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Manganese in PDB 4wtd: 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 Adp, MN2+ and Symmetrical Primer Template 5'-Auaaauuu

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 Adp, MN2+ and Symmetrical Primer Template 5'-Auaaauuu

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 Adp, MN2+ and Symmetrical Primer Template 5'-Auaaauuu:
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 Adp, MN2+ and Symmetrical Primer Template 5'-Auaaauuu, PDB code: 4wtd was solved by T.E.Edwards, D.Fox Iii, T.C.Appleby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 141.250, 141.250, 91.190, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 22.3

Other elements in 4wtd:

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

Manganese binding site 1 out of 3 in 4wtd

Go back to Manganese Binding Sites List in 4wtd
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 Adp, MN2+ and Symmetrical Primer Template 5'-Auaaauuu


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

b:43.1
occ:1.00
 OD1 A:ASP220 2.0 42.3 1.0
OD1 A:ASP319 2.0 47.9 1.0
O1A P:ADP602 2.1 45.4 1.0
O3' P:U8 2.1 74.8 1.0
OD1 A:ASP318 2.2 51.5 1.0
O P:HOH704 2.3 44.8 1.0
CG A:ASP319 2.9 49.7 1.0
PA P:ADP602 3.0 42.7 1.0
CG A:ASP220 3.0 44.3 1.0
CG A:ASP318 3.1 44.5 1.0
OD2 A:ASP319 3.3 52.4 1.0
O2A P:ADP602 3.3 45.8 1.0
OD2 A:ASP318 3.3 47.9 1.0
MN A:MN601 3.3 43.4 1.0
C3' P:U8 3.4 79.4 1.0
OD2 A:ASP220 3.4 42.7 1.0
O5' P:ADP602 3.6 49.3 1.0
C5' P:ADP602 3.9 47.2 1.0
C4' P:U8 4.2 81.2 1.0
CB A:ASP319 4.3 47.6 1.0
CB A:ASP220 4.4 43.7 1.0
C5' P:U8 4.4 77.3 1.0
C A:ASP318 4.5 44.0 1.0
CB A:ASP318 4.5 42.1 1.0
O3A P:ADP602 4.5 41.5 1.0
O5' P:U8 4.5 77.6 1.0
O A:ASP318 4.6 49.9 1.0
C2' P:U8 4.6 77.4 1.0
O1B P:ADP602 4.6 32.7 1.0
N A:ASP319 4.6 46.9 1.0
CA A:ASP319 4.7 48.0 1.0
O2' P:U8 4.7 72.5 1.0
O P:HOH705 4.8 37.3 1.0
CA A:ASP318 4.9 43.5 1.0
N A:ASP318 5.0 43.3 1.0

Manganese binding site 2 out of 3 in 4wtd

Go back to Manganese Binding Sites List in 4wtd
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 Adp, MN2+ and Symmetrical Primer Template 5'-Auaaauuu


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

b:43.4
occ:1.00
 O1A P:ADP602 2.0 45.4 1.0
O1B P:ADP602 2.1 32.7 1.0
OD2 A:ASP318 2.1 47.9 1.0
O A:THR221 2.1 46.4 1.0
OD2 A:ASP220 2.1 42.7 1.0
O P:HOH705 2.3 37.3 1.0
CG A:ASP220 2.9 44.3 1.0
CG A:ASP318 3.1 44.5 1.0
OD1 A:ASP220 3.1 42.3 1.0
C A:THR221 3.3 45.3 1.0
PA P:ADP602 3.3 42.7 1.0
PB P:ADP602 3.3 43.4 1.0
MN P:MN601 3.3 43.1 1.0
N A:THR221 3.5 48.0 1.0
OD1 A:ASP318 3.5 51.5 1.0
O3A P:ADP602 3.6 41.5 1.0
CA A:THR221 3.9 44.4 1.0
C5' P:ADP602 4.0 47.2 1.0
O2B P:ADP602 4.0 43.5 1.0
O5' P:ADP602 4.1 49.3 1.0
CB A:ASP220 4.2 43.7 1.0
C A:ASP220 4.3 46.3 1.0
N A:ARG222 4.3 48.0 1.0
CB A:ASP318 4.4 42.1 1.0
N A:HIS223 4.5 57.1 1.0
N A:PHE224 4.5 48.3 1.0
CB A:PHE224 4.5 45.7 1.0
O2A P:ADP602 4.5 45.8 1.0
O3B P:ADP602 4.6 44.5 1.0
CB A:THR221 4.6 42.7 1.0
CA A:ARG222 4.6 52.7 1.0
CA A:ASP220 4.7 43.7 1.0
O P:HOH704 4.8 44.8 1.0
O3' P:U8 4.9 74.8 1.0
C A:ARG222 4.9 55.2 1.0

Manganese binding site 3 out of 3 in 4wtd

Go back to Manganese Binding Sites List in 4wtd
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 Adp, MN2+ and Symmetrical Primer Template 5'-Auaaauuu


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

b:71.6
occ:1.00
 OE2 A:GLU237 1.9 79.7 1.0
ND1 A:HIS254 2.0 49.7 1.0
CD A:GLU237 2.8 71.0 1.0
CE1 A:HIS254 3.0 56.1 1.0
CG A:HIS254 3.0 54.1 1.0
OE1 A:GLU237 3.1 64.6 1.0
CB A:HIS254 3.4 51.0 1.0
NE2 A:GLN241 4.0 45.9 1.0
NE2 A:HIS254 4.1 58.2 1.0
CD2 A:HIS254 4.1 53.3 1.0
CA A:HIS254 4.1 45.5 1.0
CG A:GLU237 4.2 64.5 1.0
CG A:GLN241 4.6 44.5 1.0
CD A:GLN241 4.7 46.8 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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