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Strontium in PDB 2x53: Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr

Protein crystallography data

The structure of Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr, PDB code: 2x53 was solved by G.Sciara, C.Bebeacua, P.Bron, D.Tremblay, M.Ortiz-Lombardia, J.Lichiere, M.Van Heel, V.Campanacci, S.Moineau, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.31 / 3.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 300.278, 239.511, 274.782, 90.00, 124.36, 90.00
R / Rfree (%) 22.9 / 24.2

Strontium Binding Sites:

The binding sites of Strontium atom in the Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr (pdb code 2x53). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 6 binding sites of Strontium where determined in the Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr, PDB code: 2x53:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6;

Strontium binding site 1 out of 6 in 2x53

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Strontium binding site 1 out of 6 in the Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Sr1299

b:87.2
occ:1.00
OD1 S:ASN10 2.4 71.7 1.0
OD2 S:ASP12 3.0 76.9 1.0
O S:LEU11 3.3 67.6 1.0
OD1 S:ASP12 3.4 71.7 1.0
OD2 S:ASP246 3.4 65.0 1.0
CG S:ASP12 3.5 74.0 1.0
CG S:ASN10 3.5 72.2 1.0
OD1 S:ASP246 3.7 68.1 1.0
CG S:ASP246 4.0 65.8 1.0
ND2 S:ASN10 4.1 77.0 1.0
ND2 S:ASN241 4.5 64.2 1.0
C S:LEU11 4.5 66.0 1.0
CZ S:PHE91 4.7 62.5 1.0
CB S:ASN10 4.7 67.9 1.0
C S:ASN10 4.8 63.8 1.0
CA S:ASN10 4.9 63.4 1.0
N S:LEU11 4.9 61.1 1.0
CB S:ASP12 4.9 73.5 1.0

Strontium binding site 2 out of 6 in 2x53

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Strontium binding site 2 out of 6 in the Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Sr1299

b:80.3
occ:1.00
OD1 T:ASN10 2.4 62.6 1.0
OD2 T:ASP246 2.7 59.6 1.0
OD2 T:ASP12 3.0 67.0 1.0
O T:LEU11 3.3 60.1 1.0
CG T:ASN10 3.5 63.6 1.0
CG T:ASP246 3.6 60.0 1.0
OD1 T:ASP12 3.6 62.8 1.0
CG T:ASP12 3.6 64.8 1.0
OD1 T:ASP246 3.7 60.9 1.0
ND2 T:ASN10 4.2 67.3 1.0
C T:LEU11 4.5 59.8 1.0
ND2 T:ASN241 4.6 58.3 1.0
CZ T:PHE91 4.6 55.5 1.0
C T:ASN10 4.7 58.3 1.0
CB T:ASN10 4.7 61.0 1.0
CA T:ASN10 4.7 57.7 1.0
N T:LEU11 4.8 56.2 1.0
CB T:ASP12 5.0 65.1 1.0
CB T:ASP246 5.0 59.8 1.0

Strontium binding site 3 out of 6 in 2x53

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Strontium binding site 3 out of 6 in the Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Sr1299

b:82.3
occ:1.00
OD1 U:ASN10 2.4 69.5 1.0
OD2 U:ASP246 2.6 67.8 1.0
OD2 U:ASP12 3.2 77.9 1.0
OD1 U:ASP12 3.4 73.5 1.0
CG U:ASP246 3.5 67.4 1.0
O U:LEU11 3.5 69.8 1.0
CG U:ASN10 3.6 70.4 1.0
CG U:ASP12 3.7 76.0 1.0
OD1 U:ASP246 3.8 67.5 1.0
ND2 U:ASN10 4.2 74.8 1.0
ND2 U:ASN241 4.4 67.6 1.0
C U:LEU11 4.7 69.3 1.0
CB U:ASN10 4.8 66.9 1.0
CB U:ASP246 4.9 66.9 1.0
CA U:ASN10 4.9 63.4 1.0
C U:ASN10 5.0 64.9 1.0

Strontium binding site 4 out of 6 in 2x53

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Strontium binding site 4 out of 6 in the Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Sr1299

b:80.1
occ:1.00
OD1 V:ASN10 2.2 61.0 1.0
OD2 V:ASP12 3.3 65.3 1.0
CG V:ASN10 3.4 62.4 1.0
O V:LEU11 3.5 60.2 1.0
OD1 V:ASP246 3.6 63.3 1.0
OD1 V:ASP12 3.7 61.6 1.0
CG V:ASP12 3.8 63.3 1.0
OD2 V:ASP246 3.9 62.6 1.0
CG V:ASP246 3.9 62.2 1.0
ND2 V:ASN10 4.0 65.4 1.0
ND2 V:ASN241 4.3 61.6 1.0
CB V:ASN10 4.7 60.8 1.0
C V:LEU11 4.7 59.4 1.0
CZ V:PHE91 4.8 55.5 1.0
N V:LEU11 5.0 56.7 1.0
CA V:ASN10 5.0 57.5 1.0

Strontium binding site 5 out of 6 in 2x53

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Strontium binding site 5 out of 6 in the Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Sr1299

b:80.1
occ:1.00
OD1 W:ASN10 2.2 63.6 1.0
OD2 W:ASP246 2.6 62.5 1.0
CG W:ASN10 3.4 64.2 1.0
OD2 W:ASP12 3.4 76.2 1.0
CG W:ASP246 3.5 62.6 1.0
O W:LEU11 3.5 66.4 1.0
OD1 W:ASP12 3.6 71.6 1.0
OD1 W:ASP246 3.8 63.4 1.0
CG W:ASP12 3.8 74.2 1.0
ND2 W:ASN10 4.0 68.0 1.0
ND2 W:ASN241 4.6 61.4 1.0
CZ W:PHE91 4.6 55.3 1.0
CB W:ASN10 4.6 61.2 1.0
C W:LEU11 4.7 66.3 1.0
CA W:ASN10 4.8 58.3 1.0
CB W:ASP246 4.8 62.2 1.0
C W:ASN10 4.9 60.8 1.0
N W:LEU11 5.0 59.3 1.0

Strontium binding site 6 out of 6 in 2x53

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Strontium binding site 6 out of 6 in the Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Structure of the Phage P2 Baseplate in Its Activated Conformation with Sr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Sr1299

b:83.5
occ:1.00
OD1 X:ASN10 2.5 69.0 1.0
OD2 X:ASP246 2.7 66.2 1.0
OD2 X:ASP12 2.9 77.9 1.0
O X:LEU11 3.0 71.8 1.0
CG X:ASN10 3.3 69.4 1.0
CG X:ASP12 3.5 76.1 1.0
OD1 X:ASP12 3.5 72.4 1.0
ND2 X:ASN10 3.6 72.8 1.0
CG X:ASP246 3.6 66.5 1.0
OD1 X:ASP246 3.9 67.1 1.0
C X:LEU11 4.2 71.9 1.0
N X:LEU11 4.5 65.5 1.0
ND2 X:ASN241 4.5 63.4 1.0
CB X:ASN10 4.6 66.4 1.0
CZ X:PHE91 4.7 59.4 1.0
O X:ASP12 4.7 84.9 1.0
C X:ASN10 4.8 65.5 1.0
CB X:ASP12 4.8 79.2 1.0
CA X:ASN10 4.8 63.2 1.0
C X:ASP12 4.9 82.1 1.0
CB X:ASP246 4.9 66.6 1.0

Reference:

G.Sciara, C.Bebeacua, P.Bron, D.Tremblay, M.Ortiz-Lombardia, J.Lichiere, M.Van Heel, V.Campanacci, S.Moineau, C.Cambillau. Structure of Lactococcal Phage P2 Baseplate and Its Mechanism of Activation. Proc.Natl.Acad.Sci.Usa V. 107 6852 2010.
ISSN: ISSN 0027-8424
PubMed: 20351260
DOI: 10.1073/PNAS.1000232107
Page generated: Wed Dec 16 02:16:19 2020

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