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Bromine in PDB 3u6x: Phage TP901-1 Baseplate Tripod

Protein crystallography data

The structure of Phage TP901-1 Baseplate Tripod, PDB code: 3u6x was solved by D.Veesler, S.Spinelli, J.Mahony, J.Lichiere, S.Blangy, G.Bricogne, P.Legrand, M.Ortiz-Lombardia, V.I.Campanacci, D.Van Sinderen, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.74 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 149.960, 237.420, 152.210, 90.00, 115.67, 90.00
R / Rfree (%) 17.8 / 20.6

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Bromine atom in the Phage TP901-1 Baseplate Tripod (pdb code 3u6x). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 18 binding sites of Bromine where determined in the Phage TP901-1 Baseplate Tripod, PDB code: 3u6x:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 18 in 3u6x

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Bromine binding site 1 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br201

b:84.1
occ:1.00
 O L:HOH228 3.7 46.2 1.0
O E:TRP129 3.7 31.4 1.0
O F:TRP129 3.8 34.1 1.0
O D:TRP129 3.8 26.8 1.0
OD1 D:ASN130 3.9 35.9 1.0
OD1 F:ASN130 3.9 33.7 1.0
O F:HOH253 4.0 43.2 1.0
OD1 E:ASN130 4.0 28.4 1.0
O D:HOH368 4.0 62.0 1.0
C E:TRP129 4.1 31.3 1.0
C D:TRP129 4.2 27.5 1.0
C F:TRP129 4.3 33.1 1.0
CB F:TRP129 4.3 27.2 1.0
CB E:TRP129 4.3 26.1 1.0
CB D:TRP129 4.4 22.4 1.0
N E:ASN130 4.6 27.1 1.0
CA D:ASN130 4.6 22.6 1.0
CA E:ASN130 4.6 25.7 1.0
N D:ASN130 4.6 23.8 1.0
CA F:ASN130 4.7 27.8 1.0
N F:ASN130 4.7 28.0 1.0
CA E:TRP129 4.9 27.6 1.0
CG D:ASN130 4.9 40.8 1.0
CA D:TRP129 4.9 24.9 1.0
CA F:TRP129 5.0 28.7 1.0
CG E:ASN130 5.0 38.4 1.0

Bromine binding site 2 out of 18 in 3u6x

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Bromine binding site 2 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br201

b:80.8
occ:1.00
 O C:HOH3419 3.6 28.0 1.0
O C:HOH3409 4.0 24.7 1.0
OD1 C:ASN106 4.0 39.0 1.0
N E:ARG118 4.1 34.9 1.0
ND2 C:ASN106 4.2 33.6 1.0
CG E:ARG118 4.3 30.8 1.0
O C:HOH3432 4.4 51.3 1.0
CB E:ARG118 4.4 28.7 1.0
CD E:ARG118 4.4 35.5 1.0
CG C:ASN106 4.6 44.0 1.0
NH2 C:ARG107 4.6 92.7 1.0
CB E:ASN117 4.7 37.0 1.0
CA E:ASN117 4.7 38.4 1.0
NE E:ARG118 4.7 35.8 1.0
CA E:ARG118 4.9 33.0 1.0
C E:ASN117 4.9 42.5 1.0
OD1 E:ASN117 4.9 52.2 1.0

Bromine binding site 3 out of 18 in 3u6x

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Bromine binding site 3 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br202

b:0.4
occ:1.00
 O E:HOH414 2.8 39.0 1.0
OD2 F:ASP135 3.0 52.0 1.0
NE E:ARG155 3.4 29.4 1.0
CG E:ARG155 3.8 27.0 1.0
CG F:ASP135 3.9 39.9 1.0
CD E:ARG155 3.9 25.3 1.0
CE2 F:PHE145 3.9 30.1 1.0
CE1 F:HIS133 4.0 25.1 1.0
CZ F:PHE145 4.0 28.7 1.0
OD1 F:ASP135 4.1 40.9 1.0
CG2 E:VAL126 4.2 28.0 1.0
CD2 F:PHE145 4.2 27.3 1.0
CZ E:ARG155 4.3 48.2 1.0
CE1 F:PHE145 4.4 30.0 1.0
NH2 E:ARG155 4.5 35.8 1.0
NE2 F:HIS133 4.5 25.7 1.0
CG F:PHE145 4.6 27.5 1.0
NH1 F:ARG118 4.6 31.9 1.0
CD1 F:PHE145 4.7 30.0 1.0
CD F:ARG118 4.7 45.6 1.0
OG F:SER120 4.8 32.3 1.0
O E:HOH326 4.8 31.9 1.0
CB E:ARG155 5.0 22.0 1.0

Bromine binding site 4 out of 18 in 3u6x

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Bromine binding site 4 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Br201

b:61.8
occ:1.00
 O I:TRP129 3.4 39.4 1.0
O G:TRP129 3.4 40.8 1.0
O H:TRP129 3.4 35.5 1.0
OD1 I:ASN130 3.9 34.2 1.0
C H:TRP129 4.0 34.8 1.0
C I:TRP129 4.0 39.1 1.0
OD1 G:ASN130 4.0 45.8 1.0
C G:TRP129 4.0 40.5 1.0
OD1 H:ASN130 4.0 34.6 1.0
CB H:TRP129 4.2 29.3 1.0
CB I:TRP129 4.3 35.5 1.0
CB G:TRP129 4.3 35.3 1.0
CA I:ASN130 4.4 33.3 1.0
N H:ASN130 4.5 29.7 1.0
CA H:ASN130 4.5 28.1 1.0
N I:ASN130 4.5 33.7 1.0
CA G:ASN130 4.6 34.6 1.0
N G:ASN130 4.6 35.2 1.0
CA H:TRP129 4.7 31.2 1.0
CA I:TRP129 4.8 36.5 1.0
CA G:TRP129 4.8 36.2 1.0
CG I:ASN130 4.9 46.5 1.0

Bromine binding site 5 out of 18 in 3u6x

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Bromine binding site 5 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br201

b:89.1
occ:1.00
 O H:HOH403 3.4 40.3 1.0
NH2 H:ARG107 3.5 61.5 1.0
CB A:ARG118 3.9 30.5 1.0
N A:ARG118 3.9 33.4 1.0
OD1 H:ASN106 3.9 36.0 1.0
O H:HOH304 4.1 27.4 1.0
ND2 H:ASN106 4.2 38.1 1.0
O A:HOH299 4.2 52.7 1.0
CZ H:ARG107 4.3 64.2 1.0
NH1 H:ARG107 4.3 46.4 1.0
CA A:ASN117 4.6 37.0 1.0
CG H:ASN106 4.6 45.7 1.0
CA A:ARG118 4.6 32.8 1.0
OD1 A:ASN117 4.6 59.2 1.0
CB A:ASN117 4.6 38.1 1.0
CD A:ARG118 4.6 33.4 1.0
NE A:ARG118 4.7 34.6 1.0
C A:ASN117 4.8 39.6 1.0
CG A:ARG118 4.9 32.8 1.0

Bromine binding site 6 out of 18 in 3u6x

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Bromine binding site 6 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br202

b:0.9
occ:1.00
 O H:HOH308 3.7 38.1 1.0
N H:GLY73 3.7 36.1 1.0
O H:HOH389 3.9 58.9 1.0
NH2 A:ARG118 3.9 40.7 1.0
CA H:GLY72 4.0 33.8 1.0
OE1 A:GLN143 4.1 65.6 1.0
CB H:ASN106 4.1 30.4 1.0
O A:HOH303 4.2 56.7 1.0
OE2 H:GLU70 4.3 70.7 1.0
NE2 A:GLN143 4.3 65.4 1.0
C H:GLY72 4.4 38.3 1.0
N H:ASN106 4.6 36.8 1.0
O H:HOH432 4.6 62.0 1.0
CD A:GLN143 4.6 74.1 1.0
CA H:ASN106 4.7 36.0 1.0
O H:HOH402 4.7 53.8 1.0
CA H:GLY73 4.7 35.0 1.0
CG H:ASN106 4.9 45.7 1.0
CZ A:ARG118 4.9 46.3 1.0
ND2 H:ASN106 5.0 38.1 1.0

Bromine binding site 7 out of 18 in 3u6x

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Bromine binding site 7 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Br201

b:83.5
occ:1.00
 O D:HOH437 3.6 39.5 1.0
O I:HOH349 3.9 60.1 1.0
CB I:ARG118 3.9 39.9 1.0
O D:HOH319 3.9 36.4 1.0
N I:ARG118 3.9 41.8 1.0
OD1 D:ASN106 4.1 38.8 1.0
ND2 D:ASN106 4.4 28.2 1.0
OD1 I:ASN117 4.6 72.7 1.0
NH2 D:ARG107 4.6 0.6 1.0
CA I:ARG118 4.6 41.5 1.0
CD I:ARG118 4.6 44.4 1.0
CA I:ASN117 4.7 41.9 1.0
CB I:ASN117 4.7 41.6 1.0
NE I:ARG118 4.7 42.6 1.0
CG D:ASN106 4.8 41.2 1.0
C I:ASN117 4.8 46.7 1.0
CG I:ARG118 4.9 41.0 1.0

Bromine binding site 8 out of 18 in 3u6x

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Bromine binding site 8 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Br201

b:80.1
occ:1.00
 NH2 K:ARG107 3.5 52.7 1.0
O O:HOH418 3.6 31.2 1.0
CB O:ARG118 3.9 33.2 1.0
O K:HOH308 4.0 28.7 1.0
N O:ARG118 4.0 38.2 1.0
OD1 K:ASN106 4.1 45.7 1.0
O O:HOH401 4.2 55.0 1.0
ND2 K:ASN106 4.3 38.5 1.0
CD O:ARG118 4.5 44.7 1.0
OD1 O:ASN117 4.6 70.3 1.0
NE O:ARG118 4.6 40.0 1.0
CG K:ASN106 4.7 49.7 1.0
CA O:ARG118 4.7 36.8 1.0
CA O:ASN117 4.7 41.0 1.0
CZ K:ARG107 4.7 63.2 1.0
CB O:ASN117 4.7 36.7 1.0
CG O:ARG118 4.8 38.6 1.0
C O:ASN117 4.9 44.8 1.0

Bromine binding site 9 out of 18 in 3u6x

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Bromine binding site 9 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Br201

b:96.0
occ:1.00
 NH2 N:ARG107 3.3 53.2 1.0
O R:HOH2568 3.4 39.7 1.0
O N:HOH307 4.0 37.6 1.0
CB R:ARG118 4.0 45.4 1.0
OD1 N:ASN106 4.0 48.4 1.0
N R:ARG118 4.0 47.3 1.0
ND2 N:ASN106 4.3 46.5 1.0
O N:HOH407 4.3 72.2 1.0
O N:HOH431 4.3 63.1 1.0
O R:HOH2507 4.4 73.6 1.0
O N:HOH459 4.5 74.4 1.0
CG N:ASN106 4.6 51.6 1.0
CZ N:ARG107 4.6 65.1 1.0
OD1 R:ASN117 4.6 61.4 1.0
CD R:ARG118 4.7 52.0 1.0
CA R:ASN117 4.7 48.8 1.0
NE R:ARG118 4.7 47.7 1.0
CA R:ARG118 4.7 46.9 1.0
CB R:ASN117 4.8 47.8 1.0
C R:ASN117 4.9 52.3 1.0
CG R:ARG118 5.0 46.9 1.0

Bromine binding site 10 out of 18 in 3u6x

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Bromine binding site 10 out of 18 in the Phage TP901-1 Baseplate Tripod


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Phage TP901-1 Baseplate Tripod within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Br201

b:90.2
occ:1.00
 O N:HOH429 3.6 50.3 1.0
O O:TRP129 3.7 32.2 1.0
O N:TRP129 3.8 30.9 1.0
OD1 O:ASN130 3.8 30.8 1.0
O M:TRP129 3.9 33.9 1.0
OD1 M:ASN130 4.0 36.1 1.0
OD1 N:ASN130 4.1 38.8 1.0
O O:HOH330 4.1 47.6 1.0
O M:HOH215 4.2 45.8 1.0
C O:TRP129 4.2 32.9 1.0
C N:TRP129 4.2 31.3 1.0
CB N:TRP129 4.3 26.9 1.0
CB O:TRP129 4.3 29.3 1.0
C M:TRP129 4.3 33.4 1.0
CB M:TRP129 4.4 29.9 1.0
N N:ASN130 4.6 27.0 1.0
CA O:ASN130 4.7 28.1 1.0
N O:ASN130 4.7 29.1 1.0
CA N:ASN130 4.7 26.8 1.0
CA M:ASN130 4.7 27.8 1.0
N M:ASN130 4.8 27.9 1.0
CA N:TRP129 4.9 29.0 1.0
CA O:TRP129 4.9 29.6 1.0
CG O:ASN130 4.9 42.9 1.0

Reference:

D.Veesler, S.Spinelli, J.Mahony, J.Lichiere, S.Blangy, G.Bricogne, P.Legrand, M.Ortiz-Lombardia, V.Campanacci, D.Van Sinderen, C.Cambillau. Structure of the Phage TP901-1 1.8 Mda Baseplate Suggests An Alternative Host Adhesion Mechanism. Proc.Natl.Acad.Sci.Usa V. 109 8954 2012.
ISSN: ISSN 0027-8424
PubMed: 22611190
DOI: 10.1073/PNAS.1200966109
Page generated: Sat Dec 12 02:16:07 2020

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