Atomistry » Magnesium » PDB 4nm0-4nxn » 4nru
Atomistry »
  Magnesium »
    PDB 4nm0-4nxn »
      4nru »

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

Go back to Magnesium Binding Sites List in 4nru
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

Go back to Magnesium Binding Sites List in 4nru
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

Go back to Magnesium Binding Sites List in 4nru
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

Go back to Magnesium Binding Sites List in 4nru
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

Go back to Magnesium Binding Sites List in 4nru
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

Go back to Magnesium Binding Sites List in 4nru
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy