Magnesium in PDB 7k9y: Gsi-Iic Rt Template-Switching Complex (Twinned)

The structure of Gsi-Iic Rt Template-Switching Complex (Twinned), PDB code: 7k9y was solved by J.L.Stamos, A.M.Lentzsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.79 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	179.38, 107.415, 71.973, 90, 113.65, 90
R / Rfree (%)	27.1 / 32.4

The binding sites of Magnesium atom in the Gsi-Iic Rt Template-Switching Complex (Twinned) (pdb code 7k9y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Gsi-Iic Rt Template-Switching Complex (Twinned), PDB code: 7k9y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Gsi-Iic Rt Template-Switching Complex (Twinned)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gsi-Iic Rt Template-Switching Complex (Twinned) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:139.2 occ:1.00 OD1 A:ASP138 2.1 147.9 1.0 O1B A:DTP501 2.1 125.7 1.0 O1G A:DTP501 2.1 132.2 1.0 OD2 A:ASP223 2.1 126.6 1.0 O A:LEU139 2.1 142.7 1.0 O1A A:DTP501 2.1 121.9 1.0 CG A:ASP138 3.1 150.4 1.0 CG A:ASP223 3.3 123.4 1.0 C A:LEU139 3.3 139.8 1.0 PB A:DTP501 3.3 118.4 1.0 PG A:DTP501 3.4 124.4 1.0 PA A:DTP501 3.4 115.5 1.0 OD2 A:ASP138 3.5 152.3 1.0 N A:LEU139 3.7 138.7 1.0 O3A A:DTP501 3.7 114.5 1.0 O3B A:DTP501 3.8 117.3 1.0 O2G A:DTP501 3.9 122.3 1.0 OD1 A:ASP223 4.0 128.2 1.0 CA A:LEU139 4.0 139.8 1.0 C5' A:DTP501 4.1 105.4 1.0 O5' A:DTP501 4.3 108.9 1.0 CB A:PHE142 4.3 91.6 1.0 CB A:ASP223 4.4 118.9 1.0 N A:LYS141 4.4 114.6 1.0 N A:GLU140 4.4 136.1 1.0 CB A:ASP138 4.4 151.3 1.0 N A:PHE142 4.4 99.0 1.0 C A:ASP138 4.4 147.4 1.0 O2A A:DTP501 4.6 118.0 1.0 O3G A:DTP501 4.6 130.2 1.0 CB A:LEU139 4.6 139.8 1.0 O2B A:DTP501 4.6 118.4 1.0 CA A:GLU140 4.7 132.8 1.0 C A:GLU140 4.8 127.7 1.0 CA A:ASP138 4.8 150.9 1.0

Magnesium binding site 2 out of 2 in the Gsi-Iic Rt Template-Switching Complex (Twinned)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gsi-Iic Rt Template-Switching Complex (Twinned) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:131.1 occ:1.00 O1B D:DTP501 2.1 116.7 1.0 OD1 D:ASP138 2.1 142.1 1.0 O1G D:DTP501 2.1 119.2 1.0 OD2 D:ASP223 2.1 128.8 1.0 O D:LEU139 2.1 141.7 1.0 O2A D:DTP501 2.1 124.3 1.0 CG D:ASP138 3.1 146.2 1.0 PG D:DTP501 3.2 113.4 1.0 PB D:DTP501 3.2 110.0 1.0 CG D:ASP223 3.3 125.6 1.0 C D:LEU139 3.3 143.7 1.0 PA D:DTP501 3.4 121.9 1.0 OD2 D:ASP138 3.5 144.2 1.0 O3B D:DTP501 3.6 112.1 1.0 O2G D:DTP501 3.6 111.6 1.0 O3A D:DTP501 3.6 115.3 1.0 N D:LEU139 3.6 148.1 1.0 OD1 D:ASP223 4.0 125.0 1.0 CA D:LEU139 4.0 146.3 1.0 CB D:PHE142 4.2 115.2 1.0 CB D:ASP223 4.3 122.9 1.0 O1A D:DTP501 4.3 119.5 1.0 N D:PHE142 4.4 119.7 1.0 N D:GLU140 4.4 140.6 1.0 N D:LYS141 4.4 127.1 1.0 CB D:ASP138 4.4 147.3 1.0 C D:ASP138 4.4 147.4 1.0 O5' D:DTP501 4.5 118.5 1.0 C5' D:DTP501 4.5 121.0 1.0 O3G D:DTP501 4.5 112.7 1.0 O2B D:DTP501 4.6 112.5 1.0 CB D:LEU139 4.6 149.1 1.0 CA D:GLU140 4.7 137.1 1.0 C D:GLU140 4.8 133.3 1.0 CA D:ASP138 4.8 147.2 1.0 CA D:PHE142 4.9 119.5 1.0 NZ D:LYS258 5.0 166.6 1.0

A.M.Lentzsch, J.L.Stamos, J.Yao, R.Russell, A.M.Lambowitz. Structural Basis For Template Switching By A Group II Intron-Encoded Non-Ltr-Retroelement Reverse Transcriptase. J.Biol.Chem. 00971 2021.
ISSN: ESSN 1083-351X
PubMed: 34280434
DOI: 10.1016/J.JBC.2021.100971