Manganese in PDB 9d4s: Structure of G2L4 Rt in Complex with 15 Nucleotide Snapback Substrate

The structure of Structure of G2L4 Rt in Complex with 15 Nucleotide Snapback Substrate, PDB code: 9d4s was solved by M.Guo, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.30 / 2.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.398, 99.19, 157.276, 90, 90, 90
R / Rfree (%)	23.5 / 27.7

The binding sites of Manganese atom in the Structure of G2L4 Rt in Complex with 15 Nucleotide Snapback Substrate (pdb code 9d4s). 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 G2L4 Rt in Complex with 15 Nucleotide Snapback Substrate, PDB code: 9d4s:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of G2L4 Rt in Complex with 15 Nucleotide Snapback Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of G2L4 Rt in Complex with 15 Nucleotide Snapback Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:43.5 occ:1.00 OD1 A:ASP145 1.9 52.5 1.0 O2B A:DCP502 2.1 43.3 1.0 OD2 A:ASP239 2.1 48.4 1.0 O3G A:DCP502 2.2 39.3 1.0 O A:ILE146 2.2 45.3 1.0 O2A A:DCP502 2.4 48.1 1.0 CG A:ASP145 2.9 49.8 1.0 PB A:DCP502 3.1 42.9 1.0 OD2 A:ASP145 3.2 57.5 1.0 CG A:ASP239 3.3 50.0 1.0 C A:ILE146 3.3 40.1 1.0 PG A:DCP502 3.3 42.6 1.0 O3B A:DCP502 3.4 37.9 1.0 PA A:DCP502 3.4 42.4 1.0 O3A A:DCP502 3.5 44.2 1.0 N A:ILE146 3.9 43.2 1.0 OD1 A:ASP239 4.0 46.7 1.0 NZ A:LYS278 4.0 39.1 1.0 C5' A:DCP502 4.0 40.6 1.0 O1G A:DCP502 4.0 45.9 1.0 N A:PRO147 4.1 42.8 1.0 CA A:ILE146 4.2 43.0 1.0 CA A:PRO147 4.2 46.7 1.0 O5' A:DCP502 4.2 36.8 1.0 CB A:ASP145 4.2 48.1 1.0 CB A:ASP239 4.2 46.6 1.0 N A:ALA148 4.4 44.1 1.0 O1B A:DCP502 4.5 46.8 1.0 O2G A:DCP502 4.5 48.0 1.0 C A:PRO147 4.6 40.9 1.0 C A:ASP145 4.6 44.5 1.0 CE2 A:TYR270 4.6 45.9 1.0 O1A A:DCP502 4.7 47.2 1.0 N A:PHE149 4.8 42.4 1.0 CB A:ILE146 4.8 40.8 1.0 CB A:PHE149 4.9 40.6 1.0 CA A:ASP145 4.9 47.0 1.0 CE A:LYS278 5.0 42.8 1.0

Manganese binding site 2 out of 2 in the Structure of G2L4 Rt in Complex with 15 Nucleotide Snapback Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of G2L4 Rt in Complex with 15 Nucleotide Snapback Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:68.3 occ:1.00 OD2 B:ASP239 1.8 60.0 1.0 O1A B:DCP502 2.0 65.9 1.0 O1G B:DCP502 2.1 67.6 1.0 O B:ILE146 2.3 63.7 1.0 O1B B:DCP502 2.3 58.9 1.0 CG B:ASP239 2.9 60.4 1.0 OD2 B:ASP145 3.0 61.4 1.0 PA B:DCP502 3.2 54.3 1.0 PB B:DCP502 3.3 67.7 1.0 C B:ILE146 3.3 65.6 1.0 PG B:DCP502 3.4 71.0 1.0 O3B B:DCP502 3.4 61.6 1.0 O3A B:DCP502 3.5 60.6 1.0 OD1 B:ASP239 3.6 58.9 1.0 C5' B:DCP502 3.8 51.0 1.0 N B:ILE146 3.8 62.1 1.0 CB B:ASP239 3.9 55.3 1.0 O5' B:DCP502 3.9 49.5 1.0 CG B:ASP145 4.0 65.5 1.0 CB B:ASP145 4.1 66.7 1.0 N B:PRO147 4.1 69.6 1.0 CA B:ILE146 4.1 66.3 1.0 O3G B:DCP502 4.2 60.2 1.0 CA B:PRO147 4.2 68.4 1.0 N B:ALA148 4.3 63.3 1.0 O2G B:DCP502 4.4 75.7 1.0 C B:ASP145 4.4 62.8 1.0 O2A B:DCP502 4.4 55.6 1.0 C B:PRO147 4.5 66.4 1.0 N B:PHE149 4.6 58.9 1.0 O2B B:DCP502 4.7 59.7 1.0 CB B:ILE146 4.8 63.1 1.0 CB B:PHE149 4.8 55.7 1.0 CA B:ASP145 4.9 64.4 1.0

S.K.Park, M.Guo, J.L.Stamos, W.Kim, S.Lee, Y.J.Zhang, A.M.Lambowitz. Structural Basis For the Evolution of A Domesticated Group II Intron-Like Reverse Transcriptase to Function in Host Cell Dna Repair. Proc.Natl.Acad.Sci.Usa V. 122 2025.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2504208122