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Manganese in PDB 4wtc: Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu

Enzymatic activity of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu

All present enzymatic activity of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu:
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 and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu, PDB code: 4wtc 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 / 2.75
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 141.340, 141.340, 90.800, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 22.9

Other elements in 4wtc:

The structure of Crystal Structure of Hcv NS5B Genotype 2A Jfh-1 Isolate with S15G E86Q E87Q C223H V321I Mutations and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu 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 and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu (pdb code 4wtc). 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 and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu, PDB code: 4wtc:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4wtc

Go back to Manganese Binding Sites List in 4wtc
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 and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu


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 and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:54.0
occ:1.00
OD1 A:ASP220 2.1 48.4 1.0
OD1 A:ASP319 2.2 52.6 1.0
O3' P:U8 2.2 61.8 1.0
O1A A:CDP605 2.2 43.5 1.0
OD1 A:ASP318 2.2 48.4 1.0
O P:HOH102 2.5 51.7 1.0
PA A:CDP605 3.1 39.6 1.0
CG A:ASP319 3.1 51.4 1.0
CG A:ASP220 3.2 49.4 1.0
CG A:ASP318 3.2 45.9 1.0
MN A:MN602 3.3 44.6 1.0
O2A A:CDP605 3.3 43.7 1.0
OD2 A:ASP319 3.3 52.7 1.0
C3' P:U8 3.4 63.4 1.0
OD2 A:ASP318 3.5 49.5 1.0
O5' A:CDP605 3.5 47.5 1.0
OD2 A:ASP220 3.6 43.7 1.0
C5' A:CDP605 3.9 45.4 1.0
C4' P:U8 4.1 64.5 1.0
C5' P:U8 4.3 60.5 1.0
CB A:ASP220 4.4 46.0 1.0
CB A:ASP319 4.5 47.6 1.0
O5' P:U8 4.5 57.2 1.0
C A:ASP318 4.5 44.5 1.0
O3A A:CDP605 4.6 41.6 1.0
CB A:ASP318 4.6 43.3 1.0
O A:ASP318 4.6 46.4 1.0
C2' P:U8 4.6 63.1 1.0
N A:ASP319 4.6 48.6 1.0
O1B A:CDP605 4.6 35.3 1.0
O A:HOH731 4.7 44.8 1.0
O2' P:U8 4.8 62.2 1.0
CA A:ASP319 4.8 46.7 1.0
CA A:ASP318 5.0 43.2 1.0

Manganese binding site 2 out of 3 in 4wtc

Go back to Manganese Binding Sites List in 4wtc
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 and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu


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 and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:44.6
occ:1.00
O1A A:CDP605 2.0 43.5 1.0
OD2 A:ASP318 2.1 49.5 1.0
O1B A:CDP605 2.1 35.3 1.0
O A:THR221 2.2 46.0 1.0
O A:HOH731 2.3 44.8 1.0
OD2 A:ASP220 2.4 43.7 1.0
CG A:ASP220 3.0 49.4 1.0
CG A:ASP318 3.0 45.9 1.0
OD1 A:ASP220 3.1 48.4 1.0
MN A:MN601 3.3 54.0 1.0
PA A:CDP605 3.3 39.6 1.0
C A:THR221 3.3 46.4 1.0
OD1 A:ASP318 3.3 48.4 1.0
PB A:CDP605 3.4 46.8 1.0
N A:THR221 3.7 49.0 1.0
O3A A:CDP605 3.7 41.6 1.0
C5' A:CDP605 3.8 45.4 1.0
O5' A:CDP605 4.0 47.5 1.0
O3B A:CDP605 4.1 43.5 1.0
CA A:THR221 4.1 45.4 1.0
N A:ARG222 4.4 48.4 1.0
CB A:ASP318 4.4 43.3 1.0
CB A:PHE224 4.4 42.4 1.0
CB A:ASP220 4.4 46.0 1.0
C A:ASP220 4.4 46.0 1.0
N A:PHE224 4.4 46.2 1.0
O2A A:CDP605 4.5 43.7 1.0
N A:HIS223 4.5 55.8 1.0
O2B A:CDP605 4.6 44.1 1.0
CA A:ARG222 4.7 51.7 1.0
CB A:THR221 4.7 43.7 1.0
O3' P:U8 4.7 61.8 1.0
CA A:ASP220 4.7 44.9 1.0
C A:ARG222 4.8 54.3 1.0
CA A:PHE224 5.0 44.9 1.0

Manganese binding site 3 out of 3 in 4wtc

Go back to Manganese Binding Sites List in 4wtc
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 and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu


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 and DELTA8 Beta Hairpin Loop Deletion in Complex with Cdp, MN2+ and Symmetrical Primer Template 5'-Agaaauuu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:81.5
occ:1.00
OE2 A:GLU237 2.1 77.0 1.0
ND1 A:HIS254 2.1 63.6 1.0
CD A:GLU237 2.9 69.7 1.0
CE1 A:HIS254 2.9 67.5 1.0
CG A:HIS254 3.0 61.7 1.0
O A:HOH738 3.0 57.4 1.0
OE1 A:GLU237 3.1 63.6 1.0
CB A:HIS254 3.4 55.1 1.0
NE2 A:HIS254 3.9 69.2 1.0
CD2 A:HIS254 3.9 60.9 1.0
NE2 A:GLN241 4.2 43.1 1.0
CA A:HIS254 4.3 48.2 1.0
CG A:GLU237 4.4 61.2 1.0
CG A:GLN241 4.7 47.8 1.0
CD A:GLN241 4.9 49.4 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 22:51:35 2024

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