOH928 2.3 36.8 1.0 CG A:ASP81 2.6 29.4 1.0 CG A:ASP135 3.2 26.9 1.0 P C:DT3 3.2 37.7 1.0 CG A:ASP79 3.2 27.6 1.0 O A:HOH976 3.5 28.9 1.0 O5' C:DT3 3.5 43.6 1.0 CB A:ASP79 3.6 24.8 1.0 OD1 A:ASP135 3.6 24.1 1.0 MN A:MN801 3.8 37.4 1.0 OP2 C:DT3 3.8 44.9 1.0 CB A:ASP81 4.1 28.2 1.0 N A:GLY84 4.2 27.6 1.0 OD1 A:ASP79 4.4 27.7 1.0 O A:ASP135 4.4 31.0 1.0 CB A:ASP135 4.4 21.3 1.0 OD1 A:ASP223 4.5 31.4 1.0 CB A:ASP83 4.5 27.4 1.0 O3' C:DT2 4.6 38.2 1.0 CA A:GLY84 4.7 27.4 1.0 N A:ASP81 4.7 25.7 1.0 CE1 A:TYR114 4.8 27.2 1.0 O A:HOH1110 4.8 29.3 1.0 OD2 A:ASP83 4.8 28.2 1.0 CA A:ASP81 4.9 28.8 1.0 O C:HOH105 4.9 33.9 1.0 O A:HOH1161 4.9 38.5 1.0 C5' C:DT3 4.9 35.5 1.0 CA A:ASP79 5.0 25.3 1.0

K.Cheng, Y.Xu, X.Chen, H.Lu, Y.He, L.Wang, Y.Hua. Participation of Recj in the Base Excision Repair Pathway of Deinococcus Radiodurans. Nucleic Acids Res. V. 48 9859 2020.
ISSN: ESSN 1362-4962
PubMed: 32870272
DOI: 10.1093/NAR/GKAA714