Atomistry » Magnesium » PDB 5d1f-5d9c » 5d98
Atomistry »
  Magnesium »
    PDB 5d1f-5d9c »
      5d98 »

Magnesium in PDB 5d98: Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212

Enzymatic activity of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212

All present enzymatic activity of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212:
2.7.7.48;

Protein crystallography data

The structure of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212, PDB code: 5d98 was solved by N.Hengrung, K.El Omari, I.Serna Martin, F.T.Vreede, S.Cusack, R.P.Rambo, C.Vonrhein, G.Bricogne, D.I.Stuart, J.M.Grimes, E.Fodor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 3.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 185.660, 185.660, 598.220, 90.00, 90.00, 90.00
R / Rfree (%) 28.6 / 32.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 (pdb code 5d98). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212, PDB code: 5d98:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5d98

Go back to Magnesium Binding Sites List in 5d98
Magnesium binding site 1 out of 4 in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg800

b:0.6
occ:1.00
MG A:MG801 2.9 0.2 1.0
OD2 A:ASP93 3.0 0.6 1.0
OE1 A:GLU104 3.0 0.5 1.0
OD1 A:ASP93 3.1 0.9 1.0
NE2 A:HIS41 3.2 0.5 1.0
CG A:ASP93 3.5 0.5 1.0
CE1 A:HIS41 3.5 0.6 1.0
O A:ILE105 3.5 0.0 1.0
CD A:GLU104 3.7 0.6 1.0
OE2 A:GLU65 3.9 0.3 1.0
CG A:GLU104 3.9 0.8 1.0
CD2 A:HIS41 4.1 0.2 1.0
CE A:LYS119 4.1 0.7 1.0
NZ A:LYS119 4.4 0.5 1.0
ND1 A:HIS41 4.5 0.7 1.0
C A:ILE105 4.6 0.7 1.0
OE2 A:GLU104 4.7 0.5 1.0
CG A:HIS41 4.8 0.6 1.0
N A:ILE105 4.8 0.2 1.0
CB A:ASP93 5.0 0.1 1.0

Magnesium binding site 2 out of 4 in 5d98

Go back to Magnesium Binding Sites List in 5d98
Magnesium binding site 2 out of 4 in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:0.2
occ:1.00
OE2 A:GLU65 1.9 0.3 1.0
OD1 A:ASP93 2.1 0.9 1.0
MG A:MG800 2.9 0.6 1.0
CD A:GLU65 3.1 0.8 1.0
CG A:ASP93 3.3 0.5 1.0
OE1 A:GLU65 3.8 0.1 1.0
OE1 A:GLU104 3.8 0.5 1.0
O A:LEU91 3.9 0.2 1.0
OD2 A:ASP93 4.0 0.6 1.0
CG A:GLU65 4.1 0.5 1.0
CE1 A:HIS41 4.4 0.6 1.0
N A:ASP93 4.4 0.5 1.0
CB A:GLU65 4.5 0.8 1.0
CB A:ASP93 4.5 0.1 1.0
CA A:ASP93 4.5 0.4 1.0
C A:CYS92 4.5 0.3 1.0
CG A:GLU104 4.7 0.8 1.0
CD A:GLU104 4.8 0.6 1.0
O A:CYS92 4.8 0.2 1.0
NE2 A:HIS41 4.9 0.5 1.0
C A:LEU91 5.0 0.3 1.0
CA A:CYS92 5.0 0.8 1.0

Magnesium binding site 3 out of 4 in 5d98

Go back to Magnesium Binding Sites List in 5d98
Magnesium binding site 3 out of 4 in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg800

b:0.5
occ:1.00
OD2 D:ASP93 2.5 0.8 1.0
OD1 D:ASP93 2.8 0.1 1.0
OE1 D:GLU104 2.8 0.8 1.0
CG D:ASP93 3.0 1.0 1.0
NE2 D:HIS41 3.1 0.4 1.0
O D:ILE105 3.3 0.9 1.0
CD D:GLU104 3.3 0.2 1.0
CG D:GLU104 3.4 0.2 1.0
CE1 D:HIS41 3.5 0.5 1.0
MG D:MG801 3.6 0.6 1.0
OE2 D:GLU65 4.1 0.6 1.0
CE D:LYS119 4.2 0.3 1.0
CD2 D:HIS41 4.2 0.6 1.0
N D:ILE105 4.3 0.8 1.0
C D:ILE105 4.3 0.0 1.0
OE2 D:GLU104 4.4 0.4 1.0
CB D:ASP93 4.5 0.7 1.0
NZ D:LYS119 4.6 0.5 1.0
ND1 D:HIS41 4.6 0.7 1.0
CB D:GLU104 4.7 0.7 1.0
CA D:ILE105 4.9 0.8 1.0
C D:GLU104 5.0 0.1 1.0
CG D:HIS41 5.0 0.0 1.0

Magnesium binding site 4 out of 4 in 5d98

Go back to Magnesium Binding Sites List in 5d98
Magnesium binding site 4 out of 4 in the Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Influenza C Virus Rna-Dependent Rna Polymerase - Space Group P43212 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg801

b:0.6
occ:1.00
OE2 D:GLU65 2.4 0.6 1.0
OD1 D:ASP93 2.9 0.1 1.0
O D:LEU91 3.3 0.6 1.0
CD D:GLU65 3.4 0.1 1.0
MG D:MG800 3.6 0.5 1.0
OE1 D:GLU104 3.8 0.8 1.0
OE1 D:GLU65 3.9 0.6 1.0
CG D:ASP93 4.1 1.0 1.0
C D:LEU91 4.5 0.8 1.0
C D:CYS92 4.6 0.5 1.0
CG D:GLU65 4.6 0.8 1.0
O D:CYS92 4.7 0.3 1.0
OD2 D:ASP93 4.7 0.8 1.0
N D:ASP93 4.8 0.2 1.0
CD D:GLU104 4.8 0.2 1.0
CA D:CYS92 4.9 0.2 1.0
CB D:GLU65 4.9 0.3 1.0
CG D:GLU104 5.0 0.2 1.0
CA D:ASP93 5.0 1.0 1.0

Reference:

N.Hengrung, K.El Omari, I.Serna Martin, F.T.Vreede, S.Cusack, R.P.Rambo, C.Vonrhein, G.Bricogne, D.I.Stuart, J.M.Grimes, E.Fodor. Crystal Structure of the Rna-Dependent Rna Polymerase From Influenza C Virus. Nature V. 527 114 2015.
ISSN: ESSN 1476-4687
PubMed: 26503046
DOI: 10.1038/NATURE15525
Page generated: Mon Dec 14 20:10:40 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy