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Manganese in PDB 1gx6: Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese

Enzymatic activity of Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese

All present enzymatic activity of Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese:
2.7.7.48;

Protein crystallography data

The structure of Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese, PDB code: 1gx6 was solved by S.Bressanelli, F.A.Rey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.092, 96.632, 96.340, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese (pdb code 1gx6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese, PDB code: 1gx6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 1gx6

Go back to Manganese Binding Sites List in 1gx6
Manganese binding site 1 out of 5 in the Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3001

b:31.0
occ:1.00
 O3G A:UTP1001 2.1 28.5 0.8
OD1 A:ASP220 2.1 27.5 1.0
OD2 A:ASP318 2.2 30.3 1.0
O A:HOH2484 2.2 36.8 1.0
O1B A:UTP1001 2.3 39.2 0.8
O A:THR221 2.3 27.5 1.0
CG A:ASP220 3.1 27.8 1.0
CG A:ASP318 3.2 26.7 1.0
PB A:UTP1001 3.3 39.0 0.8
PG A:UTP1001 3.3 39.0 0.8
OD2 A:ASP220 3.4 26.4 1.0
C A:THR221 3.4 21.4 1.0
O3B A:UTP1001 3.6 42.2 0.8
MN A:MN3002 3.6 30.1 1.0
OD1 A:ASP318 3.7 28.8 1.0
N A:THR221 3.8 25.2 1.0
O A:HOH2265 3.9 40.8 1.0
O2B A:UTP1001 3.9 35.4 0.8
O2G A:UTP1001 4.1 36.3 0.8
CA A:THR221 4.1 27.3 1.0
O A:HOH2480 4.2 47.7 1.0
N A:PHE224 4.3 20.9 1.0
C A:ASP220 4.4 26.3 1.0
CB A:ASP220 4.4 20.5 1.0
N A:CYS223 4.4 24.1 1.0
O1G A:UTP1001 4.5 42.5 0.8
CB A:ASP318 4.5 31.5 1.0
N A:ARG222 4.5 26.7 1.0
CB A:PHE224 4.5 21.5 1.0
CA A:ARG222 4.7 29.7 1.0
CB A:THR221 4.7 21.7 1.0
O3A A:UTP1001 4.7 45.9 0.8
C A:ARG222 4.8 23.9 1.0
CA A:ASP220 4.8 21.5 1.0
O A:HOH2485 4.8 36.5 1.0
O1B A:UTP1003 4.9 74.8 0.8
O2A A:UTP1001 4.9 43.6 0.8

Manganese binding site 2 out of 5 in 1gx6

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Manganese binding site 2 out of 5 in the Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3002

b:30.1
occ:1.00
 O2A A:UTP1001 2.0 43.6 0.8
OD1 A:ASP318 2.1 28.8 1.0
OD1 A:ASP319 2.2 23.3 1.0
OD2 A:ASP220 2.2 26.4 1.0
O1B A:UTP1001 2.3 39.2 0.8
O A:HOH2485 2.4 36.5 1.0
CG A:ASP318 3.0 26.7 1.0
CG A:ASP319 3.0 28.5 1.0
PA A:UTP1001 3.2 53.4 0.8
OD2 A:ASP318 3.3 30.3 1.0
CG A:ASP220 3.3 27.8 1.0
OD2 A:ASP319 3.3 33.9 1.0
PB A:UTP1001 3.4 39.0 0.8
O3A A:UTP1001 3.6 45.9 0.8
MN A:MN3001 3.6 31.0 1.0
O A:HOH2333 3.7 45.9 1.0
OD1 A:ASP220 3.7 27.5 1.0
O1A A:UTP1001 4.0 51.2 0.8
N A:ASP319 4.2 22.5 1.0
C A:ASP318 4.3 23.5 1.0
CB A:ASP319 4.3 27.6 1.0
O2B A:UTP1001 4.3 35.4 0.8
CB A:ASP318 4.4 31.5 1.0
O3B A:UTP1001 4.4 42.2 0.8
O A:HOH2332 4.5 31.0 1.0
O5' A:UTP1001 4.5 49.9 0.8
CA A:ASP319 4.5 22.1 1.0
O A:ASP318 4.6 29.0 1.0
CB A:ASP220 4.6 20.5 1.0
CA A:ASP318 4.8 24.1 1.0
C5' A:UTP1001 4.8 53.0 0.8
O3G A:UTP1001 4.8 28.5 0.8
O A:HOH2484 4.9 36.8 1.0
N A:ASP318 4.9 26.1 1.0
O A:HOH2394 4.9 55.5 1.0

Manganese binding site 3 out of 5 in 1gx6

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Manganese binding site 3 out of 5 in the Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3003

b:66.1
occ:0.66
 O5' A:UTP1002 2.3 61.6 0.7
O1A A:UTP1001 2.4 51.2 0.8
O1B A:UTP1002 2.5 66.2 0.7
MN A:MN3004 2.6 64.6 0.5
O A:HOH2394 2.8 55.5 1.0
O A:HOH2482 3.1 61.5 1.0
PA A:UTP1002 3.4 65.2 0.7
O2A A:UTP1002 3.5 63.8 0.7
PB A:UTP1002 3.6 65.8 0.7
O3A A:UTP1002 3.8 64.5 0.7
PA A:UTP1001 3.8 53.4 0.8
OG A:SER367 3.8 35.7 1.0
NH2 A:ARG158 4.3 76.0 1.0
O2B A:UTP1002 4.3 67.0 0.7
O A:HOH2485 4.4 36.5 1.0
O3A A:UTP1001 4.5 45.9 0.8
O5' A:UTP1001 4.6 49.9 0.8
O1A A:UTP1002 4.7 59.4 0.7
O3G A:UTP1002 4.8 72.9 0.7
O3B A:UTP1002 4.9 68.5 0.7
O2A A:UTP1001 4.9 43.6 0.8
CB A:SER367 5.0 29.4 1.0
CZ A:ARG158 5.0 76.2 1.0

Manganese binding site 4 out of 5 in 1gx6

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Manganese binding site 4 out of 5 in the Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3004

b:64.6
occ:0.53
 O1B A:UTP1002 2.5 66.2 0.7
MN A:MN3003 2.6 66.1 0.7
O5' A:UTP1002 2.9 61.6 0.7
O3G A:UTP1002 3.2 72.9 0.7
NH2 A:ARG158 3.3 76.0 1.0
O1A A:UTP1003 3.6 71.6 0.8
O1G A:UTP1002 3.6 72.6 0.7
PB A:UTP1002 3.6 65.8 0.7
O2A A:UTP1003 3.7 71.0 0.8
PG A:UTP1002 3.8 73.6 0.7
O3A A:UTP1002 3.9 64.5 0.7
OG A:SER367 4.0 35.7 1.0
O A:HOH2394 4.0 55.5 1.0
O1A A:UTP1001 4.0 51.2 0.8
O3B A:UTP1002 4.1 68.5 0.7
PA A:UTP1003 4.1 76.2 0.8
PA A:UTP1002 4.2 65.2 0.7
MN A:MN3005 4.3 82.4 0.6
CZ A:ARG158 4.5 76.2 1.0
O A:HOH2485 4.6 36.5 1.0
O2B A:UTP1001 4.8 35.4 0.8
O2B A:UTP1002 4.9 67.0 0.7

Manganese binding site 5 out of 5 in 1gx6

Go back to Manganese Binding Sites List in 1gx6
Manganese binding site 5 out of 5 in the Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Hepatitis C Virus Rna Polymerase in Complex with Utp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3005

b:82.4
occ:0.62
 O1B A:UTP1003 1.9 74.8 0.8
O2B A:UTP1001 2.3 35.4 0.8
O2A A:UTP1003 2.6 71.0 0.8
O1G A:UTP1003 2.6 76.7 0.8
PB A:UTP1003 2.8 77.4 0.8
PA A:UTP1003 3.1 76.2 0.8
O3A A:UTP1003 3.1 74.0 0.8
O3B A:UTP1003 3.3 75.7 0.8
O A:HOH2484 3.4 36.8 1.0
O1A A:UTP1003 3.5 71.6 0.8
PG A:UTP1003 3.5 77.8 0.8
PB A:UTP1001 3.7 39.0 0.8
O A:HOH2477 3.7 50.8 1.0
O A:HOH2480 4.1 47.7 1.0
O2B A:UTP1003 4.2 74.4 0.8
O1B A:UTP1001 4.3 39.2 0.8
NH2 A:ARG158 4.3 76.0 1.0
MN A:MN3004 4.3 64.6 0.5
O3A A:UTP1001 4.5 45.9 0.8
O3G A:UTP1003 4.5 77.2 0.8
O2G A:UTP1003 4.6 77.8 0.8
O2G A:UTP1001 4.6 36.3 0.8
O5' A:UTP1003 4.6 73.5 0.8
O3B A:UTP1001 4.6 42.2 0.8
O A:HOH2485 4.8 36.5 1.0

Reference:

S.Bressanelli, L.Tomei, F.A.Rey, R.De Francesco. A Structural Analysis of the Hepatitis C Virus Rna Polymerase in Complex with Ribonucleotides J.Virol. V. 76 3482 2002.
ISSN: ISSN 0022-538X
PubMed: 11884572
DOI: 10.1128/JVI.76.7.3482-3492.2002
Page generated: Sat Oct 5 10:49:07 2024

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