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

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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp

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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp:
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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp, PDB code: 4wti 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 / 2.80
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 140.150, 140.150, 92.760, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 23.4

Other elements in 4wti:

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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp 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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp (pdb code 4wti). 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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp, PDB code: 4wti:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4wti

Go back to Manganese Binding Sites List in 4wti
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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp


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

b:65.1
occ:1.00
 OD1 A:ASP319 2.1 57.3 1.0
OD1 A:ASP318 2.2 66.7 1.0
O1A A:GDP605 2.2 62.8 1.0
O3' P:C2 2.3 94.0 1.0
O A:HOH749 2.4 58.2 1.0
OD1 A:ASP220 2.5 58.5 1.0
CG A:ASP319 3.1 59.6 1.0
PA A:GDP605 3.2 56.9 1.0
CG A:ASP318 3.3 63.7 1.0
C3' P:C2 3.4 89.4 1.0
MN A:MN602 3.5 58.5 1.0
O2A A:GDP605 3.6 62.8 1.0
OD2 A:ASP319 3.6 68.7 1.0
CG A:ASP220 3.7 57.3 1.0
O5' A:GDP605 3.7 61.4 1.0
OD2 A:ASP318 3.8 60.0 1.0
C5' A:GDP605 4.2 60.1 1.0
N A:ASP319 4.2 58.9 1.0
CB A:ASP319 4.3 57.7 1.0
C4' P:C2 4.3 87.4 1.0
C A:ASP318 4.4 59.2 1.0
OD2 A:ASP220 4.5 59.1 1.0
C5' P:C2 4.5 86.6 1.0
O5' P:C2 4.5 90.6 1.0
CA A:ASP319 4.6 57.8 1.0
CB A:ASP318 4.6 61.0 1.0
C2' P:C2 4.6 90.4 1.0
CB A:ASP220 4.6 52.5 1.0
O A:HOH750 4.7 58.5 1.0
O3A A:GDP605 4.7 58.5 1.0
O A:ASP318 4.7 64.0 1.0
CA A:ASP318 4.9 58.5 1.0
O1B A:GDP605 4.9 47.5 1.0
O2' P:C2 4.9 85.6 1.0
N A:ASP318 5.0 57.6 1.0

Manganese binding site 2 out of 3 in 4wti

Go back to Manganese Binding Sites List in 4wti
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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp


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

b:58.5
occ:1.00
 O A:HOH750 2.0 58.5 1.0
O1A A:GDP605 2.1 62.8 1.0
O1B A:GDP605 2.1 47.5 1.0
O A:THR221 2.3 59.1 1.0
OD2 A:ASP318 2.3 60.0 1.0
OD1 A:ASP220 2.6 58.5 1.0
OD2 A:ASP220 2.9 59.1 1.0
CG A:ASP220 3.1 57.3 1.0
CG A:ASP318 3.1 63.7 1.0
OD1 A:ASP318 3.2 66.7 1.0
PA A:GDP605 3.3 56.9 1.0
PB A:GDP605 3.4 58.1 1.0
C A:THR221 3.4 56.9 1.0
MN A:MN601 3.5 65.1 1.0
O3A A:GDP605 3.6 58.5 1.0
N A:THR221 3.8 54.0 1.0
C5' A:GDP605 3.9 60.1 1.0
O2B A:GDP605 4.1 58.1 1.0
O5' A:GDP605 4.1 61.4 1.0
CA A:THR221 4.2 56.2 1.0
C A:ASP220 4.5 54.1 1.0
CB A:ASP220 4.5 52.5 1.0
N A:ARG222 4.5 61.5 1.0
N A:HIS223 4.5 65.9 1.0
N A:PHE224 4.5 59.1 1.0
CB A:ASP318 4.6 61.0 1.0
CB A:PHE224 4.6 57.4 1.0
O2A A:GDP605 4.6 62.8 1.0
O3B A:GDP605 4.6 60.0 1.0
CA A:ARG222 4.7 66.6 1.0
CB A:THR221 4.8 57.6 1.0
CA A:ASP220 4.8 51.9 1.0
OD1 A:ASP319 4.8 57.3 1.0
C A:ARG222 4.9 67.6 1.0

Manganese binding site 3 out of 3 in 4wti

Go back to Manganese Binding Sites List in 4wti
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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp


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'-Acgg, Rna Primer 5'-Pcc, MN2+, and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:91.0
occ:1.00
 OE2 A:GLU237 2.2 81.1 1.0
ND1 A:HIS254 2.2 59.6 1.0
CG A:HIS254 3.0 61.1 1.0
CD A:GLU237 3.0 82.0 1.0
CE1 A:HIS254 3.1 63.6 1.0
OE1 A:GLU237 3.1 76.0 1.0
CB A:HIS254 3.3 61.6 1.0
CD2 A:HIS254 4.0 59.5 1.0
NE2 A:HIS254 4.0 62.7 1.0
CA A:HIS254 4.2 58.3 1.0
NE2 A:GLN241 4.2 56.0 1.0
CG A:GLU237 4.4 77.2 1.0
CG A:GLN241 4.8 55.9 1.0
CD A:GLN241 4.8 55.5 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 22:52:12 2024

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