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Manganese in PDB 4wtl: Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp

Enzymatic activity of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp

All present enzymatic activity of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp, PDB code: 4wtl was solved by T.E.Edwards, T.C.Appleby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 2.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 140.410, 140.410, 92.080, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 23.5

Other elements in 4wtl:

The structure of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp (pdb code 4wtl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp, PDB code: 4wtl:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4wtl

Go back to Manganese Binding Sites List in 4wtl
Manganese binding site 1 out of 2 in the Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:22.6
occ:1.00
OD1 A:ASP319 2.0 28.1 1.0
OD2 A:ASP220 2.0 26.7 1.0
OD2 A:ASP318 2.1 22.8 1.0
O1A A:UDP604 2.2 19.2 1.0
O3' P:G2 2.2 27.3 1.0
O A:HOH852 2.2 27.7 1.0
CG A:ASP220 3.0 25.1 1.0
CG A:ASP319 3.1 25.4 1.0
CG A:ASP318 3.1 23.0 1.0
PA A:UDP604 3.3 21.1 1.0
OD1 A:ASP220 3.3 23.6 1.0
OD1 A:ASP318 3.4 20.2 1.0
C3' P:G2 3.5 30.2 1.0
MN A:MN602 3.6 19.8 1.0
OD2 A:ASP319 3.7 29.5 1.0
O2A A:UDP604 3.7 20.3 1.0
O5' A:UDP604 4.0 23.6 1.0
C5' A:UDP604 4.1 21.4 1.0
CB A:ASP319 4.2 22.7 1.0
N A:ASP319 4.2 21.7 1.0
C4' P:G2 4.2 32.3 1.0
C A:ASP318 4.2 22.3 1.0
C5' P:G2 4.3 31.0 1.0
CB A:ASP220 4.4 23.5 1.0
CB A:ASP318 4.4 21.8 1.0
O A:ASP318 4.5 22.5 1.0
CA A:ASP319 4.5 21.5 1.0
O A:HOH861 4.6 47.9 1.0
O5' P:G2 4.6 30.9 1.0
C2' P:G2 4.7 28.9 1.0
O2' P:G2 4.7 27.5 1.0
CA A:ASP318 4.7 22.1 1.0
O A:HOH1055 4.7 36.0 1.0
OP1 P:G2 4.7 33.8 1.0
O3A A:UDP604 4.8 22.8 1.0
O A:HOH862 4.8 22.7 1.0
N A:ASP318 4.8 20.4 1.0
O1B A:UDP604 4.9 19.9 1.0

Manganese binding site 2 out of 2 in 4wtl

Go back to Manganese Binding Sites List in 4wtl
Manganese binding site 2 out of 2 in the Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Uacc, Rna Primer 5'-Pgg, MN2+, and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:19.8
occ:1.00
OD1 A:ASP220 2.1 23.6 1.0
OD1 A:ASP318 2.1 20.2 1.0
O1B A:UDP604 2.1 19.9 1.0
O A:THR221 2.2 22.3 1.0
O A:HOH862 2.2 22.7 1.0
O1A A:UDP604 2.2 19.2 1.0
CG A:ASP220 3.1 25.1 1.0
CG A:ASP318 3.2 23.0 1.0
PB A:UDP604 3.3 23.4 1.0
PA A:UDP604 3.3 21.1 1.0
C A:THR221 3.3 21.0 1.0
O3A A:UDP604 3.5 22.8 1.0
MN A:MN601 3.6 22.6 1.0
OD2 A:ASP318 3.6 22.8 1.0
OD2 A:ASP220 3.6 26.7 1.0
N A:THR221 3.8 22.4 1.0
O2B A:UDP604 3.9 22.0 1.0
O A:HOH903 4.0 30.6 1.0
C5' A:UDP604 4.1 21.4 1.0
CA A:THR221 4.1 21.1 1.0
O5' A:UDP604 4.2 23.6 1.0
O A:HOH1055 4.2 36.0 1.0
N A:HIS223 4.3 21.9 1.0
CB A:ASP220 4.4 23.5 1.0
N A:ARG222 4.4 20.8 1.0
C A:ASP220 4.4 22.8 1.0
N A:PHE224 4.4 20.5 1.0
CB A:ASP318 4.5 21.8 1.0
CB A:PHE224 4.5 21.1 1.0
CA A:ARG222 4.6 23.1 1.0
O2A A:UDP604 4.6 20.3 1.0
O3B A:UDP604 4.6 22.8 1.0
CB A:THR221 4.6 22.0 1.0
O A:HOH852 4.6 27.7 1.0
C A:ARG222 4.7 23.6 1.0
CA A:ASP220 4.8 21.6 1.0

Reference:

T.C.Appleby, J.Perry, E.Murakami, O.Barauskas, J.Feng, A.Cho, D.Fox Iii, D.R.Wetmore, M.E.Mcgrath, A.S.Ray, M.J.Sofia, S.Swaminathan, T.E.Edwards. Structural Basis For Rna Replication By the Hepatitis C Virus Polymerase To Be Published.
Page generated: Sat Oct 5 22:53:23 2024

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