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

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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp

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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp:
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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp, PDB code: 4wtk 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) 50.00 / 2.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 140.230, 140.230, 92.540, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 22.4

Other elements in 4wtk:

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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp 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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp (pdb code 4wtk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp, PDB code: 4wtk:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4wtk

Go back to Manganese Binding Sites List in 4wtk
Manganese binding site 1 out of 3 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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp


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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:47.5
occ:1.00
OD1 A:ASP319 2.0 46.2 1.0
OD2 A:ASP220 2.0 48.2 1.0
O1A A:CDP605 2.1 49.4 1.0
OD1 A:ASP318 2.2 55.6 1.0
O3' P:G2 2.2 71.8 1.0
O A:HOH766 2.3 47.3 1.0
CG A:ASP319 3.0 50.0 1.0
CG A:ASP220 3.1 41.2 1.0
PA A:CDP605 3.1 45.6 1.0
CG A:ASP318 3.1 52.4 1.0
OD1 A:ASP220 3.4 45.3 1.0
O2A A:CDP605 3.4 49.9 1.0
OD2 A:ASP318 3.4 55.3 1.0
MN A:MN602 3.4 45.7 1.0
OD2 A:ASP319 3.5 56.5 1.0
C3' P:G2 3.6 85.1 1.0
O5' A:CDP605 3.9 48.7 1.0
C5' A:CDP605 4.1 49.3 1.0
C4' P:G2 4.2 87.5 1.0
CB A:ASP319 4.3 46.9 1.0
C5' P:G2 4.3 90.8 1.0
CB A:ASP220 4.4 38.4 1.0
C A:ASP318 4.4 47.5 1.0
N A:ASP319 4.5 47.2 1.0
CB A:ASP318 4.5 50.7 1.0
O A:HOH799 4.5 54.3 1.0
O3A A:CDP605 4.5 47.1 1.0
O A:ASP318 4.6 52.1 1.0
CA A:ASP319 4.7 47.8 1.0
O5' P:G2 4.7 92.4 1.0
C2' P:G2 4.7 86.8 1.0
O1B A:CDP605 4.7 35.2 1.0
CA A:ASP318 4.9 49.3 1.0
O2' P:G2 4.9 80.1 1.0

Manganese binding site 2 out of 3 in 4wtk

Go back to Manganese Binding Sites List in 4wtk
Manganese binding site 2 out of 3 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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp


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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:45.7
occ:1.00
OD1 A:ASP220 2.1 45.3 1.0
OD2 A:ASP318 2.1 55.3 1.0
O A:HOH799 2.1 54.3 1.0
O1A A:CDP605 2.1 49.4 1.0
O1B A:CDP605 2.2 35.2 1.0
O A:THR221 2.2 43.7 1.0
CG A:ASP220 3.0 41.2 1.0
CG A:ASP318 3.1 52.4 1.0
PA A:CDP605 3.3 45.6 1.0
PB A:CDP605 3.3 47.1 1.0
OD2 A:ASP220 3.4 48.2 1.0
C A:THR221 3.4 47.1 1.0
MN A:MN601 3.4 47.5 1.0
OD1 A:ASP318 3.5 55.6 1.0
O3A A:CDP605 3.5 47.1 1.0
N A:THR221 3.7 46.1 1.0
C5' A:CDP605 3.9 49.3 1.0
O3B A:CDP605 4.0 48.1 1.0
O5' A:CDP605 4.1 48.7 1.0
CA A:THR221 4.1 45.7 1.0
N A:HIS223 4.3 52.7 1.0
CB A:ASP220 4.3 38.4 1.0
CB A:ASP318 4.4 50.7 1.0
N A:ARG222 4.4 48.1 1.0
N A:PHE224 4.4 44.4 1.0
C A:ASP220 4.5 42.9 1.0
CB A:PHE224 4.5 41.9 1.0
O2A A:CDP605 4.6 49.9 1.0
CA A:ARG222 4.6 51.8 1.0
O2B A:CDP605 4.6 47.4 1.0
CB A:THR221 4.7 46.8 1.0
C A:ARG222 4.7 54.0 1.0
CA A:ASP220 4.8 42.0 1.0
O3' P:G2 4.9 71.8 1.0

Manganese binding site 3 out of 3 in 4wtk

Go back to Manganese Binding Sites List in 4wtk
Manganese binding site 3 out of 3 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'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations in Complex with Rna Template 5'-Agcc, Rna Primer 5'-Pgg, MN2+, and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:81.1
occ:1.00
OE2 A:GLU237 2.0 63.5 1.0
ND1 A:HIS254 2.1 50.5 1.0
O1 A:EDO608 2.9 63.7 1.0
CD A:GLU237 2.9 64.3 1.0
CG A:HIS254 3.0 55.4 1.0
CE1 A:HIS254 3.0 52.3 1.0
OE1 A:GLU237 3.3 57.3 1.0
CB A:HIS254 3.3 55.6 1.0
O2 A:EDO608 3.6 70.5 1.0
CD2 A:HIS254 4.0 53.6 1.0
NE2 A:HIS254 4.0 55.0 1.0
CA A:HIS254 4.0 52.5 1.0
NE2 A:GLN241 4.1 44.6 1.0
C1 A:EDO608 4.2 73.2 1.0
CG A:GLU237 4.3 59.3 1.0
C2 A:EDO608 4.5 73.8 1.0
CG A:GLN241 5.0 44.6 1.0
CD A:GLN241 5.0 46.1 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: Tue Dec 15 04:33:06 2020

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