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Potassium in PDB 3zed: X-Ray Structure of the Birnavirus VP1-VP3 Complex

Enzymatic activity of X-Ray Structure of the Birnavirus VP1-VP3 Complex

All present enzymatic activity of X-Ray Structure of the Birnavirus VP1-VP3 Complex:
2.7.7.48;

Protein crystallography data

The structure of X-Ray Structure of the Birnavirus VP1-VP3 Complex, PDB code: 3zed was solved by M.W.Bahar, L.P.Sarin, S.C.Graham, J.Pang, D.H.Bamford, D.I.Stuart, J.M.Grimes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.13 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.270, 341.870, 59.700, 90.00, 90.00, 90.00
R / Rfree (%) 17.93 / 21.45

Potassium Binding Sites:

The binding sites of Potassium atom in the X-Ray Structure of the Birnavirus VP1-VP3 Complex (pdb code 3zed). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the X-Ray Structure of the Birnavirus VP1-VP3 Complex, PDB code: 3zed:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 3zed

Go back to Potassium Binding Sites List in 3zed
Potassium binding site 1 out of 6 in the X-Ray Structure of the Birnavirus VP1-VP3 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of X-Ray Structure of the Birnavirus VP1-VP3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1002

b:34.1
occ:1.00
 O A:ASN182 2.6 38.9 1.0
O A:GLY512 2.7 35.0 1.0
O A:VAL177 2.7 36.5 1.0
OD1 A:ASN409 2.8 28.8 1.0
OD1 A:ASN184 2.8 32.7 1.0
OD1 A:ASN514 2.8 31.5 1.0
C A:GLY512 3.7 34.5 1.0
CG A:ASN514 3.8 38.0 1.0
C A:VAL177 3.8 35.4 1.0
N A:ASN184 3.8 32.0 1.0
CG A:ASN409 3.8 34.4 1.0
C A:ASN182 3.8 38.7 1.0
CG A:ASN184 4.0 38.4 1.0
ND2 A:ASN182 4.0 34.2 1.0
C A:PRO183 4.0 35.2 1.0
CA A:ASN184 4.0 31.8 1.0
N A:ASN514 4.1 33.6 1.0
CG1 A:VAL177 4.2 32.3 1.0
CA A:ILE513 4.3 28.3 1.0
N A:ILE513 4.3 29.6 1.0
O A:PRO183 4.3 32.7 1.0
CB A:ASN409 4.4 25.0 1.0
O A:HOH2128 4.4 32.4 1.0
CA A:ASN409 4.4 27.3 1.0
ND2 A:ASN514 4.5 33.3 1.0
CA A:ALA178 4.5 31.9 1.0
N A:ALA178 4.5 31.9 1.0
CG A:ASN182 4.6 49.6 1.0
CA A:PRO183 4.6 32.2 1.0
O A:HOH2141 4.6 29.0 1.0
C A:ILE513 4.6 36.2 1.0
CB A:ASN182 4.6 31.2 1.0
CB A:ASN514 4.6 27.4 1.0
CB A:ASN184 4.6 24.7 1.0
O A:ALA178 4.7 32.9 1.0
CA A:GLY512 4.7 31.3 1.0
N A:PRO183 4.7 33.3 1.0
CA A:VAL177 4.8 30.7 1.0
C A:ALA178 4.8 35.3 1.0
CA A:ASN182 4.8 37.5 1.0
ND2 A:ASN409 4.9 32.9 1.0
CA A:ASN514 5.0 32.2 1.0
ND2 A:ASN184 5.0 28.0 1.0

Potassium binding site 2 out of 6 in 3zed

Go back to Potassium Binding Sites List in 3zed
Potassium binding site 2 out of 6 in the X-Ray Structure of the Birnavirus VP1-VP3 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of X-Ray Structure of the Birnavirus VP1-VP3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1003

b:37.9
occ:1.00
 O A:LYS704 2.5 42.1 1.0
O A:HOH2274 2.7 36.4 1.0
O A:PRO702 2.7 43.6 1.0
OE1 A:GLN203 2.7 41.0 1.0
OG1 A:THR698 2.9 36.7 1.0
O A:SER701 2.9 47.3 1.0
C A:PRO702 3.3 45.3 1.0
O A:HOH2440 3.3 51.1 1.0
CA A:PRO702 3.6 43.2 1.0
C A:LYS704 3.6 44.0 1.0
CD A:GLN203 3.7 43.5 1.0
NE2 A:GLN203 3.8 34.0 1.0
C A:SER701 3.9 48.0 1.0
N A:LYS704 4.0 42.5 1.0
O A:HOH2166 4.0 42.9 1.0
CB A:THR698 4.0 39.1 1.0
CG2 A:THR698 4.2 35.4 1.0
N A:THR698 4.2 36.8 1.0
N A:LYS703 4.3 42.2 1.0
N A:PRO702 4.3 44.4 1.0
CA A:LYS704 4.3 42.3 1.0
C A:LYS703 4.5 46.8 1.0
O A:ARG700 4.6 43.5 1.0
N A:THR705 4.7 42.0 1.0
O A:GLN351 4.7 42.0 1.0
CA A:THR698 4.7 35.6 1.0
CA A:LYS703 4.8 43.5 1.0
CB A:GLN697 4.9 42.1 1.0
CA A:THR705 4.9 41.0 1.0
CB A:LYS704 4.9 45.0 1.0
CB A:PRO702 5.0 45.8 1.0

Potassium binding site 3 out of 6 in 3zed

Go back to Potassium Binding Sites List in 3zed
Potassium binding site 3 out of 6 in the X-Ray Structure of the Birnavirus VP1-VP3 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of X-Ray Structure of the Birnavirus VP1-VP3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1002

b:43.7
occ:1.00
 O B:GLY512 2.6 44.9 1.0
O B:ASN182 2.6 45.4 1.0
O B:VAL177 2.7 40.0 1.0
OD1 B:ASN184 2.7 48.6 1.0
OD1 B:ASN409 2.8 39.5 1.0
OD1 B:ASN514 2.8 42.1 1.0
C B:GLY512 3.7 46.4 1.0
CG B:ASN514 3.7 46.4 1.0
C B:VAL177 3.8 41.3 1.0
CG B:ASN409 3.8 44.0 1.0
N B:ASN184 3.9 44.0 1.0
C B:ASN182 3.9 48.2 1.0
CG B:ASN184 3.9 51.4 1.0
ND2 B:ASN182 4.0 44.8 1.0
C B:PRO183 4.1 47.7 1.0
N B:ASN514 4.1 41.7 1.0
CA B:ASN184 4.1 42.8 1.0
CG1 B:VAL177 4.1 41.1 1.0
O B:HOH2071 4.2 38.0 1.0
CA B:ILE513 4.3 40.2 1.0
N B:ILE513 4.3 42.0 1.0
CB B:ASN409 4.4 36.7 1.0
O B:PRO183 4.4 47.8 1.0
CA B:ASN409 4.4 39.4 1.0
ND2 B:ASN514 4.4 40.2 1.0
CA B:ALA178 4.5 39.9 1.0
N B:ALA178 4.5 38.6 1.0
CG B:ASN182 4.6 58.1 1.0
C B:ILE513 4.6 45.0 1.0
CA B:PRO183 4.6 44.9 1.0
CB B:ASN514 4.6 37.6 1.0
CB B:ASN184 4.6 41.9 1.0
O B:HOH2081 4.6 40.6 1.0
CB B:ASN182 4.6 47.9 1.0
O B:ALA178 4.7 51.8 1.0
CA B:GLY512 4.7 43.9 1.0
N B:PRO183 4.7 45.9 1.0
CA B:VAL177 4.8 40.0 1.0
C B:ALA178 4.8 49.2 1.0
CA B:ASN182 4.9 46.1 1.0
ND2 B:ASN409 4.9 34.2 1.0
CA B:ASN514 4.9 40.9 1.0
ND2 B:ASN184 4.9 41.2 1.0

Potassium binding site 4 out of 6 in 3zed

Go back to Potassium Binding Sites List in 3zed
Potassium binding site 4 out of 6 in the X-Ray Structure of the Birnavirus VP1-VP3 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of X-Ray Structure of the Birnavirus VP1-VP3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1003

b:56.6
occ:1.00
 O B:LYS704 2.5 62.2 1.0
O B:PRO702 2.7 67.5 1.0
OE1 B:GLN203 2.7 60.4 1.0
O B:HOH2162 2.8 45.6 1.0
OG1 B:THR698 2.8 51.2 1.0
O B:SER701 2.8 65.9 1.0
C B:PRO702 3.3 68.8 1.0
O B:HOH2288 3.6 59.6 1.0
CA B:PRO702 3.6 62.9 1.0
CD B:GLN203 3.6 68.6 1.0
C B:LYS704 3.7 64.4 1.0
NE2 B:GLN203 3.8 54.7 1.0
C B:SER701 3.8 67.2 1.0
CB B:THR698 4.0 55.5 1.0
N B:LYS704 4.0 65.6 1.0
O B:HOH2098 4.1 57.2 1.0
CG2 B:THR698 4.1 44.8 1.0
N B:PRO702 4.2 63.7 1.0
N B:THR698 4.2 55.0 1.0
N B:LYS703 4.3 68.0 1.0
CA B:LYS704 4.4 64.0 1.0
O B:ARG700 4.5 61.3 1.0
C B:LYS703 4.6 71.9 1.0
CA B:THR698 4.7 53.4 1.0
O B:GLN351 4.7 54.4 1.0
N B:THR705 4.7 59.9 1.0
CA B:LYS703 4.9 68.9 1.0
CB B:GLN697 4.9 57.2 1.0
CB B:PRO702 4.9 66.0 1.0
CB B:LYS704 5.0 66.4 1.0
CA B:THR705 5.0 56.6 1.0

Potassium binding site 5 out of 6 in 3zed

Go back to Potassium Binding Sites List in 3zed
Potassium binding site 5 out of 6 in the X-Ray Structure of the Birnavirus VP1-VP3 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of X-Ray Structure of the Birnavirus VP1-VP3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1002

b:38.7
occ:1.00
 O C:GLY512 2.6 38.8 1.0
O C:ASN182 2.6 42.3 1.0
O C:VAL177 2.7 37.4 1.0
OD1 C:ASN514 2.8 43.2 1.0
OD1 C:ASN184 2.8 39.5 1.0
OD1 C:ASN409 2.8 34.8 1.0
C C:GLY512 3.6 42.1 1.0
CG C:ASN514 3.7 47.3 1.0
C C:VAL177 3.8 38.2 1.0
CG C:ASN409 3.8 44.2 1.0
N C:ASN184 3.8 38.5 1.0
C C:ASN182 3.9 42.6 1.0
CG C:ASN184 3.9 40.9 1.0
ND2 C:ASN182 4.0 41.0 1.0
C C:PRO183 4.0 41.5 1.0
N C:ASN514 4.1 37.5 1.0
CA C:ASN184 4.1 38.3 1.0
CG1 C:VAL177 4.2 36.6 1.0
CA C:ILE513 4.3 35.6 1.0
N C:ILE513 4.3 37.9 1.0
O C:PRO183 4.3 41.3 1.0
O C:HOH2073 4.4 40.2 1.0
CB C:ASN409 4.4 29.6 1.0
CA C:ASN409 4.4 34.3 1.0
ND2 C:ASN514 4.5 33.8 1.0
CA C:ALA178 4.5 36.7 1.0
CG C:ASN182 4.5 55.3 1.0
N C:ALA178 4.6 35.9 1.0
C C:ILE513 4.6 41.9 1.0
CA C:PRO183 4.6 38.4 1.0
CB C:ASN182 4.6 39.7 1.0
O C:HOH2082 4.6 33.5 1.0
CB C:ASN184 4.6 34.5 1.0
CB C:ASN514 4.6 34.2 1.0
O C:ALA178 4.7 43.1 1.0
CA C:GLY512 4.7 40.4 1.0
N C:PRO183 4.7 39.5 1.0
CA C:VAL177 4.8 34.9 1.0
C C:ALA178 4.8 43.1 1.0
CA C:ASN182 4.8 42.4 1.0
ND2 C:ASN409 4.9 33.5 1.0
CA C:ASN514 4.9 37.7 1.0
ND2 C:ASN184 5.0 32.2 1.0

Potassium binding site 6 out of 6 in 3zed

Go back to Potassium Binding Sites List in 3zed
Potassium binding site 6 out of 6 in the X-Ray Structure of the Birnavirus VP1-VP3 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of X-Ray Structure of the Birnavirus VP1-VP3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1003

b:70.5
occ:1.00
 O C:LYS704 2.4 71.4 1.0
OE1 C:GLN203 2.6 71.2 1.0
O C:HOH2163 2.7 54.7 1.0
O C:PRO702 2.8 74.4 1.0
O C:SER701 2.8 68.9 1.0
OG1 C:THR698 2.9 67.3 1.0
C C:PRO702 3.4 76.2 1.0
CD C:GLN203 3.5 75.1 1.0
C C:LYS704 3.5 75.5 1.0
CA C:PRO702 3.7 71.0 1.0
NE2 C:GLN203 3.7 61.5 1.0
C C:SER701 3.9 71.7 1.0
N C:LYS704 4.0 75.9 1.0
CB C:THR698 4.1 62.4 1.0
CG2 C:THR698 4.2 51.5 1.0
CA C:LYS704 4.3 74.4 1.0
N C:PRO702 4.3 70.6 1.0
N C:THR698 4.3 61.9 1.0
N C:LYS703 4.3 76.3 1.0
C C:LYS703 4.6 81.4 1.0
N C:THR705 4.6 73.5 1.0
O C:ARG700 4.6 65.1 1.0
O C:GLN351 4.7 60.0 1.0
CA C:THR698 4.8 60.2 1.0
CA C:THR705 4.8 71.4 1.0
CB C:LYS704 4.9 76.3 1.0
CA C:LYS703 4.9 78.4 1.0
CG C:GLN203 4.9 63.6 1.0

Reference:

M.W.Bahar, L.P.Sarin, S.C.Graham, J.Pang, D.H.Bamford, D.I.Stuart, J.M.Grimes. Structure of A VP1-VP3 Complex Suggests How Birnaviruses Package the VP1 Polymerase. J.Virol. V. 87 3229 2013.
ISSN: ISSN 0022-538X
PubMed: 23283942
DOI: 10.1128/JVI.02939-12
Page generated: Mon Aug 12 09:56:10 2024

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