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Manganese in PDB 4wta: 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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu

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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu

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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu:
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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu, PDB code: 4wta 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 (°) 140.620, 140.620, 91.000, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 22.4

Other elements in 4wta:

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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu 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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu (pdb code 4wta). 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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu, PDB code: 4wta:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4wta

Go back to Manganese Binding Sites List in 4wta
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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu


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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:42.5
occ:1.00
 O3' P:U6 2.1 73.5 1.0
OD1 A:ASP319 2.1 51.4 1.0
OD1 A:ASP220 2.1 44.3 1.0
O1A A:UDP605 2.2 45.2 1.0
OD1 A:ASP318 2.3 42.5 1.0
O P:HOH101 2.5 52.8 1.0
CG A:ASP319 3.0 52.2 1.0
PA A:UDP605 3.0 43.7 1.0
CG A:ASP220 3.1 42.3 1.0
OD2 A:ASP319 3.2 52.4 1.0
CG A:ASP318 3.2 40.0 1.0
O2A A:UDP605 3.2 47.9 1.0
C3' P:U6 3.3 73.8 1.0
MN A:MN602 3.3 43.7 1.0
OD2 A:ASP318 3.3 42.8 1.0
OD2 A:ASP220 3.4 39.8 1.0
O5' A:UDP605 3.5 48.7 1.0
C5' A:UDP605 3.9 46.5 1.0
C4' P:U6 4.0 77.5 1.0
C5' P:U6 4.2 72.9 1.0
CB A:ASP319 4.4 48.5 1.0
CB A:ASP220 4.4 40.9 1.0
O5' P:U6 4.5 68.7 1.0
O3A A:UDP605 4.5 40.2 1.0
C2' P:U6 4.5 73.1 1.0
CB A:ASP318 4.6 39.5 1.0
C A:ASP318 4.6 40.7 1.0
O1B A:UDP605 4.6 32.3 1.0
O A:ASP318 4.6 42.5 1.0
O A:HOH716 4.7 33.3 1.0
O2' P:U6 4.7 72.8 1.0
N A:ASP319 4.8 43.1 1.0
CA A:ASP319 4.8 45.7 1.0

Manganese binding site 2 out of 3 in 4wta

Go back to Manganese Binding Sites List in 4wta
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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu


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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:43.7
occ:1.00
 O1A A:UDP605 1.9 45.2 1.0
OD2 A:ASP318 2.0 42.8 1.0
O A:THR221 2.1 40.9 1.0
O1B A:UDP605 2.1 32.3 1.0
OD2 A:ASP220 2.2 39.8 1.0
O A:HOH716 2.3 33.3 1.0
CG A:ASP220 3.0 42.3 1.0
CG A:ASP318 3.1 40.0 1.0
C A:THR221 3.2 42.5 1.0
PA A:UDP605 3.3 43.7 1.0
OD1 A:ASP220 3.3 44.3 1.0
MN A:MN601 3.3 42.5 1.0
PB A:UDP605 3.4 43.8 1.0
OD1 A:ASP318 3.5 42.5 1.0
O3A A:UDP605 3.7 40.2 1.0
N A:THR221 3.7 45.1 1.0
O A:HOH745 3.9 44.4 1.0
C5' A:UDP605 3.9 46.5 1.0
CA A:THR221 4.0 43.7 1.0
O5' A:UDP605 4.1 48.7 1.0
O2B A:UDP605 4.2 40.0 1.0
N A:ARG222 4.3 45.6 1.0
CB A:ASP220 4.3 40.9 1.0
N A:PHE224 4.3 44.9 1.0
C A:ASP220 4.3 43.8 1.0
CB A:ASP318 4.4 39.5 1.0
CB A:PHE224 4.4 41.2 1.0
N A:HIS223 4.4 51.8 1.0
O2A A:UDP605 4.5 47.9 1.0
CA A:ARG222 4.5 50.0 1.0
O3B A:UDP605 4.6 42.1 1.0
CB A:THR221 4.7 43.2 1.0
CA A:ASP220 4.7 41.4 1.0
O3' P:U6 4.7 73.5 1.0
C A:ARG222 4.8 52.1 1.0
CA A:PHE224 4.9 42.8 1.0

Manganese binding site 3 out of 3 in 4wta

Go back to Manganese Binding Sites List in 4wta
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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu


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 Udp, MN2+ and Symmetrical Primer Template 5'-Caaaauuu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:87.6
occ:1.00
 OE2 A:GLU237 1.8 74.9 1.0
ND1 A:HIS254 2.3 55.9 1.0
CD A:GLU237 3.0 68.3 1.0
CG A:HIS254 3.1 53.7 1.0
CE1 A:HIS254 3.3 59.0 1.0
CB A:HIS254 3.4 52.0 1.0
OE1 A:GLU237 3.6 69.2 1.0
NE2 A:GLN241 3.9 42.9 1.0
CG A:GLU237 4.1 60.3 1.0
CA A:HIS254 4.2 48.2 1.0
CD2 A:HIS254 4.2 55.3 1.0
NE2 A:HIS254 4.3 59.0 1.0
CD A:GLN241 4.7 45.0 1.0
CG A:GLN241 4.7 44.6 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 22:51:35 2024

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