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Sodium in PDB 3ddk: Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase

Protein crystallography data

The structure of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase, PDB code: 3ddk was solved by G.Campagnola, M.H.Weygandt, K.E.Scoggin, O.B.Peersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.58 / 2.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.360, 74.360, 288.050, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase (pdb code 3ddk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase, PDB code: 3ddk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3ddk

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Sodium binding site 1 out of 9 in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na901

b:52.6
occ:1.00
OE2 A:GLU4 3.4 51.0 1.0
NH1 A:ARG284 3.8 56.6 1.0
ND2 A:ASN65 3.9 35.8 1.0
O A:HOH546 3.9 31.3 1.0
OD1 A:ASN67 4.0 55.2 1.0
ND2 A:ASN67 4.0 56.3 1.0
CD A:ARG284 4.1 50.6 1.0
CD A:GLU4 4.3 49.4 1.0
OE1 A:GLU4 4.3 51.8 1.0
CB A:ASN65 4.4 35.5 1.0
CG A:GLU2 4.5 44.9 1.0
CG A:ASN67 4.5 55.3 1.0
CB A:GLU2 4.6 38.1 1.0
CG A:ASN65 4.7 34.6 1.0
CZ A:ARG284 4.8 56.6 1.0
NE A:ARG284 4.9 54.5 1.0

Sodium binding site 2 out of 9 in 3ddk

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Sodium binding site 2 out of 9 in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:51.3
occ:1.00
NZ A:LYS38 3.7 33.7 1.0
O A:ASP397 3.9 27.9 1.0
OD1 A:ASP397 4.0 38.0 1.0
CB A:ASP397 4.2 32.3 1.0
CB A:GLU400 4.2 28.2 1.0
CA A:ASP397 4.4 30.9 1.0
CD A:LYS38 4.4 31.0 1.0
O A:HOH695 4.4 52.3 1.0
CE A:LYS38 4.4 31.3 1.0
CG A:ASP397 4.5 35.7 1.0
NZ A:LYS376 4.5 52.4 1.0
C A:ASP397 4.6 29.3 1.0
CG A:GLU400 4.9 28.9 1.0
N A:SER401 4.9 28.9 1.0

Sodium binding site 3 out of 9 in 3ddk

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Sodium binding site 3 out of 9 in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:51.3
occ:1.00
O A:HOH565 3.0 36.7 1.0
OG A:SER292 3.2 24.5 1.0
O2 A:SO4923 3.4 0.2 1.0
O3 A:SO4923 3.5 0.1 1.0
N A:GLY293 3.5 26.6 1.0
NH1 A:ARG188 3.6 28.6 1.0
CA A:SER292 3.8 25.3 1.0
CB A:SER292 3.8 24.9 1.0
CE2 A:TYR195 3.9 28.3 1.0
S A:SO4923 4.0 0.6 1.0
CG A:ARG188 4.1 29.4 1.0
C A:SER292 4.1 26.2 1.0
CD A:ARG188 4.3 26.8 1.0
CD2 A:TYR195 4.3 26.2 1.0
CA A:GLY293 4.5 25.1 1.0
CZ A:ARG188 4.6 30.5 1.0
CZ A:TYR195 4.6 27.9 1.0
O1 A:SO4923 4.7 0.5 1.0
OH A:TYR195 4.9 29.0 1.0
NE A:ARG188 4.9 31.2 1.0

Sodium binding site 4 out of 9 in 3ddk

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Sodium binding site 4 out of 9 in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:47.5
occ:1.00
O A:VAL367 2.9 38.2 1.0
O A:LEU229 2.9 31.1 1.0
O A:HOH625 3.0 36.6 1.0
O3 A:SO4924 3.2 0.1 1.0
OE2 A:GLU366 3.2 69.5 1.0
OE1 A:GLU366 3.5 67.4 1.0
CD A:GLU366 3.5 67.2 1.0
N A:LEU229 3.5 31.9 1.0
O A:HOH627 3.8 34.2 1.0
C A:LEU229 3.8 31.4 1.0
N A:VAL367 3.8 46.9 1.0
C A:VAL367 3.9 39.5 1.0
CA A:LEU229 4.0 31.2 1.0
O2 A:SO4924 4.1 0.6 1.0
C A:HIS228 4.2 33.1 1.0
CB A:VAL367 4.2 40.5 1.0
CB A:LEU229 4.2 30.4 1.0
S A:SO4924 4.2 0.5 1.0
CA A:VAL367 4.2 41.5 1.0
CB A:HIS228 4.3 36.8 1.0
CA A:HIS228 4.4 34.3 1.0
CG A:GLU366 4.5 63.6 1.0
ND1 A:HIS228 4.6 39.9 1.0
O1 A:SO4924 4.7 0.6 1.0
O A:HOH675 4.7 58.2 1.0
C A:GLU366 4.8 52.8 1.0
O A:HOH754 4.8 56.4 1.0
O A:HIS228 4.9 33.2 1.0
CG A:HIS228 5.0 39.4 1.0
CA A:GLU366 5.0 56.6 1.0

Sodium binding site 5 out of 9 in 3ddk

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Sodium binding site 5 out of 9 in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:54.4
occ:1.00
O A:HOH548 2.9 55.0 1.0
N A:GLU72 3.4 35.0 1.0
CB A:ASP71 3.7 35.6 1.0
CA A:ASP71 3.8 36.1 1.0
NE2 A:HIS69 3.9 63.0 1.0
C A:ASP71 4.0 35.4 1.0
CG A:GLU72 4.1 46.4 1.0
CB A:GLU72 4.1 38.8 1.0
OE2 A:GLU72 4.2 51.9 1.0
CE1 A:HIS69 4.3 62.9 1.0
CA A:GLU72 4.3 36.3 1.0
CD A:GLU72 4.6 50.7 1.0

Sodium binding site 6 out of 9 in 3ddk

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Sodium binding site 6 out of 9 in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na912

b:48.6
occ:1.00
O A:HOH594 2.8 53.7 1.0
NE2 A:HIS199 2.9 31.1 1.0
O A:HOH565 3.1 36.7 1.0
O A:HOH655 3.2 22.9 1.0
CE1 A:HIS199 3.5 31.6 1.0
CG1 A:VAL210 3.5 29.4 1.0
CD2 A:HIS199 4.1 29.5 1.0
O A:HOH656 4.2 32.7 1.0
CD1 A:ILE296 4.5 22.8 1.0
CG1 A:ILE296 4.7 19.9 1.0
O A:HOH568 4.7 37.5 1.0
ND1 A:HIS199 4.7 31.1 1.0
CB A:SER295 4.8 23.8 1.0
CB A:VAL210 5.0 29.6 1.0

Sodium binding site 7 out of 9 in 3ddk

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Sodium binding site 7 out of 9 in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na913

b:31.2
occ:1.00
N A:GLU35 3.3 39.8 1.0
O A:HOH713 3.4 39.6 1.0
ND1 A:HIS399 3.4 28.3 1.0
CE1 A:HIS399 3.5 27.9 1.0
CD1 A:PHE34 3.8 32.2 1.0
CG A:GLU35 3.8 52.3 1.0
CA A:PHE34 3.8 37.2 1.0
NZ A:LYS436 4.0 41.7 1.0
CG A:HIS399 4.1 27.7 1.0
CB A:GLU35 4.1 44.8 1.0
C A:PHE34 4.1 38.1 1.0
CB A:PHE34 4.1 35.8 1.0
NE2 A:HIS399 4.1 29.9 1.0
CA A:GLU35 4.3 42.2 1.0
CG A:PHE34 4.4 33.7 1.0
CD2 A:HIS399 4.5 27.1 1.0
O A:GLU35 4.6 41.0 1.0
CE1 A:PHE34 4.7 32.3 1.0
O A:VAL33 4.8 38.8 1.0
CB A:HIS399 4.8 24.5 1.0
OE2 A:GLU35 4.9 61.2 1.0
CD A:GLU35 4.9 57.7 1.0
C A:GLU35 5.0 41.5 1.0
CD A:LYS436 5.0 37.9 1.0

Sodium binding site 8 out of 9 in 3ddk

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Sodium binding site 8 out of 9 in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na916

b:48.4
occ:1.00
OH A:TYR385 3.4 38.4 1.0
CE1 A:TYR385 4.2 35.3 1.0
CZ A:TYR385 4.3 37.0 1.0
CD1 A:LEU459 4.7 29.4 1.0
NE A:ARG455 4.9 40.7 1.0

Sodium binding site 9 out of 9 in 3ddk

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Sodium binding site 9 out of 9 in the Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na918

b:27.8
occ:1.00
O A:LYS315 2.7 46.8 1.0
O A:HOH659 3.0 42.9 1.0
C A:LYS315 3.7 42.8 1.0
C A:TYR314 3.7 35.9 1.0
N A:LYS315 3.8 38.0 1.0
CA A:TYR314 3.8 33.7 1.0
CB A:TYR314 4.1 30.3 1.0
CD1 A:TYR314 4.3 28.1 1.0
O A:TYR314 4.3 36.3 1.0
CA A:LYS315 4.4 41.8 1.0
N A:GLY316 4.6 41.8 1.0
CA A:GLY316 4.7 40.2 1.0
CG A:TYR314 4.7 29.3 1.0
O A:VAL313 4.8 33.5 1.0
C A:GLY316 4.9 39.3 1.0

Reference:

G.Campagnola, M.H.Weygandt, K.E.Scoggin, O.B.Peersen. Crystal Structure of Coxsackievirus B3 3DPOL Highlights Functional Importance of Residue 5 in Picornaviral Polymerases J.Virol. V. 82 9458 2008.
ISSN: ISSN 0022-538X
PubMed: 18632862
DOI: 10.1128/JVI.00647-08
Page generated: Tue Dec 15 06:08:39 2020

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