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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

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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

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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: Thu Oct 3 10:22:46 2024

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