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Magnesium in PDB 4nru: Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative

Protein crystallography data

The structure of Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative, PDB code: 4nru was solved by M.Milani, R.Croci, M.Pezzullo, D.Tarantino, E.Mastrangelo, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.09 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 109.220, 162.420, 122.960, 90.00, 97.04, 90.00
R / Rfree (%) 19.1 / 25.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative (pdb code 4nru). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative, PDB code: 4nru:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4nru

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Magnesium binding site 1 out of 6 in the Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:34.9
occ:1.00
 OD2 A:ASP240 2.3 29.6 1.0
O A:SER389 2.4 21.3 1.0
O A:GLU345 2.5 26.9 1.0
O A:HOH1252 2.5 20.6 1.0
OD1 A:ASP344 2.6 29.3 1.0
CG A:ASP240 3.0 26.5 1.0
OD1 A:ASP240 3.4 27.2 1.0
C A:SER389 3.6 26.7 1.0
C A:GLU345 3.6 23.2 1.0
N A:GLU345 3.7 30.9 1.0
CG A:ASP344 3.8 27.1 1.0
O A:HOH1550 3.9 42.2 1.0
CB A:ASP240 4.1 26.9 1.0
CA A:GLU345 4.2 28.1 1.0
O A:HOH1240 4.3 35.5 1.0
OG A:SER389 4.3 50.9 1.0
CA A:PHE390 4.4 27.8 1.0
N A:PHE390 4.4 25.0 1.0
OD2 A:ASP344 4.4 24.3 1.0
CG2 A:VAL346 4.5 26.2 1.0
CA A:SER389 4.6 32.7 1.0
C A:ASP344 4.6 31.1 1.0
CD1 A:PHE390 4.6 22.9 1.0
N A:SER389 4.7 26.7 1.0
N A:VAL346 4.7 27.7 1.0
CA A:ASP344 4.7 30.0 1.0
CB A:ASP344 4.9 26.8 1.0
CG2 A:ILE388 4.9 32.4 1.0
CB A:PHE390 4.9 24.3 1.0
CG A:GLU345 4.9 31.5 1.0
CB A:SER389 4.9 37.9 1.0

Magnesium binding site 2 out of 6 in 4nru

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Magnesium binding site 2 out of 6 in the Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:31.8
occ:1.00
 O B:SER389 2.3 34.5 1.0
OD1 B:ASP344 2.4 34.7 1.0
OD2 B:ASP240 2.4 30.4 1.0
O B:GLU345 2.5 24.2 1.0
O B:HOH1478 2.7 44.9 1.0
O B:HOH1473 2.8 24.2 1.0
CG B:ASP240 3.2 38.6 1.0
C B:SER389 3.4 30.7 1.0
OD1 B:ASP240 3.5 33.4 1.0
C B:GLU345 3.6 25.3 1.0
CG B:ASP344 3.6 30.2 1.0
N B:GLU345 3.6 26.9 1.0
O B:HOH1403 3.8 46.4 1.0
CA B:PHE390 3.9 28.7 1.0
N B:PHE390 4.1 28.0 1.0
O B:HOH1452 4.1 27.9 1.0
CD1 B:PHE390 4.2 27.2 1.0
CA B:GLU345 4.2 28.4 1.0
OD2 B:ASP344 4.2 32.7 1.0
CB B:ASP240 4.4 26.9 1.0
O B:HOH1392 4.4 41.6 1.0
CG2 B:VAL346 4.4 28.9 1.0
CB B:PHE390 4.5 24.7 1.0
CA B:SER389 4.5 33.8 1.0
C B:ASP344 4.5 22.6 1.0
N B:VAL346 4.6 28.1 1.0
CA B:ASP344 4.7 27.7 1.0
CB B:ASP344 4.7 29.8 1.0
N B:SER389 4.7 32.8 1.0
CB B:SER389 4.7 37.8 1.0
CG B:PHE390 4.8 23.8 1.0
CG2 B:ILE388 4.9 42.4 1.0
CG B:GLU345 5.0 36.0 1.0

Magnesium binding site 3 out of 6 in 4nru

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Magnesium binding site 3 out of 6 in the Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1102

b:37.5
occ:1.00
 OD2 C:ASP240 2.1 42.5 1.0
OD1 C:ASP344 2.4 37.1 1.0
O C:SER389 2.4 40.8 1.0
O C:GLU345 2.5 30.8 1.0
O C:HOH1504 2.5 29.6 1.0
CG C:ASP240 3.0 43.5 1.0
OD1 C:ASP240 3.4 37.0 1.0
C C:SER389 3.6 38.0 1.0
C C:GLU345 3.6 31.4 1.0
CG C:ASP344 3.6 34.9 1.0
N C:GLU345 3.7 30.6 1.0
O C:HOH1399 4.0 38.6 1.0
CB C:ASP240 4.1 38.1 1.0
CA C:GLU345 4.2 32.0 1.0
OD2 C:ASP344 4.3 34.8 1.0
CA C:PHE390 4.3 30.0 1.0
N C:PHE390 4.3 31.1 1.0
CD1 C:PHE390 4.5 28.6 1.0
CG2 C:VAL346 4.5 34.3 1.0
CA C:SER389 4.6 46.5 1.0
C C:ASP344 4.6 32.4 1.0
N C:VAL346 4.6 32.0 1.0
CB C:PHE390 4.7 32.2 1.0
CA C:ASP344 4.8 33.6 1.0
N C:SER389 4.8 37.0 1.0
CB C:ASP344 4.8 34.1 1.0
CB C:SER389 4.8 55.6 1.0

Magnesium binding site 4 out of 6 in 4nru

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Magnesium binding site 4 out of 6 in the Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1102

b:50.8
occ:1.00
 OD1 D:ASP344 2.3 31.1 1.0
O D:SER389 2.5 34.6 1.0
OD2 D:ASP240 2.6 37.6 1.0
O D:GLU345 2.7 41.4 1.0
O D:HOH1430 2.8 26.8 1.0
CG D:ASP240 3.4 40.7 1.0
C D:SER389 3.5 38.6 1.0
CG D:ASP344 3.5 34.0 1.0
C D:GLU345 3.8 31.2 1.0
OD1 D:ASP240 3.8 35.0 1.0
N D:GLU345 3.8 36.7 1.0
CA D:PHE390 4.1 35.8 1.0
O D:HOH1353 4.1 46.1 1.0
N D:PHE390 4.2 31.8 1.0
OD2 D:ASP344 4.2 39.0 1.0
O D:HOH1436 4.3 45.4 1.0
CD1 D:PHE390 4.3 33.7 1.0
CB D:ASP240 4.4 34.4 1.0
CA D:GLU345 4.4 35.8 1.0
CG2 D:VAL346 4.5 43.0 1.0
CA D:SER389 4.6 43.1 1.0
CA D:ASP344 4.6 32.7 1.0
CB D:ASP344 4.6 34.4 1.0
C D:ASP344 4.7 32.1 1.0
CB D:PHE390 4.7 31.6 1.0
CB D:SER389 4.7 49.8 1.0
N D:SER389 4.8 43.9 1.0
N D:VAL346 4.9 36.6 1.0

Magnesium binding site 5 out of 6 in 4nru

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Magnesium binding site 5 out of 6 in the Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1103

b:48.5
occ:1.00
 OD1 E:ASP344 2.4 32.5 1.0
OD2 E:ASP240 2.4 45.7 1.0
O E:GLU345 2.5 29.5 1.0
O E:SER389 2.5 39.2 1.0
CG E:ASP240 3.1 48.4 1.0
OD1 E:ASP240 3.4 45.0 1.0
N E:GLU345 3.5 32.4 1.0
C E:GLU345 3.6 32.6 1.0
C E:SER389 3.6 33.4 1.0
CG E:ASP344 3.6 34.6 1.0
CA E:GLU345 4.1 32.7 1.0
CA E:PHE390 4.2 38.5 1.0
N E:PHE390 4.3 36.8 1.0
OD2 E:ASP344 4.3 34.8 1.0
CD1 E:PHE390 4.3 34.1 1.0
CB E:ASP240 4.4 39.9 1.0
C E:ASP344 4.5 32.8 1.0
CG2 E:VAL346 4.5 36.5 1.0
CA E:ASP344 4.6 37.5 1.0
CA E:SER389 4.6 36.3 1.0
N E:VAL346 4.7 32.0 1.0
O E:HOH1447 4.7 40.0 1.0
CB E:ASP344 4.7 36.5 1.0
CB E:PHE390 4.7 32.5 1.0
N E:SER389 4.7 43.4 1.0
CG2 E:ILE388 4.8 45.1 1.0
O E:HOH1276 4.8 40.6 1.0
CB E:SER389 4.8 41.3 1.0
CG E:GLU345 4.9 34.4 1.0

Magnesium binding site 6 out of 6 in 4nru

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Magnesium binding site 6 out of 6 in the Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Murine Norovirus Rna-Dependent-Rna-Polymerase in Complex with Compound 6, A Suramin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1102

b:56.0
occ:1.00
 OD2 F:ASP240 2.1 55.3 1.0
O F:SER389 2.3 44.1 1.0
O F:GLU345 2.4 38.6 1.0
OD1 F:ASP344 2.7 43.9 1.0
O F:HOH1225 3.0 36.9 1.0
CG F:ASP240 3.0 63.9 1.0
C F:SER389 3.4 48.1 1.0
OD1 F:ASP240 3.6 62.3 1.0
O F:HOH1315 3.6 49.4 1.0
C F:GLU345 3.6 51.4 1.0
CG F:ASP344 3.8 47.1 1.0
N F:GLU345 3.9 44.6 1.0
CA F:PHE390 4.0 43.9 1.0
N F:PHE390 4.1 42.7 1.0
CG2 F:VAL346 4.1 38.2 1.0
CB F:ASP240 4.1 64.0 1.0
OD2 F:ASP344 4.2 44.1 1.0
CD1 F:PHE390 4.3 35.2 1.0
CA F:GLU345 4.4 48.7 1.0
CA F:SER389 4.5 51.5 1.0
CB F:PHE390 4.5 44.2 1.0
N F:VAL346 4.6 48.2 1.0
N F:SER389 4.7 54.0 1.0
CB F:SER389 4.8 60.1 1.0
C F:ASP344 4.9 44.1 1.0
CG F:PHE390 4.9 40.2 1.0
CA F:VAL346 5.0 41.4 1.0
CB F:ASP344 5.0 42.6 1.0

Reference:

R.Croci, M.Pezzullo, D.Tarantino, M.Milani, S.C.Tsay, R.Sureshbabu, Y.J.Tsai, E.Mastrangelo, J.Rohayem, M.Bolognesi, J.R.Hwu. Structural Bases of Norovirus Rna Dependent Rna Polymerase Inhibition By Novel Suramin-Related Compounds. Plos One V. 9 91765 2014.
ISSN: ESSN 1932-6203
PubMed: 24622391
DOI: 10.1371/JOURNAL.PONE.0091765
Page generated: Mon Aug 19 23:44:55 2024

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