Magnesium in PDB 7om2: Thosea Asigna Virus Rdrp Domain in Complex with Mg+2

Protein crystallography data

The structure of Thosea Asigna Virus Rdrp Domain in Complex with Mg+2, PDB code: 7om2 was solved by D.S.Ferrero, M.Falqui, N.Verdaguer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.51 / 2.07
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 134.844, 149.003, 100.368, 90, 90, 90
R / Rfree (%) 17.2 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thosea Asigna Virus Rdrp Domain in Complex with Mg+2 (pdb code 7om2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thosea Asigna Virus Rdrp Domain in Complex with Mg+2, PDB code: 7om2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7om2

Go back to Magnesium Binding Sites List in 7om2
Magnesium binding site 1 out of 2 in the Thosea Asigna Virus Rdrp Domain in Complex with Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thosea Asigna Virus Rdrp Domain in Complex with Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:27.9
occ:1.00
O A:HOH923 2.0 25.0 1.0
O A:HOH832 2.0 22.4 1.0
OD1 A:ASP352 2.1 28.9 1.0
O A:HOH824 2.1 25.5 1.0
O A:HOH1183 2.1 33.5 1.0
O A:HOH987 2.1 25.0 1.0
CG A:ASP352 3.2 25.6 1.0
O A:THR353 3.8 28.3 1.0
OD2 A:ASP352 3.8 25.6 1.0
O A:PRO368 3.8 26.1 1.0
OD1 A:ASP369 3.9 33.1 1.0
O A:LYS511 4.0 28.6 1.0
N A:THR353 4.1 24.9 1.0
O A:CYS367 4.2 28.6 1.0
O A:HOH1108 4.3 32.3 1.0
CB A:CYS367 4.3 28.1 1.0
O A:HOH952 4.4 50.1 1.0
CB A:ASP352 4.4 26.5 1.0
CA A:ASP352 4.4 20.9 1.0
C A:CYS367 4.4 26.7 1.0
O A:HOH1361 4.6 55.2 1.0
CA A:CYS367 4.7 24.3 1.0
O A:HOH949 4.7 25.7 1.0
C A:THR353 4.8 27.9 1.0
C A:ASP352 4.8 28.2 1.0
C A:PRO368 4.8 26.9 1.0
CD1 A:PHE512 4.9 25.2 1.0
CA A:PHE512 5.0 22.2 1.0

Magnesium binding site 2 out of 2 in 7om2

Go back to Magnesium Binding Sites List in 7om2
Magnesium binding site 2 out of 2 in the Thosea Asigna Virus Rdrp Domain in Complex with Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thosea Asigna Virus Rdrp Domain in Complex with Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:31.5
occ:1.00
OD1 B:ASP352 2.1 34.4 1.0
O B:HOH870 2.1 24.1 1.0
O B:HOH851 2.1 23.9 1.0
O B:HOH833 2.1 30.2 1.0
O B:HOH930 2.2 31.2 1.0
O B:HOH1149 2.2 35.1 1.0
CG B:ASP352 3.2 30.2 1.0
OD1 B:ASP369 3.7 36.5 1.0
OD2 B:ASP352 3.8 27.7 1.0
O B:THR353 3.8 34.2 1.0
O B:PRO368 3.9 24.4 1.0
O B:LYS511 4.0 33.3 1.0
N B:THR353 4.2 25.2 1.0
O B:CYS367 4.2 34.6 1.0
CB B:CYS367 4.3 26.7 1.0
O B:HOH932 4.3 30.8 1.0
CB B:ASP352 4.4 27.9 1.0
O B:HOH996 4.4 43.8 1.0
CA B:ASP352 4.4 21.4 1.0
C B:CYS367 4.4 30.7 1.0
CA B:CYS367 4.7 30.7 1.0
C B:PRO368 4.8 24.2 1.0
C B:ASP352 4.8 23.3 1.0
C B:THR353 4.8 36.5 1.0
O B:HOH955 4.9 31.7 1.0
CD1 B:PHE512 4.9 29.7 1.0
CG B:ASP369 5.0 35.6 1.0
C B:LYS511 5.0 26.2 1.0

Reference:

D.S.Ferrero, M.Falqui, N.Verdaguer. Snapshots of A Non-Canonical Rdrp in Action. Viruses V. 13 2021.
ISSN: ESSN 1999-4915
PubMed: 34203380
DOI: 10.3390/V13071260
Page generated: Sat Aug 21 16:47:58 2021

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