Chlorine in PDB 6xd0: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434

Protein crystallography data

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434, PDB code: 6xd0 was solved by R.Arora, T.E.Benson, C.W.Liew, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.01
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 161.660, 176.240, 57.760, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.4

Other elements in 6xd0:

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434 (pdb code 6xd0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434, PDB code: 6xd0:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6xd0

Go back to Chlorine Binding Sites List in 6xd0
Chlorine binding site 1 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1008

b:69.8
occ:1.00
CL1 A:V0M1008 0.0 69.8 1.0
C19 A:V0M1008 1.7 68.0 1.0
C18 A:V0M1008 2.7 67.3 1.0
C14 A:V0M1008 2.8 67.0 1.0
N2 A:V0M1008 3.0 65.8 1.0
C13 A:V0M1008 3.2 65.1 1.0
C20 A:V0M1008 3.3 64.9 1.0
CG A:ARG481 3.6 52.3 1.0
CB A:ARG481 3.9 45.5 1.0
O A:ARG481 4.0 41.0 1.0
C17 A:V0M1008 4.0 66.9 1.0
C15 A:V0M1008 4.1 67.0 1.0
C12 A:V0M1008 4.2 64.6 1.0
CE1 A:PHE398 4.2 44.5 1.0
C21 A:V0M1008 4.2 64.7 1.0
C A:ARG481 4.4 40.9 1.0
CB A:PHE485 4.5 35.7 1.0
CA A:ARG481 4.5 42.1 1.0
C16 A:V0M1008 4.5 66.8 1.0
CB A:VAL603 4.6 70.7 1.0
CD A:ARG481 4.7 58.3 1.0
CG2 A:VAL603 4.7 71.3 1.0
C11 A:V0M1008 5.0 63.9 1.0
C23 A:V0M1008 5.0 64.6 1.0
C22 A:V0M1008 5.0 64.7 1.0
CD1 A:PHE398 5.0 44.0 1.0

Chlorine binding site 2 out of 2 in 6xd0

Go back to Chlorine Binding Sites List in 6xd0
Chlorine binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1008

b:67.2
occ:1.00
CL2 A:V0M1008 0.0 67.2 1.0
C15 A:V0M1008 1.7 67.0 1.0
C16 A:V0M1008 2.7 66.8 1.0
C14 A:V0M1008 2.8 67.0 1.0
N2 A:V0M1008 3.1 65.8 1.0
O1 A:V0M1008 3.4 63.0 1.0
ND2 A:ASN492 3.5 50.8 1.0
CB A:ASN492 3.6 41.5 1.0
CG1 A:VAL603 3.7 71.3 1.0
CG A:ASN492 3.8 49.0 1.0
OE2 A:GLU493 3.8 49.7 1.0
CD1 A:PHE485 3.9 38.1 1.0
C17 A:V0M1008 4.0 66.9 1.0
O A:HOH1320 4.0 51.4 1.0
C19 A:V0M1008 4.1 68.0 1.0
CE1 A:PHE485 4.2 39.0 1.0
C13 A:V0M1008 4.3 65.1 1.0
CA A:GLY489 4.4 34.8 1.0
C10 A:V0M1008 4.4 63.4 1.0
O A:GLY489 4.5 35.3 1.0
C18 A:V0M1008 4.5 67.3 1.0
CB A:VAL603 4.6 70.7 1.0
CE A:LYS401 4.7 53.1 1.0
OD1 A:ASN492 4.7 51.8 1.0
NZ A:LYS401 4.7 53.8 1.0
CD A:GLU493 4.8 48.0 1.0
C2 A:V0M1008 4.9 63.8 1.0
CA A:ASN492 5.0 37.9 1.0
CG A:GLU493 5.0 41.1 1.0
C A:GLY489 5.0 35.0 1.0
C20 A:V0M1008 5.0 64.9 1.0

Reference:

R.Arora, T.E.Benson, C.W.Liew, J.Lescar. Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-434 To Be Published.
Page generated: Sat Dec 12 14:35:27 2020

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