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

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'-Uagg, Rna Primer 5'-Pcc, MN2+, and Udp

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'-Uagg, Rna Primer 5'-Pcc, MN2+, and Udp:
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'-Uagg, Rna Primer 5'-Pcc, MN2+, and Udp, PDB code: 4wtm was solved by T.E.Edwards, T.C.Appleby, D.Fox Iii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.99 / 2.15
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 140.370, 140.370, 92.430, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 21.6

Other elements in 4wtm:

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

Manganese binding site 1 out of 3 in 4wtm

Go back to Manganese Binding Sites List in 4wtm
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'-Uagg, Rna Primer 5'-Pcc, MN2+, and Udp


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

b:33.2
occ:1.00
 OD1 A:ASP319 1.9 33.7 1.0
O1A A:UDP605 2.0 31.4 1.0
OD2 A:ASP220 2.0 38.9 1.0
OD1 A:ASP318 2.2 35.6 1.0
O A:HOH822 2.2 35.7 1.0
O3' P:C2 2.3 40.4 1.0
CG A:ASP220 3.0 33.7 1.0
CG A:ASP318 3.0 36.6 1.0
CG A:ASP319 3.0 34.7 1.0
OD1 A:ASP220 3.2 31.2 1.0
OD2 A:ASP318 3.2 33.6 1.0
PA A:UDP605 3.3 35.7 1.0
MN A:MN602 3.4 32.8 1.0
C3' P:C2 3.6 44.4 1.0
OD2 A:ASP319 3.6 39.6 1.0
O2A A:UDP605 3.7 37.8 1.0
O5' A:UDP605 4.1 38.7 1.0
C5' A:UDP605 4.1 40.7 1.0
CB A:ASP319 4.2 32.4 1.0
N A:ASP319 4.3 28.8 1.0
C A:ASP318 4.3 33.7 1.0
CB A:ASP220 4.3 32.4 1.0
C4' P:C2 4.3 45.2 1.0
CB A:ASP318 4.4 34.0 1.0
CA A:ASP319 4.5 30.4 1.0
O A:HOH828 4.5 35.8 1.0
O A:ASP318 4.5 32.6 1.0
C5' P:C2 4.5 43.2 1.0
O3A A:UDP605 4.6 34.7 1.0
C2' P:C2 4.7 46.7 1.0
O1B A:UDP605 4.7 27.7 1.0
O2' P:C2 4.8 46.4 1.0
CA A:ASP318 4.8 33.5 1.0
O5' P:C2 4.8 42.6 1.0
N A:ASP318 4.9 32.0 1.0
OP1 P:C2 5.0 51.2 1.0

Manganese binding site 2 out of 3 in 4wtm

Go back to Manganese Binding Sites List in 4wtm
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'-Uagg, Rna Primer 5'-Pcc, MN2+, and Udp


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

b:32.8
occ:1.00
 OD2 A:ASP318 2.0 33.6 1.0
O A:HOH828 2.0 35.8 1.0
O1B A:UDP605 2.1 27.7 1.0
OD1 A:ASP220 2.1 31.2 1.0
O A:THR221 2.2 38.0 1.0
O1A A:UDP605 2.3 31.4 1.0
CG A:ASP318 3.1 36.6 1.0
CG A:ASP220 3.2 33.7 1.0
PB A:UDP605 3.3 34.3 1.0
PA A:UDP605 3.3 35.7 1.0
C A:THR221 3.4 35.3 1.0
O3A A:UDP605 3.4 34.7 1.0
MN A:MN601 3.4 33.2 1.0
OD1 A:ASP318 3.6 35.6 1.0
OD2 A:ASP220 3.6 38.9 1.0
O A:HOH891 3.7 55.7 1.0
N A:THR221 3.8 32.7 1.0
O2B A:UDP605 4.0 33.9 1.0
CA A:THR221 4.1 31.9 1.0
C5' A:UDP605 4.1 40.7 1.0
O5' A:UDP605 4.2 38.7 1.0
N A:HIS223 4.3 36.1 1.0
N A:PHE224 4.4 31.4 1.0
CB A:ASP318 4.4 34.0 1.0
N A:ARG222 4.4 34.5 1.0
CB A:ASP220 4.4 32.4 1.0
C A:ASP220 4.4 31.8 1.0
O3B A:UDP605 4.6 37.5 1.0
CB A:PHE224 4.6 32.1 1.0
O2A A:UDP605 4.6 37.8 1.0
CA A:ARG222 4.6 37.5 1.0
CB A:THR221 4.6 32.8 1.0
O A:HOH822 4.7 35.7 1.0
C A:ARG222 4.7 37.6 1.0
CA A:ASP220 4.8 30.6 1.0

Manganese binding site 3 out of 3 in 4wtm

Go back to Manganese Binding Sites List in 4wtm
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'-Uagg, Rna Primer 5'-Pcc, MN2+, and Udp


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

b:51.6
occ:1.00
 ND1 A:HIS254 1.9 38.6 1.0
OE2 A:GLU237 2.2 54.6 1.0
CG A:HIS254 2.8 43.0 1.0
OE1 A:GLU237 2.8 47.8 1.0
CD A:GLU237 2.8 46.3 1.0
CE1 A:HIS254 3.0 46.4 1.0
CB A:HIS254 3.1 42.3 1.0
CA A:HIS254 3.8 37.8 1.0
CD2 A:HIS254 4.0 43.8 1.0
O A:HOH900 4.0 58.1 1.0
NE2 A:HIS254 4.0 47.1 1.0
NE2 A:GLN241 4.1 32.0 1.0
CG A:GLU237 4.3 47.0 1.0
N A:HIS254 4.8 41.8 1.0
C A:HIS254 4.9 37.9 1.0
CD A:GLN241 5.0 37.6 1.0
CG A:GLN241 5.0 38.0 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 22:53:37 2024

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