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Potassium in PDB 2yi9: Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium

Enzymatic activity of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium

All present enzymatic activity of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium:
2.7.7.48; 2.7.7.49;

Protein crystallography data

The structure of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium, PDB code: 2yi9 was solved by S.C.Graham, L.P.Sarin, M.W.Bahar, R.A.Myers, D.I.Stuart, D.H.Bamford, J.M.Grimes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.21 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.048, 183.874, 244.521, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.1

Other elements in 2yi9:

The structure of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Magnesium (Mg) 5 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium (pdb code 2yi9). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium, PDB code: 2yi9:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 2yi9

Go back to Potassium Binding Sites List in 2yi9
Potassium binding site 1 out of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1794

b:24.4
occ:1.00
 O A:GLY512 2.6 21.9 1.0
OD1 A:ASN184 2.6 19.1 1.0
O A:ASN182 2.7 24.7 1.0
O A:VAL177 2.7 22.6 1.0
OD1 A:ASN514 2.7 23.8 1.0
OD1 A:ASN409 2.7 20.3 1.0
C A:GLY512 3.6 23.6 1.0
CG A:ASN514 3.7 25.5 1.0
C A:VAL177 3.8 23.7 1.0
CG A:ASN409 3.8 25.1 1.0
CG A:ASN184 3.8 27.5 1.0
N A:ASN184 3.8 22.5 1.0
C A:ASN182 3.9 26.7 1.0
ND2 A:ASN182 3.9 18.0 1.0
C A:PRO183 4.0 25.5 1.0
N A:ASN514 4.0 20.3 1.0
CA A:ASN184 4.1 21.8 1.0
CG1 A:VAL177 4.2 19.3 1.0
CA A:ILE513 4.3 18.0 1.0
O A:HOH2141 4.3 21.3 1.0
O A:PRO183 4.3 23.4 1.0
N A:ILE513 4.3 20.2 1.0
CB A:ASN409 4.3 17.4 1.0
CA A:ASN409 4.4 19.1 1.0
CA A:ALA178 4.4 21.2 1.0
ND2 A:ASN514 4.5 18.8 1.0
CG A:ASN182 4.5 25.8 1.0
N A:ALA178 4.5 21.1 1.0
CB A:ASN182 4.5 22.7 1.0
C A:ILE513 4.6 23.1 1.0
CB A:ASN184 4.6 22.6 1.0
CA A:PRO183 4.6 22.2 1.0
O A:HOH2153 4.6 20.2 1.0
CB A:ASN514 4.6 14.1 1.0
O A:ALA178 4.6 24.0 1.0
CA A:GLY512 4.7 22.0 1.0
C A:ALA178 4.7 25.5 1.0
N A:PRO183 4.7 23.4 1.0
CA A:VAL177 4.7 18.9 1.0
CA A:ASN182 4.8 25.1 1.0
ND2 A:ASN184 4.8 15.7 1.0
ND2 A:ASN409 4.9 15.1 1.0
CA A:ASN514 4.9 19.1 1.0

Potassium binding site 2 out of 5 in 2yi9

Go back to Potassium Binding Sites List in 2yi9
Potassium binding site 2 out of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1794

b:23.3
occ:1.00
 O B:GLY512 2.6 17.9 1.0
OD1 B:ASN184 2.6 9.9 1.0
O B:ASN182 2.7 14.8 1.0
O B:VAL177 2.7 16.3 1.0
OD1 B:ASN409 2.7 12.2 1.0
OD1 B:ASN514 2.7 14.3 1.0
C B:GLY512 3.7 18.0 1.0
CG B:ASN514 3.7 24.9 1.0
C B:VAL177 3.8 15.8 1.0
CG B:ASN409 3.8 16.0 1.0
CG B:ASN184 3.8 17.1 1.0
N B:ASN184 3.8 15.4 1.0
C B:ASN182 3.9 17.9 1.0
ND2 B:ASN182 3.9 11.4 1.0
C B:PRO183 4.0 17.8 1.0
N B:ASN514 4.0 16.0 1.0
CA B:ASN184 4.1 15.4 1.0
CG1 B:VAL177 4.2 12.9 1.0
O B:HOH2170 4.2 11.4 1.0
CA B:ILE513 4.3 13.1 1.0
CB B:ASN409 4.3 12.9 1.0
O B:PRO183 4.4 17.7 1.0
N B:ILE513 4.4 13.8 1.0
CA B:ASN409 4.4 14.4 1.0
CA B:ALA178 4.4 13.3 1.0
ND2 B:ASN514 4.5 12.0 1.0
N B:ALA178 4.5 12.9 1.0
CG B:ASN182 4.5 22.9 1.0
CB B:ASN182 4.6 17.1 1.0
C B:ILE513 4.6 17.7 1.0
CB B:ASN184 4.6 13.2 1.0
CA B:PRO183 4.6 13.6 1.0
O B:ALA178 4.6 16.4 1.0
CB B:ASN514 4.6 12.1 1.0
O B:HOH2188 4.7 11.3 1.0
C B:ALA178 4.7 17.0 1.0
CA B:GLY512 4.7 15.2 1.0
N B:PRO183 4.7 14.7 1.0
CA B:VAL177 4.7 11.8 1.0
ND2 B:ASN184 4.8 10.3 1.0
CA B:ASN182 4.8 16.5 1.0
ND2 B:ASN409 4.9 11.6 1.0
CA B:ASN514 4.9 14.5 1.0

Potassium binding site 3 out of 5 in 2yi9

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Potassium binding site 3 out of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1794

b:26.2
occ:1.00
 O C:GLY512 2.6 21.3 1.0
OD1 C:ASN184 2.6 17.9 1.0
O C:ASN182 2.7 21.9 1.0
O C:VAL177 2.7 19.4 1.0
OD1 C:ASN514 2.7 22.1 1.0
OD1 C:ASN409 2.7 18.8 1.0
C C:GLY512 3.7 21.8 1.0
C C:VAL177 3.8 21.4 1.0
CG C:ASN514 3.8 30.0 1.0
CG C:ASN409 3.8 28.4 1.0
CG C:ASN184 3.8 21.9 1.0
N C:ASN184 3.9 22.0 1.0
C C:ASN182 3.9 24.1 1.0
ND2 C:ASN182 3.9 16.2 1.0
C C:PRO183 4.0 24.3 1.0
N C:ASN514 4.1 21.1 1.0
CA C:ASN184 4.1 21.0 1.0
CG1 C:VAL177 4.2 20.2 1.0
O C:HOH2155 4.2 20.9 1.0
CA C:ILE513 4.3 18.2 1.0
O C:PRO183 4.3 21.7 1.0
CB C:ASN409 4.3 17.6 1.0
N C:ILE513 4.3 19.5 1.0
CA C:ASN409 4.4 18.1 1.0
CA C:ALA178 4.4 17.4 1.0
ND2 C:ASN514 4.5 16.1 1.0
N C:ALA178 4.5 17.8 1.0
CG C:ASN182 4.5 32.3 1.0
CB C:ASN182 4.5 19.6 1.0
CB C:ASN184 4.6 14.8 1.0
C C:ILE513 4.6 24.0 1.0
CA C:PRO183 4.6 20.4 1.0
CB C:ASN514 4.6 17.9 1.0
O C:ALA178 4.6 20.3 1.0
O C:HOH2170 4.6 16.8 1.0
CA C:GLY512 4.7 18.0 1.0
C C:ALA178 4.7 21.5 1.0
N C:PRO183 4.7 21.4 1.0
CA C:VAL177 4.7 17.9 1.0
ND2 C:ASN184 4.8 16.2 1.0
CA C:ASN182 4.8 22.4 1.0
ND2 C:ASN409 4.9 15.1 1.0
CA C:ASN514 4.9 20.7 1.0

Potassium binding site 4 out of 5 in 2yi9

Go back to Potassium Binding Sites List in 2yi9
Potassium binding site 4 out of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1794

b:18.9
occ:1.00
 O D:GLY512 2.6 17.4 1.0
OD1 D:ASN184 2.6 13.3 1.0
O D:ASN182 2.7 15.9 1.0
O D:VAL177 2.7 17.2 1.0
OD1 D:ASN409 2.7 13.5 1.0
OD1 D:ASN514 2.7 12.7 1.0
C D:GLY512 3.6 16.6 1.0
CG D:ASN514 3.7 19.0 1.0
C D:VAL177 3.8 18.1 1.0
CG D:ASN409 3.8 17.9 1.0
CG D:ASN184 3.8 24.3 1.0
N D:ASN184 3.8 17.0 1.0
C D:ASN182 3.9 18.6 1.0
ND2 D:ASN182 3.9 13.5 1.0
C D:PRO183 4.0 20.5 1.0
N D:ASN514 4.0 13.9 1.0
CA D:ASN184 4.0 16.7 1.0
CG1 D:VAL177 4.2 16.9 1.0
CA D:ILE513 4.3 11.4 1.0
O D:HOH2179 4.3 15.0 1.0
O D:PRO183 4.3 21.2 1.0
CB D:ASN409 4.3 12.2 1.0
N D:ILE513 4.3 11.6 1.0
CA D:ASN409 4.4 11.6 1.0
CA D:ALA178 4.5 14.5 1.0
ND2 D:ASN514 4.5 13.5 1.0
CG D:ASN182 4.5 23.4 1.0
N D:ALA178 4.5 14.4 1.0
CB D:ASN184 4.6 13.6 1.0
C D:ILE513 4.6 17.2 1.0
CB D:ASN182 4.6 13.7 1.0
CA D:PRO183 4.6 15.4 1.0
O D:ALA178 4.6 15.5 1.0
O D:HOH2197 4.6 12.7 1.0
CB D:ASN514 4.6 12.0 1.0
CA D:GLY512 4.7 14.7 1.0
C D:ALA178 4.7 18.6 1.0
N D:PRO183 4.7 16.1 1.0
CA D:VAL177 4.8 15.3 1.0
ND2 D:ASN184 4.8 10.9 1.0
CA D:ASN182 4.8 17.8 1.0
ND2 D:ASN409 4.9 13.3 1.0
CA D:ASN514 4.9 13.8 1.0

Potassium binding site 5 out of 5 in 2yi9

Go back to Potassium Binding Sites List in 2yi9
Potassium binding site 5 out of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K1794

b:19.2
occ:1.00
 O E:GLY512 2.6 16.2 1.0
OD1 E:ASN184 2.6 11.4 1.0
O E:ASN182 2.7 16.7 1.0
O E:VAL177 2.7 15.6 1.0
OD1 E:ASN514 2.7 13.8 1.0
OD1 E:ASN409 2.7 13.0 1.0
C E:GLY512 3.7 16.3 1.0
CG E:ASN514 3.8 17.4 1.0
C E:VAL177 3.8 16.6 1.0
CG E:ASN409 3.8 16.2 1.0
CG E:ASN184 3.8 16.9 1.0
N E:ASN184 3.8 14.9 1.0
C E:ASN182 3.9 18.1 1.0
ND2 E:ASN182 3.9 10.4 1.0
C E:PRO183 4.0 19.6 1.0
N E:ASN514 4.0 13.1 1.0
CA E:ASN184 4.1 14.1 1.0
O E:HOH2182 4.2 10.2 1.0
CG1 E:VAL177 4.2 15.5 1.0
CA E:ILE513 4.3 10.9 1.0
CB E:ASN409 4.3 11.5 1.0
O E:PRO183 4.3 18.6 1.0
N E:ILE513 4.4 11.0 1.0
CA E:ASN409 4.4 14.1 1.0
CA E:ALA178 4.4 12.8 1.0
ND2 E:ASN514 4.5 14.2 1.0
N E:ALA178 4.5 13.3 1.0
CG E:ASN182 4.5 25.1 1.0
CB E:ASN182 4.6 15.2 1.0
C E:ILE513 4.6 14.8 1.0
CB E:ASN184 4.6 13.7 1.0
CA E:PRO183 4.6 13.7 1.0
O E:ALA178 4.6 15.5 1.0
CB E:ASN514 4.6 11.7 1.0
O E:HOH2200 4.6 10.1 1.0
CA E:GLY512 4.7 14.0 1.0
C E:ALA178 4.7 16.8 1.0
N E:PRO183 4.7 15.1 1.0
CA E:VAL177 4.8 13.9 1.0
ND2 E:ASN184 4.8 9.8 1.0
CA E:ASN182 4.8 15.9 1.0
ND2 E:ASN409 4.9 12.7 1.0
CA E:ASN514 4.9 12.6 1.0

Reference:

S.C.Graham, L.P.Sarin, M.W.Bahar, R.A.Myers, D.I.Stuart, D.H.Bamford, J.M.Grimes. The N-Terminus of the Rna Polymerase From Infectious Pancreatic Necrosis Virus Is the Determinant of Genome Attachment. Plos Pathog. V. 7 2085 2011.
ISSN: ISSN 1553-7366
PubMed: 21731487
DOI: 10.1371/JOURNAL.PPAT.1002085
Page generated: Mon Aug 12 07:43:42 2024

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