Magnesium in PDB 7vb4: A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase

Enzymatic activity of A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase

All present enzymatic activity of A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase:
2.7.7.48;

Protein crystallography data

The structure of A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase, PDB code: 7vb4 was solved by Y.B.Tan, D.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 1.86
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 67, 68.29, 71.07, 115.97, 106.71, 95.9
R / Rfree (%) 18.7 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase (pdb code 7vb4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase, PDB code: 7vb4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7vb4

Go back to Magnesium Binding Sites List in 7vb4
Magnesium binding site 1 out of 4 in the A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:27.4
occ:1.00
 O A:HOH1031 2.0 20.3 1.0
O A:HOH818 2.0 17.9 0.8
O A:HOH805 2.1 23.4 1.0
OD1 A:ASP466 2.2 35.1 1.0
O A:HOH889 2.2 19.7 0.8
O A:HOH1107 2.2 20.8 0.8
CG A:ASP466 3.3 28.6 1.0
OD2 A:ASP466 3.9 28.5 1.0
OE1 A:GLU368 3.9 23.9 1.0
O A:ASN467 4.0 18.4 1.0
O A:TYR503 4.1 16.1 1.0
CB A:GLU368 4.2 24.4 1.0
O A:HOH958 4.3 22.8 1.0
O A:HOH1182 4.4 35.8 1.0
N A:ASN467 4.4 15.0 1.0
CD A:GLU368 4.4 34.7 1.0
CB A:ASP466 4.5 20.9 1.0
CG A:GLU368 4.6 26.0 1.0
CA A:ASP466 4.6 20.6 1.0
O A:THR369 4.6 27.3 1.0
O A:HOH1042 4.6 35.8 0.7
C A:TYR503 5.0 17.9 1.0

Magnesium binding site 2 out of 4 in 7vb4

Go back to Magnesium Binding Sites List in 7vb4
Magnesium binding site 2 out of 4 in the A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:18.5
occ:1.00
 O A:HOH967 2.0 19.8 1.0
O A:HOH998 2.0 18.9 1.0
OD1 A:ASP392 2.1 17.0 1.0
O A:HOH874 2.1 22.7 1.0
O A:HOH1199 2.2 19.8 1.0
O A:HOH935 2.2 17.5 1.0
CG A:ASP392 3.1 19.3 1.0
OD2 A:ASP392 3.5 17.7 1.0
O A:MET388 4.1 13.7 1.0
O A:HOH870 4.3 22.3 1.0
OE1 A:GLU391 4.3 29.1 1.0
O A:HOH1175 4.3 22.5 1.0
CB A:ASP392 4.4 12.6 1.0
NH2 A:ARG228 4.6 20.7 1.0
CA A:ASP392 4.7 16.6 1.0
N A:ASP392 4.7 16.7 1.0
CD A:GLU391 4.8 27.1 1.0
CG A:GLU391 4.9 21.7 1.0

Magnesium binding site 3 out of 4 in 7vb4

Go back to Magnesium Binding Sites List in 7vb4
Magnesium binding site 3 out of 4 in the A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:26.7
occ:1.00
 O B:HOH1060 2.1 19.4 1.0
O B:HOH1064 2.1 25.7 1.0
O B:HOH814 2.1 22.6 1.0
O B:HOH909 2.1 21.3 1.0
O B:HOH841 2.1 24.7 1.0
OD1 B:ASP466 2.3 22.3 1.0
CG B:ASP466 3.5 23.1 1.0
OE1 B:GLU368 4.0 27.8 1.0
O B:ASN467 4.1 14.7 1.0
O B:HOH903 4.1 20.5 1.0
OD2 B:ASP466 4.1 15.7 1.0
CB B:GLU368 4.3 17.0 1.0
O B:TYR503 4.3 14.6 1.0
O B:HOH1130 4.3 34.4 1.0
O B:HOH1132 4.4 34.7 1.0
N B:ASN467 4.4 9.7 1.0
O B:THR369 4.4 20.9 1.0
CA B:ASP466 4.6 12.0 1.0
CB B:ASP466 4.6 12.5 1.0
CD B:GLU368 4.7 29.7 1.0
CG B:GLU368 4.9 21.1 1.0
CA B:ASP370 4.9 20.9 1.0

Magnesium binding site 4 out of 4 in 7vb4

Go back to Magnesium Binding Sites List in 7vb4
Magnesium binding site 4 out of 4 in the A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A Crystal Structure of Alphavirus Nonstructural Protein 4 (NSP4) Reveals An Intrinsically Dynamic Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:19.9
occ:1.00
 O B:HOH1194 2.0 20.3 1.0
OD1 B:ASP392 2.1 13.8 1.0
O B:HOH973 2.1 18.5 1.0
O B:HOH1030 2.1 16.3 1.0
O B:HOH854 2.1 21.8 1.0
O B:HOH823 2.2 16.4 1.0
CG B:ASP392 3.0 16.3 1.0
OD2 B:ASP392 3.4 13.2 1.0
O B:MET388 4.1 10.0 1.0
OE1 B:GLU391 4.1 30.8 1.0
O B:HOH978 4.4 14.5 1.0
CB B:ASP392 4.4 11.2 1.0
O B:HOH1164 4.5 25.6 1.0
NH2 B:ARG228 4.6 17.8 1.0
O B:HOH1173 4.6 38.3 1.0
CD B:GLU391 4.6 32.5 1.0
CA B:ASP392 4.7 12.8 1.0
O B:HOH1135 4.7 33.0 1.0
N B:ASP392 4.7 10.7 1.0
CB B:MET388 4.8 10.8 1.0
CG B:GLU391 4.9 20.5 1.0
C B:MET388 5.0 15.4 1.0

Reference:

Y.B.Tan, L.S.Lello, X.Liu, Y.S.Law, C.Kang, J.Lescar, J.Zheng, A.Merits, D.Luo. Crystal Structures of Alphavirus Nonstructural Protein 4 (NSP4) Reveal An Intrinsically Dynamic Rna-Dependent Rna Polymerase Fold. Nucleic Acids Res. V. 50 1000 2022.
ISSN: ESSN 1362-4962
PubMed: 35037043
DOI: 10.1093/NAR/GKAB1302
Page generated: Fri Apr 7 00:23:13 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy