Chlorine in PDB 8iib: Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)

Protein crystallography data

The structure of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546), PDB code: 8iib was solved by X.Fang, G.Lu, C.Hou, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.41 / 2.69
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.51, 150.51, 104.626, 90, 90, 120
R / Rfree (%) 21.3 / 25.4

Other elements in 8iib:

The structure of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) also contains other interesting chemical elements:

Cadmium (Cd) 4 atoms
Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) (pdb code 8iib). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546), PDB code: 8iib:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8iib

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Chlorine binding site 1 out of 7 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:30.4
occ:1.00
 CD A:CD601 2.6 29.9 1.0
O A:HOH720 3.3 26.6 1.0
OE1 A:GLN449 3.4 33.5 1.0
CL A:CL607 3.8 30.1 1.0
CB A:CYS469 3.8 17.2 1.0
CG A:LYS454 3.8 26.3 1.0
CE A:LYS454 3.9 35.0 1.0
CA A:CYS469 4.0 22.6 1.0
CD A:GLN449 4.3 26.6 1.0
SG A:CYS469 4.3 18.8 1.0
CG A:GLN449 4.3 19.1 1.0
CD A:LYS454 4.4 36.6 1.0
N A:CYS469 4.5 23.9 1.0
SG B:CYS480 4.6 29.0 1.0
O A:HOH774 4.7 33.2 1.0
CB A:GLN449 4.9 19.9 1.0
O A:LYS452 4.9 24.1 1.0
CB A:LYS454 5.0 20.2 1.0

Chlorine binding site 2 out of 7 in 8iib

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Chlorine binding site 2 out of 7 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:30.1
occ:1.00
 CD A:CD601 2.7 29.9 1.0
N A:MET470 3.3 21.5 1.0
N B:ARG481 3.3 33.0 1.0
CG A:MET470 3.7 23.9 1.0
CL A:CL606 3.8 30.4 1.0
CA A:CYS469 3.8 22.6 1.0
CA B:CYS480 4.0 25.0 1.0
O A:HOH720 4.0 26.6 1.0
CB A:MET470 4.0 21.8 1.0
O A:HOH774 4.1 33.2 1.0
C A:CYS469 4.1 22.8 1.0
CB B:ARG481 4.1 29.0 1.0
C B:CYS480 4.2 29.9 1.0
CE1 A:HIS504 4.2 23.8 1.0
CA A:MET470 4.2 25.4 1.0
CA B:ARG481 4.3 36.3 1.0
SG A:CYS469 4.3 18.8 1.0
CG B:ARG481 4.3 33.4 1.0
SG B:CYS480 4.4 29.0 1.0
CD B:ARG481 4.4 44.1 1.0
CB A:CYS469 4.5 17.2 1.0
CB B:CYS480 4.6 28.6 1.0
O B:TRP479 4.8 36.6 1.0
O A:LEU468 4.8 21.8 1.0
C B:ARG481 4.8 42.2 1.0
N A:CYS469 4.9 23.9 1.0
ND1 A:HIS504 5.0 19.7 1.0

Chlorine binding site 3 out of 7 in 8iib

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Chlorine binding site 3 out of 7 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl608

b:24.8
occ:1.00
 CD A:CD602 2.6 24.4 1.0
N B:MET470 3.1 17.9 1.0
N A:ARG481 3.1 26.3 1.0
CG A:ARG481 3.6 30.2 1.0
CA B:CYS469 3.7 20.8 1.0
CG B:MET470 3.7 32.8 1.0
O B:HOH745 3.8 18.9 1.0
CA A:CYS480 3.8 16.7 1.0
CB B:MET470 3.9 21.4 1.0
C B:CYS469 3.9 20.7 1.0
C A:CYS480 3.9 23.0 1.0
CL B:CL608 3.9 30.1 1.0
CB A:ARG481 4.0 20.9 1.0
CA B:MET470 4.1 23.8 1.0
CA A:ARG481 4.1 28.8 1.0
SG B:CYS469 4.2 24.9 1.0
SG A:CYS480 4.3 20.0 1.0
CB B:CYS469 4.3 26.4 1.0
CE1 B:HIS504 4.3 23.7 1.0
CD A:ARG481 4.5 33.4 1.0
CB A:CYS480 4.5 17.4 1.0
N A:GLY482 4.6 27.0 1.0
O A:TRP479 4.7 23.0 1.0
O B:HOH712 4.8 29.4 1.0
C A:ARG481 4.8 29.0 1.0
N B:CYS469 4.8 24.2 1.0
O B:LEU468 4.9 21.9 1.0
N A:CYS480 4.9 18.2 1.0

Chlorine binding site 4 out of 7 in 8iib

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Chlorine binding site 4 out of 7 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl609

b:75.9
occ:1.00
 CD A:CD603 3.1 76.8 1.0
N A:VAL299 4.1 57.7 1.0
O A:LEU297 4.1 59.5 1.0
CB A:VAL299 4.6 35.6 1.0
CA A:ASN298 4.7 52.7 1.0
CA A:VAL299 4.8 55.8 1.0
C A:ASN298 4.8 57.3 1.0
N A:CYS300 4.8 42.9 1.0

Chlorine binding site 5 out of 7 in 8iib

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Chlorine binding site 5 out of 7 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl608

b:30.1
occ:1.00
 CD A:CD602 2.5 24.4 1.0
NE2 B:GLN449 3.0 23.6 1.0
O B:HOH745 3.4 18.9 1.0
CG B:LYS454 3.7 32.1 1.0
CB B:CYS469 3.8 26.4 1.0
CL A:CL608 3.9 24.8 1.0
CD B:GLN449 4.0 23.0 1.0
CA B:CYS469 4.1 20.8 1.0
CG B:GLN449 4.1 22.4 1.0
CE B:LYS454 4.2 44.6 1.0
SG B:CYS469 4.2 24.9 1.0
CD1 A:LEU484 4.3 30.2 1.0
CD B:LYS454 4.4 38.6 1.0
SG A:CYS480 4.5 20.0 1.0
CB B:GLN449 4.5 22.8 1.0
N B:CYS469 4.7 24.2 1.0
O B:LYS452 4.9 20.4 1.0
CB B:LYS454 4.9 25.8 1.0

Chlorine binding site 6 out of 7 in 8iib

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Chlorine binding site 6 out of 7 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl609

b:59.5
occ:1.00
 CD B:CD601 2.7 77.5 1.0
O B:HOH752 3.1 47.8 1.0
O B:LEU297 3.4 74.7 1.0
N B:VAL299 3.9 62.1 1.0
CA B:ASN298 4.3 55.9 1.0
C B:LEU297 4.5 66.7 1.0
C B:ASN298 4.5 59.3 1.0
N B:CYS300 4.6 51.3 1.0
CB B:VAL299 4.7 46.1 1.0
CA B:VAL299 4.7 55.4 1.0
N B:ASN298 4.9 61.3 1.0

Chlorine binding site 7 out of 7 in 8iib

Go back to Chlorine Binding Sites List in 8iib
Chlorine binding site 7 out of 7 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl610

b:75.1
occ:1.00
 CD B:CD601 3.1 77.5 1.0
SG B:CYS300 3.2 53.7 1.0
CA B:CYS300 4.1 57.4 1.0
N B:CYS300 4.2 51.3 1.0
O B:VAL299 4.2 62.9 1.0
C B:VAL299 4.2 51.2 1.0
CB B:CYS300 4.2 72.0 1.0
CB B:VAL299 4.5 46.1 1.0
CA B:VAL299 5.0 55.4 1.0

Reference:

X.Fang, G.Lu, Y.Deng, S.Yang, C.Hou, P.Gong. Unusual Substructure Conformations Observed in Crystal Structures of A Dicistrovirus Rna-Dependent Rna Polymerase Suggest Contribution of the N-Terminal Extension in Proper Folding. Virol Sin 2023.
ISSN: ISSN 1995-820X
PubMed: 37156298
DOI: 10.1016/J.VIRS.2023.05.002
Page generated: Tue Jul 30 10:31:50 2024

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