Phosphorus in PDB 1a1v: Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna

Protein crystallography data

The structure of Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna, PDB code: 1a1v was solved by J.L.Kim, K.A.Morgenstern, J.P.Griffith, M.D.Dwyer, J.A.Thomson, M.A.Murcko, C.Lin, P.R.Caron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.100, 117.500, 63.400, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 28.7

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna (pdb code 1a1v). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna, PDB code: 1a1v:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6;

Phosphorus binding site 1 out of 6 in 1a1v

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Phosphorus binding site 1 out of 6 in the Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P3

b:64.6
occ:1.00
P B:DU3 0.0 64.6 1.0
OP2 B:DU3 1.5 65.4 1.0
OP1 B:DU3 1.5 64.5 1.0
O5' B:DU3 1.6 61.4 1.0
O3' B:DU2 1.6 62.9 1.0
C5' B:DU3 2.6 58.9 1.0
HE2 A:HIS369 2.7 0.0 1.0
H2 B:HOH164 2.9 0.0 1.0
NE2 A:HIS369 3.6 29.7 1.0
O B:HOH164 3.8 50.0 1.0
C4' B:DU3 3.9 57.5 1.0
H1 B:HOH93 4.0 0.0 1.0
O4' B:DU3 4.1 58.0 1.0
CD2 A:HIS369 4.3 28.6 1.0
H1 B:HOH164 4.3 0.0 1.0
OG1 A:THR450 4.4 26.7 1.0
HG1 A:THR450 4.4 0.0 1.0
C3' B:DU3 4.6 55.5 1.0
C2' B:DU3 4.7 57.2 1.0
CE1 A:HIS369 4.7 29.2 1.0
O B:HOH93 4.7 24.1 1.0
C1' B:DU3 4.8 57.8 1.0

Phosphorus binding site 2 out of 6 in 1a1v

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Phosphorus binding site 2 out of 6 in the Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P4

b:51.1
occ:1.00
P B:DU4 0.0 51.1 1.0
OP2 B:DU4 1.5 52.6 1.0
OP1 B:DU4 1.5 52.5 1.0
O5' B:DU4 1.6 51.5 1.0
O3' B:DU3 1.6 53.3 1.0
C5' B:DU4 2.6 50.3 1.0
C3' B:DU3 2.6 55.5 1.0
H A:LYS371 3.3 0.0 1.0
H1 B:HOH165 3.6 0.0 1.0
C2' B:DU3 3.6 57.2 1.0
O B:HOH165 3.7 47.7 1.0
C4' B:DU3 3.8 57.5 1.0
C4' B:DU4 3.9 50.0 1.0
C3' B:DU4 4.1 50.5 1.0
CD A:LYS371 4.1 28.0 1.0
N A:LYS371 4.3 23.6 1.0
CB A:SER370 4.4 24.6 1.0
CA A:SER370 4.4 24.1 1.0
CG A:LYS371 4.5 27.1 1.0
C1' B:DU3 4.5 57.8 1.0
H2 B:HOH165 4.5 0.0 1.0
C2' B:DU4 4.5 50.0 1.0
O4' B:DU4 4.6 49.0 1.0
O4' B:DU3 4.7 58.0 1.0
C6 B:DU4 4.7 47.1 1.0
C5' B:DU3 4.8 58.9 1.0
C A:SER370 4.9 23.0 1.0
CB A:LYS371 4.9 24.9 1.0

Phosphorus binding site 3 out of 6 in 1a1v

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Phosphorus binding site 3 out of 6 in the Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P5

b:47.9
occ:1.00
P B:DU5 0.0 47.9 1.0
OP1 B:DU5 1.5 48.6 1.0
OP2 B:DU5 1.5 48.9 1.0
O5' B:DU5 1.6 49.2 1.0
O3' B:DU4 1.6 50.7 1.0
C3' B:DU4 2.6 50.5 1.0
C5' B:DU5 2.6 52.1 1.0
C2' B:DU4 2.9 50.0 1.0
H A:ARG393 3.0 0.0 1.0
OG1 A:THR411 3.5 18.6 1.0
CB A:ARG393 3.7 40.7 1.0
C4' B:DU5 3.9 53.5 1.0
N A:ARG393 3.9 35.7 1.0
C1' B:DU4 3.9 47.7 1.0
C4' B:DU4 3.9 50.0 1.0
HG1 A:THR411 4.0 0.0 1.0
C3' B:DU5 4.1 53.7 1.0
CB A:ALA413 4.2 31.3 1.0
C6 B:DU5 4.2 59.8 1.0
CB A:THR411 4.2 16.5 1.0
H A:ALA413 4.3 0.0 1.0
C2' B:DU5 4.4 54.9 1.0
CA A:ARG393 4.4 36.1 1.0
O4' B:DU4 4.5 49.0 1.0
CG2 A:THR411 4.5 18.0 1.0
O4' B:DU5 4.5 55.0 1.0
HZ3 A:LYS371 4.6 0.0 1.0
CB A:TYR392 4.6 31.0 1.0
CD A:LYS371 4.7 28.0 1.0
C5 B:DU5 4.8 60.6 1.0
N A:ALA413 4.8 28.2 1.0
CG A:LYS371 4.9 27.1 1.0
CD A:ARG393 4.9 50.1 1.0
CG A:ARG393 4.9 46.0 1.0
HE A:ARG393 4.9 0.0 1.0
CA A:ALA413 4.9 31.9 1.0
C A:TYR392 4.9 33.2 1.0
C1' B:DU5 5.0 56.5 1.0

Phosphorus binding site 4 out of 6 in 1a1v

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Phosphorus binding site 4 out of 6 in the Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P6

b:55.5
occ:1.00
P B:DU6 0.0 55.5 1.0
OP1 B:DU6 1.5 56.1 1.0
OP2 B:DU6 1.5 54.7 1.0
O5' B:DU6 1.6 56.3 1.0
O3' B:DU5 1.6 53.6 1.0
C3' B:DU5 2.6 53.7 1.0
C5' B:DU6 2.6 55.6 1.0
HH21 A:ARG393 2.8 0.0 1.0
C2' B:DU5 3.1 54.9 1.0
HE A:ARG393 3.5 0.0 1.0
NH2 A:ARG393 3.7 57.6 1.0
C4' B:DU6 3.9 56.6 1.0
C4' B:DU5 3.9 53.5 1.0
O A:ALA413 4.0 38.9 1.0
C1' B:DU5 4.1 56.5 1.0
NE A:ARG393 4.2 53.8 1.0
CA A:ALA413 4.3 31.9 1.0
C3' B:DU6 4.3 57.4 1.0
HH22 A:ARG393 4.3 0.0 1.0
CZ A:ARG393 4.4 56.0 1.0
O4' B:DU6 4.5 57.2 1.0
O4' B:DU5 4.6 55.0 1.0
C A:ALA413 4.7 35.4 1.0
CB A:ALA413 4.7 31.3 1.0
C2' B:DU6 4.7 58.2 1.0

Phosphorus binding site 5 out of 6 in 1a1v

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Phosphorus binding site 5 out of 6 in the Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P7

b:55.4
occ:1.00
P B:DU7 0.0 55.4 1.0
OP2 B:DU7 1.5 55.5 1.0
OP1 B:DU7 1.5 55.4 1.0
O5' B:DU7 1.6 54.3 1.0
O3' B:DU6 1.6 57.1 1.0
C3' B:DU6 2.6 57.4 1.0
C5' B:DU7 2.6 51.5 1.0
H2 B:HOH11 2.9 0.0 1.0
H A:VAL232 3.3 0.0 1.0
C2' B:DU6 3.5 58.2 1.0
C4' B:DU7 3.6 49.4 1.0
C3' B:DU7 3.8 48.2 1.0
O B:HOH11 3.9 24.2 1.0
C4' B:DU6 3.9 56.6 1.0
CG2 A:VAL232 4.0 20.8 1.0
C2' B:DU7 4.0 49.2 1.0
O4' B:DU7 4.1 49.0 1.0
N A:VAL232 4.2 24.6 1.0
H1 B:HOH11 4.3 0.0 1.0
CB A:VAL232 4.3 25.0 1.0
O A:PRO230 4.4 25.4 1.0
C1' B:DU6 4.5 58.9 1.0
C6 B:DU7 4.5 49.7 1.0
C1' B:DU7 4.6 49.6 1.0
O4' B:DU6 4.8 57.2 1.0
N1 B:DU7 4.8 50.0 1.0
C5' B:DU6 4.8 55.6 1.0
HG A:SER231 4.9 0.0 1.0
CA A:SER231 4.9 24.3 1.0
CA A:VAL232 4.9 24.8 1.0

Phosphorus binding site 6 out of 6 in 1a1v

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Phosphorus binding site 6 out of 6 in the Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Hepatitis C Virus NS3 Helicase Domain Complexed with Single Stranded Sdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:43.2
occ:1.00
P B:DU8 0.0 43.2 1.0
OP1 B:DU8 1.5 44.4 1.0
OP2 B:DU8 1.5 44.7 1.0
O5' B:DU8 1.6 45.7 1.0
O3' B:DU7 1.6 45.7 1.0
C3' B:DU7 2.6 48.2 1.0
C5' B:DU8 2.6 46.2 1.0
H A:GLY255 2.9 0.0 1.0
C2' B:DU7 3.3 49.2 1.0
HG1 A:THR269 3.4 0.0 1.0
N A:GLY255 3.6 37.2 1.0
CG2 A:VAL232 3.7 20.8 1.0
OG1 A:THR269 3.7 19.5 1.0
H A:LYS272 3.8 0.0 1.0
C4' B:DU8 3.9 46.5 1.0
CA A:GLY255 3.9 38.9 1.0
C4' B:DU7 3.9 49.4 1.0
O4' B:DU8 4.3 45.8 1.0
N A:LYS272 4.3 21.0 1.0
CB A:THR269 4.4 22.7 1.0
C1' B:DU7 4.4 49.6 1.0
C3' B:DU8 4.5 46.5 1.0
H2 A:HOH1003 4.5 0.0 1.0
CG2 A:THR269 4.5 20.7 1.0
C A:THR254 4.7 35.3 1.0
CA A:GLY271 4.7 19.1 1.0
O5' B:DU7 4.7 54.3 1.0
O4' B:DU7 4.8 49.0 1.0
C A:GLY271 4.8 19.2 1.0
CB A:LYS272 4.8 24.1 1.0
C2' B:DU8 4.9 46.8 1.0
C5' B:DU7 4.9 51.5 1.0
H A:GLY271 4.9 0.0 1.0
H A:VAL256 4.9 0.0 1.0

Reference:

J.L.Kim, K.A.Morgenstern, J.P.Griffith, M.D.Dwyer, J.A.Thomson, M.A.Murcko, C.Lin, P.R.Caron. Hepatitis C Virus NS3 Rna Helicase Domain with A Bound Oligonucleotide: the Crystal Structure Provides Insights Into the Mode of Unwinding. Structure V. 6 89 1998.
ISSN: ISSN 0969-2126
PubMed: 9493270
DOI: 10.1016/S0969-2126(98)00010-0
Page generated: Fri Sep 25 12:01:47 2020

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