Atomistry » Chlorine » PDB 2yc5-2yj8 » 2yi8
Atomistry »
  Chlorine »
    PDB 2yc5-2yj8 »
      2yi8 »

Chlorine in PDB 2yi8: Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus

Enzymatic activity of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus

All present enzymatic activity of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus:
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, PDB code: 2yi8 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) 90.33 / 2.30
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 (%) 16.6 / 18.7

Other elements in 2yi8:

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

Potassium (K) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus (pdb code 2yi8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus, PDB code: 2yi8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 2yi8

Go back to Chlorine Binding Sites List in 2yi8
Chlorine binding site 1 out of 6 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:21.9
occ:1.00
 O A:HOH2029 3.0 11.1 1.0
O A:HOH2147 3.1 13.4 1.0
ND2 A:ASN320 3.3 4.3 1.0
O A:HOH2380 3.4 31.6 1.0
CG A:MET174 3.6 12.1 1.0
CB A:ASN320 3.7 5.7 1.0
CE A:MET174 3.9 11.4 1.0
CG A:ASN320 4.0 16.1 1.0
CG A:ARG170 4.0 18.2 1.0
CD2 A:LEU171 4.1 9.0 1.0
SD A:MET174 4.2 15.8 1.0
NE A:ARG170 4.5 29.4 1.0
N A:ASN320 4.6 10.2 1.0
CA A:ASN320 4.7 9.7 1.0
O A:ASN320 4.7 15.3 1.0
O A:HOH2379 4.7 9.6 1.0
CD1 A:LEU302 4.7 6.7 1.0
O A:HOH2377 4.8 9.3 1.0
CB A:MET174 4.8 9.6 1.0
CD A:ARG170 4.8 20.6 1.0

Chlorine binding site 2 out of 6 in 2yi8

Go back to Chlorine Binding Sites List in 2yi8
Chlorine binding site 2 out of 6 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1003

b:14.1
occ:1.00
 O B:HOH2168 3.0 15.3 1.0
O B:HOH2034 3.1 7.7 1.0
ND2 B:ASN320 3.3 3.0 1.0
O B:HOH2435 3.3 45.2 1.0
CG B:MET174 3.6 4.8 1.0
CB B:ASN320 3.7 3.5 1.0
CE B:MET174 3.9 5.1 1.0
CG B:ASN320 4.0 16.4 1.0
CG B:ARG170 4.0 9.9 1.0
CD2 B:LEU171 4.1 3.0 1.0
SD B:MET174 4.2 7.8 1.0
NE B:ARG170 4.4 27.8 1.0
N B:ASN320 4.6 6.4 1.0
CA B:ASN320 4.6 5.7 1.0
O B:ASN320 4.7 12.9 1.0
O B:HOH2432 4.7 6.9 1.0
CD1 B:LEU302 4.7 4.3 1.0
O B:HOH2434 4.7 6.8 1.0
CD B:ARG170 4.8 12.2 1.0
CB B:MET174 4.9 4.4 1.0

Chlorine binding site 3 out of 6 in 2yi8

Go back to Chlorine Binding Sites List in 2yi8
Chlorine binding site 3 out of 6 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1003

b:17.4
occ:1.00
 O C:HOH2151 2.9 15.2 1.0
O C:HOH2028 3.0 8.6 1.0
O C:HOH2415 3.2 53.3 1.0
ND2 C:ASN320 3.3 5.5 1.0
CG C:MET174 3.6 10.0 1.0
CB C:ASN320 3.7 3.0 1.0
CE C:MET174 3.9 9.9 1.0
CG C:ASN320 4.0 12.4 1.0
CG C:ARG170 4.0 11.6 1.0
CD2 C:LEU171 4.1 6.2 1.0
SD C:MET174 4.2 13.5 1.0
NE C:ARG170 4.5 32.7 1.0
N C:ASN320 4.6 6.0 1.0
CA C:ASN320 4.6 5.8 1.0
O C:ASN320 4.7 9.8 1.0
O C:HOH2411 4.7 15.3 1.0
CD1 C:LEU302 4.7 9.4 1.0
O C:HOH2413 4.8 10.3 1.0
CB C:MET174 4.8 8.2 1.0
CD C:ARG170 4.9 13.1 1.0
C C:ASN320 5.0 9.3 1.0

Chlorine binding site 4 out of 6 in 2yi8

Go back to Chlorine Binding Sites List in 2yi8
Chlorine binding site 4 out of 6 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1003

b:16.2
occ:1.00
 O D:HOH2170 2.9 15.2 1.0
O D:HOH2030 3.1 8.0 1.0
ND2 D:ASN320 3.3 3.0 1.0
O D:HOH2434 3.4 33.4 1.0
CG D:MET174 3.6 7.5 1.0
CB D:ASN320 3.7 4.0 1.0
CE D:MET174 3.9 7.0 1.0
CG D:ARG170 4.0 15.0 1.0
CG D:ASN320 4.0 12.0 1.0
CD2 D:LEU171 4.1 7.7 1.0
SD D:MET174 4.2 11.2 1.0
NE D:ARG170 4.4 33.3 1.0
N D:ASN320 4.6 5.8 1.0
CA D:ASN320 4.7 5.5 1.0
O D:ASN320 4.7 9.9 1.0
O D:HOH2429 4.7 7.9 1.0
CD1 D:LEU302 4.8 4.5 1.0
O D:HOH2432 4.8 8.8 1.0
CD D:ARG170 4.8 15.8 1.0
CB D:MET174 4.8 4.9 1.0

Chlorine binding site 5 out of 6 in 2yi8

Go back to Chlorine Binding Sites List in 2yi8
Chlorine binding site 5 out of 6 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1003

b:14.2
occ:1.00
 O E:HOH2187 3.0 11.5 1.0
O E:HOH2030 3.0 14.1 1.0
ND2 E:ASN320 3.3 3.4 1.0
CG E:MET174 3.6 6.5 1.0
CB E:ASN320 3.7 3.3 1.0
CE E:MET174 3.9 5.0 1.0
CG E:ASN320 4.0 10.1 1.0
CG E:ARG170 4.0 7.3 1.0
CD2 E:LEU171 4.1 4.3 1.0
SD E:MET174 4.2 9.0 1.0
NE E:ARG170 4.5 15.6 1.0
N E:ASN320 4.6 6.2 1.0
CA E:ASN320 4.6 6.2 1.0
O E:ASN320 4.7 10.0 1.0
CD1 E:LEU302 4.8 5.9 1.0
O E:HOH2471 4.8 4.1 1.0
O E:HOH2473 4.8 4.8 1.0
CB E:MET174 4.8 4.3 1.0
CD E:ARG170 4.8 14.7 1.0

Chlorine binding site 6 out of 6 in 2yi8

Go back to Chlorine Binding Sites List in 2yi8
Chlorine binding site 6 out of 6 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1005

b:14.1
occ:1.00
 NE2 E:GLN769 3.1 22.0 1.0
NH1 E:ARG727 3.1 8.4 1.0
O E:HOH2655 3.2 13.1 1.0
NE2 E:GLN731 3.4 25.6 1.0
CD E:ARG727 3.6 10.6 1.0
CG E:GLN769 3.6 18.4 1.0
CD E:GLN769 3.8 26.8 1.0
CB E:ALA765 4.2 8.6 1.0
CZ E:ARG727 4.2 18.4 1.0
O E:HOH2660 4.3 21.0 1.0
NE E:ARG727 4.3 10.6 1.0
CB E:ARG727 4.4 6.8 1.0
O E:ALA765 4.4 11.9 1.0
CG E:ARG727 4.5 7.8 1.0
CD E:GLN731 4.6 26.8 1.0
C E:ALA765 4.7 11.9 1.0
OE1 E:GLN769 4.9 23.8 1.0
CA E:ALA765 4.9 8.4 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: Sat Jul 20 15:03:38 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy