Magnesium in PDB 7oma: Thosea Asigna Virus Rdrp Domain Elongation Complex

Protein crystallography data

The structure of Thosea Asigna Virus Rdrp Domain Elongation Complex, PDB code: 7oma 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) 67.78 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.794, 207.305, 115.98, 90, 91.1, 90
R / Rfree (%) 23.1 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thosea Asigna Virus Rdrp Domain Elongation Complex (pdb code 7oma). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Thosea Asigna Virus Rdrp Domain Elongation Complex, PDB code: 7oma:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7oma

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Magnesium binding site 1 out of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:47.3
occ:1.00
OD2 B:ASP369 1.9 59.0 1.0
CG B:ASP369 2.8 66.0 1.0
OD1 B:ASP369 3.1 79.6 1.0
OD2 B:ASP352 3.3 41.5 1.0
CG B:ASP352 3.3 47.2 1.0
OP1 G:U8 3.3 37.8 1.0
CB B:ASP352 3.5 47.4 1.0
OD1 B:ASP351 3.7 44.1 1.0
C5' G:U8 3.7 39.0 1.0
OD1 B:ASP352 3.8 51.0 1.0
CA B:ASP352 4.0 44.9 1.0
CB B:ASP369 4.2 57.7 1.0
O5' G:U8 4.3 37.6 1.0
OP1 G:U9 4.3 40.7 1.0
N B:ASP352 4.4 46.1 1.0
P G:U8 4.4 38.9 1.0
O3' G:U8 4.5 43.8 1.0
C4' G:U8 4.7 41.0 1.0
CG B:ASP351 4.7 46.1 1.0
P G:U9 4.9 44.1 1.0

Magnesium binding site 2 out of 5 in 7oma

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Magnesium binding site 2 out of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex


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 Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:48.2
occ:1.00
OD2 B:ASP351 2.0 47.0 1.0
O B:PHE370 2.1 45.9 1.0
O1 B:POP701 2.5 66.4 1.0
OP1 G:U9 2.8 40.7 1.0
O4 B:POP701 3.0 44.7 1.0
CG B:ASP351 3.1 46.1 1.0
C B:PHE370 3.2 45.3 1.0
N B:PHE370 3.4 49.0 1.0
CB B:ASP369 3.6 57.7 1.0
OD1 B:ASP351 3.7 44.1 1.0
OD2 B:ASP369 3.7 59.0 1.0
P1 B:POP701 3.8 62.7 1.0
CA B:PHE370 3.8 47.9 1.0
P2 B:POP701 3.9 55.9 1.0
O6 B:POP701 4.0 70.3 1.0
C B:ASP369 4.1 47.0 1.0
CG B:ASP369 4.1 66.0 1.0
O2 B:POP701 4.2 65.2 1.0
CE B:LYS488 4.2 70.5 1.0
N B:LYS371 4.2 44.6 1.0
O B:POP701 4.3 59.0 1.0
CB B:ASP351 4.3 42.1 1.0
P G:U9 4.3 44.1 1.0
CA B:ASP369 4.3 51.5 1.0
CA B:LYS371 4.6 48.9 1.0
CB B:PHE370 4.7 48.6 1.0
O5' G:U9 4.8 51.8 1.0
O3 B:POP701 5.0 64.8 1.0
N B:GLN372 5.0 44.2 1.0

Magnesium binding site 3 out of 5 in 7oma

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Magnesium binding site 3 out of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thosea Asigna Virus Rdrp Domain Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:45.8
occ:1.00
OD2 A:ASP351 1.9 40.1 1.0
O4 A:POP701 2.1 69.8 1.0
OP1 E:U9 2.2 35.0 1.0
OD2 A:ASP369 2.3 53.3 1.0
O A:PHE370 2.5 54.9 1.0
O3 A:POP701 2.7 45.2 1.0
CG A:ASP351 3.0 41.1 1.0
CG A:ASP369 3.0 56.4 1.0
OD1 A:ASP369 3.1 63.9 1.0
O2 A:POP701 3.4 46.4 1.0
P2 A:POP701 3.4 69.2 1.0
P1 A:POP701 3.4 44.6 1.0
OD1 A:ASP351 3.4 40.6 1.0
P E:U9 3.6 35.8 1.0
C A:PHE370 3.7 50.5 1.0
O A:POP701 3.7 55.3 1.0
O6 A:POP701 4.0 73.8 1.0
O5' E:U9 4.0 33.7 1.0
N A:PHE370 4.0 50.6 1.0
CB A:ASP351 4.2 40.8 1.0
CB A:ASP369 4.4 51.0 1.0
CA A:PHE370 4.4 48.4 1.0
O5 A:POP701 4.5 76.3 1.0
OP2 E:U9 4.5 36.7 1.0
O3' E:U8 4.6 30.4 1.0
C5' E:U9 4.6 34.5 1.0
N A:LYS371 4.7 49.3 1.0
CE A:LYS488 4.8 65.1 1.0
NZ A:LYS488 4.8 70.1 1.0
O1 A:POP701 4.8 62.0 1.0
CA A:LYS371 4.9 50.1 1.0
C A:ASP369 4.9 44.0 1.0

Magnesium binding site 4 out of 5 in 7oma

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Magnesium binding site 4 out of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thosea Asigna Virus Rdrp Domain Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:52.9
occ:1.00
N D:GLN372 3.1 56.7 1.0
OP1 L:U9 3.3 73.3 1.0
CA D:GLN372 3.4 60.7 1.0
O5' L:U9 3.7 75.7 1.0
O D:PHE370 3.7 65.3 1.0
NH1 D:ARG280 3.7 98.0 1.0
N D:MET373 3.7 56.7 1.0
OD2 D:ASP351 3.9 44.4 1.0
P L:U9 4.0 62.2 1.0
C D:GLN372 4.1 60.5 1.0
C D:LYS371 4.1 60.4 1.0
C5' L:U9 4.3 77.9 1.0
O3' L:U9 4.3 78.4 1.0
NH2 D:ARG280 4.4 93.0 1.0
CA D:LYS371 4.5 54.5 1.0
CZ D:ARG280 4.5 90.6 1.0
OE1 D:GLN372 4.6 74.1 1.0
C D:PHE370 4.7 53.1 1.0
CB D:GLN372 4.7 64.9 1.0
C3' L:U9 4.7 76.0 1.0
OP2 L:U9 4.8 56.7 1.0
NH2 D:ARG164 4.9 74.8 1.0
CD D:GLN372 4.9 76.3 1.0
CA D:MET373 5.0 54.2 1.0

Magnesium binding site 5 out of 5 in 7oma

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Magnesium binding site 5 out of 5 in the Thosea Asigna Virus Rdrp Domain Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thosea Asigna Virus Rdrp Domain Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg101

b:89.4
occ:1.00
OP1 I:U9 1.5 90.0 1.0
OD2 C:ASP351 1.8 65.3 1.0
O3 C:POP701 2.0 112.7 1.0
O6 C:POP701 2.0 64.1 1.0
O C:POP701 2.4 100.5 1.0
P1 C:POP701 2.5 129.2 1.0
CG C:ASP351 2.7 65.7 1.0
P2 C:POP701 2.7 67.7 1.0
P I:U9 2.8 88.2 1.0
OD1 C:ASP351 2.9 65.9 1.0
O1 C:POP701 3.0 136.0 1.0
O5' I:U9 3.3 90.1 1.0
O C:PHE370 3.4 62.5 1.0
O4 C:POP701 3.6 62.4 1.0
O3' I:U8 3.9 84.1 1.0
OP2 I:U9 3.9 86.6 1.0
OD1 C:ASP369 3.9 84.8 1.0
C5' I:U9 3.9 89.3 1.0
O2 C:POP701 3.9 132.0 1.0
O5 C:POP701 4.0 68.5 1.0
CB C:ASP351 4.0 61.6 1.0
CG C:ASP369 4.2 84.6 1.0
OD2 C:ASP369 4.5 90.4 1.0
C C:PHE370 4.6 60.2 1.0
N C:PHE370 4.7 64.2 1.0
CB C:ASP369 4.8 76.5 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 16:48:02 2021

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