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Strontium in PDB 2pn4: Crystal Structure of Hepatitis C Virus Ires Subdomain Iia

Protein crystallography data

The structure of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia, PDB code: 2pn4 was solved by Q.Zhao, Q.Han, C.R.Kissinger, P.A.Thompson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.98 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.286, 48.730, 119.999, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 32

Other elements in 2pn4:

The structure of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia also contains other interesting chemical elements:

Bromine (Br) 4 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia (pdb code 2pn4). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 10 binding sites of Strontium where determined in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia, PDB code: 2pn4:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 10 in 2pn4

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Strontium binding site 1 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1001

b:58.1
occ:1.00
 O A:HOH1046 2.3 50.0 1.0
O B:HOH126 2.5 45.8 1.0
O2 A:C55 2.6 47.2 1.0
O A:HOH1047 3.8 44.4 1.0
C2 A:C55 3.8 47.4 1.0
C1' A:C55 4.4 49.6 1.0
O2' A:C55 4.5 54.1 1.0
OP2 B:C108 4.6 56.7 1.0
N1 A:C55 4.6 48.1 1.0
N3 A:C55 4.7 45.9 1.0
C2' A:C55 4.7 52.1 1.0
C2 A:A54 4.7 45.7 1.0
N1 A:A54 4.8 44.8 1.0
OP2 B:A109 4.8 52.7 1.0
O6 B:G110 4.9 39.0 1.0
N7 B:A109 4.9 43.7 1.0
OP1 B:G107 5.0 52.5 1.0

Strontium binding site 2 out of 10 in 2pn4

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Strontium binding site 2 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1002

b:56.2
occ:1.00
 O A:HOH1038 2.7 35.6 1.0
O6 A:G60 2.8 38.5 1.0
O4 A:U61 2.8 51.9 1.0
O6 B:G107 2.9 44.4 1.0
O6 B:G105 3.5 58.8 1.0
C4 A:U61 3.6 49.0 1.0
N3 A:U61 3.8 48.8 1.0
C6 A:G60 3.8 38.3 1.0
C6 B:G107 4.0 45.7 1.0
N4 B:C108 4.1 47.8 1.0
C6 B:G105 4.2 59.2 1.0
O4 A:U59 4.4 43.8 1.0
N7 A:G60 4.4 40.5 1.0
C5 A:G60 4.5 38.9 1.0
N4 A:C62 4.5 55.3 1.0
N7 B:G107 4.7 45.3 1.0
C5 B:G107 4.8 45.4 1.0
C5 A:U61 4.9 46.7 1.0
N1 A:G60 4.9 38.1 1.0
C4 A:U59 4.9 43.2 1.0
C5 B:G105 4.9 59.0 1.0
N1 B:G105 5.0 59.5 1.0

Strontium binding site 3 out of 10 in 2pn4

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Strontium binding site 3 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1006

b:57.1
occ:0.70
 O A:HOH1044 2.8 42.2 1.0
O A:HOH1042 3.7 51.8 1.0
OP2 A:A53 4.4 42.3 1.0
O A:HOH1043 4.4 45.4 1.0
OP1 A:A53 4.6 40.6 1.0

Strontium binding site 4 out of 10 in 2pn4

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Strontium binding site 4 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1027

b:61.9
occ:0.60
 OP1 A:A54 2.2 47.7 1.0
O A:HOH1036 3.0 40.8 1.0
P A:A54 3.6 47.5 1.0
O3' A:A53 4.1 46.7 1.0
C5' A:A54 4.4 48.0 1.0
O5' A:A54 4.5 48.3 1.0
OP2 A:A54 4.6 46.0 1.0
O C:HOH1025 4.8 45.3 1.0

Strontium binding site 5 out of 10 in 2pn4

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Strontium binding site 5 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1005

b:56.8
occ:0.60
 O A:HOH1045 2.5 41.0 1.0
O A:HOH1032 2.6 49.6 1.0
N7 A:G51 4.3 37.5 1.0
O6 A:G51 4.6 39.2 1.0
N7 A:G52 4.9 38.6 1.0
O6 A:G52 5.0 38.5 1.0

Strontium binding site 6 out of 10 in 2pn4

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Strontium binding site 6 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr1003

b:55.1
occ:1.00
 O C:HOH1032 2.7 30.8 1.0
O6 C:G60 2.7 42.4 1.0
O6 D:G107 2.8 46.0 1.0
O4 C:U61 2.8 52.1 1.0
O6 D:G105 3.6 62.0 1.0
C4 C:U61 3.6 51.4 1.0
N3 C:U61 3.8 51.4 1.0
C6 C:G60 3.8 40.9 1.0
C6 D:G107 4.0 46.7 1.0
N4 D:C108 4.1 47.9 1.0
C6 D:G105 4.3 61.6 1.0
O4 C:U59 4.4 38.2 1.0
N7 C:G60 4.4 43.8 1.0
C5 C:G60 4.5 41.2 1.0
N7 D:G107 4.6 47.4 1.0
N4 C:C62 4.6 52.4 1.0
C5 D:G107 4.7 46.9 1.0
N1 C:G60 4.9 42.5 1.0
O C:HOH1027 4.9 33.6 1.0
C5 C:U61 4.9 51.0 1.0
C5 D:G105 4.9 61.5 1.0
N1 D:G105 5.0 61.5 1.0
C4 C:U59 5.0 37.0 1.0

Strontium binding site 7 out of 10 in 2pn4

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Strontium binding site 7 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr1004

b:56.3
occ:1.00
 O2 C:C55 2.6 43.3 1.0
O D:HOH130 3.6 45.9 1.0
C2 C:C55 3.7 43.8 1.0
O C:HOH1029 4.1 42.3 1.0
N3 C:C55 4.4 44.4 1.0
OP2 D:C108 4.5 52.5 1.0
C1' C:C55 4.6 48.4 1.0
O2' C:C55 4.6 52.7 1.0
N1 C:C55 4.7 46.1 1.0
C2' C:C55 4.8 51.8 1.0
C2 C:A54 4.8 45.1 1.0
N1 C:A54 4.9 44.2 1.0
OP1 D:G107 4.9 55.5 1.0
N7 D:A109 4.9 43.3 1.0
O6 D:G110 4.9 36.2 1.0
OP2 D:A109 5.0 52.5 1.0

Strontium binding site 8 out of 10 in 2pn4

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Strontium binding site 8 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr1009

b:52.6
occ:0.70
 O C:HOH1033 2.7 29.7 0.7
OP2 C:A53 4.4 41.0 1.0
OP1 C:A53 4.4 41.5 1.0
P C:A53 5.0 41.0 1.0

Strontium binding site 9 out of 10 in 2pn4

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Strontium binding site 9 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr1022

b:59.8
occ:0.60
 OP1 C:A54 2.3 49.1 1.0
O A:HOH1035 3.0 47.1 1.0
P C:A54 3.7 49.2 1.0
O3' C:A53 4.2 47.3 1.0
C5' C:A54 4.4 48.3 1.0
O5' C:A54 4.5 49.1 1.0
OP2 C:A54 4.8 47.0 1.0

Strontium binding site 10 out of 10 in 2pn4

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Strontium binding site 10 out of 10 in the Crystal Structure of Hepatitis C Virus Ires Subdomain Iia


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Crystal Structure of Hepatitis C Virus Ires Subdomain Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr1008

b:58.9
occ:0.60
 O C:HOH1034 2.7 40.4 1.0
O C:HOH1028 2.9 36.1 1.0
N7 C:G51 4.4 38.6 1.0
O6 C:G51 4.7 37.9 1.0
N7 C:G52 4.9 34.9 1.0
O6 C:G52 4.9 36.1 1.0

Reference:

Q.Zhao, Q.Han, C.R.Kissinger, T.Hermann, P.A.Thompson. Structure of Hepatitis C Virus Ires Subdomain Iia. Acta Crystallogr.,Sect.D V. 64 436 2008.
ISSN: ISSN 0907-4449
PubMed: 18391410
DOI: 10.1107/S0907444908002011
Page generated: Thu Oct 10 21:22:11 2024

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