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Bromine in PDB 1sr4: Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin

Protein crystallography data

The structure of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin, PDB code: 1sr4 was solved by D.Nesic, Y.Hsu, C.E.Stebbins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.652, 75.653, 121.637, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.4

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin (pdb code 1sr4). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 26 binding sites of Bromine where determined in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin, PDB code: 1sr4:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 26 in 1sr4

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Bromine binding site 1 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br503

b:41.0
occ:1.00
 O A:HOH613 3.0 40.2 1.0
ND2 A:ASN112 3.2 11.2 1.0
CB A:ASN112 3.8 9.2 1.0
CA A:SER133 3.8 13.8 1.0
O A:GLN132 3.9 10.6 1.0
CG A:GLN132 4.0 11.0 1.0
CG A:ASN112 4.0 12.7 1.0
CB A:SER133 4.2 14.4 1.0
N A:SER133 4.3 12.0 1.0
C A:GLN132 4.3 11.5 1.0
O A:HOH567 4.4 27.0 1.0
CD A:GLN132 4.4 12.7 1.0
OG A:SER133 4.5 16.8 1.0
NE2 A:GLN132 4.6 10.9 1.0
O A:HOH621 4.7 31.7 1.0
O A:HOH568 4.8 17.2 1.0
O A:HOH559 4.9 20.4 1.0
C A:SER133 4.9 14.1 1.0
OE1 A:GLN132 5.0 13.7 1.0
O A:SER133 5.0 13.4 1.0
CB A:GLN132 5.0 8.0 1.0

Bromine binding site 2 out of 26 in 1sr4

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Bromine binding site 2 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br505

b:44.0
occ:1.00
 O A:HOH585 2.9 14.4 1.0
O A:HOH541 3.1 9.5 1.0
NE1 A:TRP100 3.5 12.1 1.0
CE3 A:TRP91 3.9 28.8 1.0
CZ2 A:TRP100 4.0 15.4 1.0
CE2 A:TRP100 4.1 13.3 1.0
CZ3 A:TRP91 4.1 31.5 1.0
CD1 A:TRP98 4.2 17.2 1.0
CB A:TRP98 4.3 11.6 1.0
O A:HOH665 4.6 47.7 1.0
CD1 A:TRP100 4.6 13.2 1.0
N A:TRP98 4.6 11.8 1.0
CG A:TRP98 4.7 16.5 1.0
O A:TRP98 4.7 11.1 1.0
OD1 A:ASN97 4.8 18.6 1.0
CA A:TRP98 5.0 12.5 1.0

Bromine binding site 3 out of 26 in 1sr4

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Bromine binding site 3 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br507

b:72.6
occ:1.00
 O A:HOH620 3.1 30.1 1.0
NE2 A:GLN132 3.5 10.9 1.0
O A:HOH568 3.5 17.2 1.0
CG A:PRO74 3.5 11.6 1.0
O A:HOH605 4.0 30.6 1.0
CD A:PRO74 4.0 12.5 1.0
O A:HOH567 4.0 27.0 1.0
N A:PRO74 4.1 13.3 1.0
CD1 A:LEU217 4.2 9.7 1.0
CA A:PRO74 4.2 11.2 1.0
CB A:GLU73 4.3 21.7 1.0
CG A:GLU73 4.3 30.5 1.0
CB A:PRO74 4.4 12.1 1.0
C A:GLU73 4.6 16.2 1.0
CD2 A:LEU217 4.6 10.5 1.0
CD A:GLN132 4.8 12.7 1.0

Bromine binding site 4 out of 26 in 1sr4

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Bromine binding site 4 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br508

b:66.8
occ:1.00
 ND2 A:ASN76 3.3 17.4 1.0
OG A:SER72 3.5 24.6 1.0
CG B:GLU56 3.7 31.5 1.0
N B:GLU56 3.8 18.2 1.0
CB A:SER72 3.9 21.9 1.0
OD1 A:ASN76 3.9 17.4 1.0
O A:SER72 4.0 21.6 1.0
CG A:ASN76 4.1 16.3 1.0
C A:SER72 4.2 19.5 1.0
C B:GLY55 4.2 17.0 1.0
CA B:GLU56 4.3 19.5 1.0
OE2 B:GLU56 4.4 39.6 1.0
CA B:GLY55 4.4 16.2 1.0
CB B:GLU56 4.4 24.1 1.0
CD B:GLU56 4.5 35.5 1.0
N A:GLU73 4.6 19.7 1.0
CA A:SER72 4.7 20.6 1.0
CA A:GLU73 4.8 18.4 1.0
OE1 A:GLU73 4.8 37.0 1.0

Bromine binding site 5 out of 26 in 1sr4

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Bromine binding site 5 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br510

b:70.6
occ:1.00
 O A:HOH611 3.0 28.2 1.0
N A:LEU93 3.2 14.4 1.0
CA A:ALA92 3.8 16.3 1.0
CG A:LEU93 3.8 16.0 1.0
CB A:LEU93 3.9 16.9 1.0
C A:ALA92 3.9 15.2 1.0
CA A:LEU93 4.1 15.5 1.0
CB A:ALA92 4.4 15.0 1.0
CD1 A:LEU93 4.4 17.3 1.0
O A:TRP91 4.5 13.2 1.0
N A:ALA94 4.8 17.4 1.0
N A:ALA92 5.0 13.7 1.0
C A:LEU93 5.0 16.9 1.0

Bromine binding site 6 out of 26 in 1sr4

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Bromine binding site 6 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br511

b:80.0
occ:1.00
 N A:LYS95 3.2 17.5 1.0
NZ A:LYS95 3.2 36.6 1.0
CE A:LYS95 3.6 33.7 1.0
CG A:LYS95 3.7 26.5 1.0
CA A:ALA94 3.7 18.6 1.0
O A:HOH671 3.9 41.4 1.0
CB A:LYS95 3.9 23.0 1.0
C A:ALA94 4.0 18.7 1.0
CB A:ALA94 4.1 21.1 1.0
CA A:LYS95 4.2 19.5 1.0
CD A:LYS95 4.2 32.6 1.0
O A:HOH659 4.4 36.4 1.0
O A:LEU93 4.9 15.6 1.0
N A:ALA94 5.0 17.4 1.0

Bromine binding site 7 out of 26 in 1sr4

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Bromine binding site 7 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br515

b:80.0
occ:1.00
 OH A:TYR141 3.4 28.2 1.0
CE2 A:TYR141 3.9 22.4 1.0
CZ A:TYR141 4.2 25.3 1.0
CZ2 A:TRP98 4.6 18.7 1.0
O A:HOH632 4.6 33.8 1.0

Bromine binding site 8 out of 26 in 1sr4

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Bromine binding site 8 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br517

b:34.1
occ:1.00
 NH1 A:ARG67 3.2 24.7 1.0
N A:LEU70 3.4 17.9 1.0
NH2 A:ARG67 3.6 27.5 1.0
C A:LEU70 3.7 16.5 1.0
N A:PRO71 3.7 17.5 1.0
O A:LEU70 3.8 18.0 1.0
CZ A:ARG67 3.8 27.1 1.0
NH2 B:ARG100 3.9 11.8 1.0
CA A:VAL69 4.0 19.4 1.0
O A:HOH566 4.0 20.1 1.0
CA A:PRO71 4.0 17.8 1.0
CG1 A:VAL69 4.0 21.9 1.0
C A:VAL69 4.2 18.6 1.0
CA A:LEU70 4.2 16.1 1.0
CB A:VAL69 4.5 20.5 1.0
CD A:PRO71 4.7 16.7 1.0
O A:GLN68 4.7 15.4 1.0
O A:HOH590 4.7 35.6 1.0
CG A:PRO71 4.8 20.3 1.0
CB A:PRO71 4.9 18.1 1.0
CG2 A:VAL69 5.0 23.1 1.0

Bromine binding site 9 out of 26 in 1sr4

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Bromine binding site 9 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br518

b:58.1
occ:1.00
 ND2 A:ASN58 3.0 19.8 1.0
O A:HOH561 3.3 18.9 1.0
O A:HOH588 3.6 27.1 1.0
CB A:SER61 3.7 16.6 1.0
CA A:SER61 4.0 14.1 1.0
CG A:ASN58 4.0 20.4 1.0
CB A:ASN58 4.0 19.9 1.0
O A:LEU60 4.8 13.4 1.0
N A:SER61 4.9 12.8 1.0
ND2 A:ASN66 5.0 18.9 1.0

Bromine binding site 10 out of 26 in 1sr4

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Bromine binding site 10 out of 26 in the Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of the Haemophilus Ducreyi Cytolethal Distending Toxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br525

b:71.2
occ:1.00
 N A:ARG124 3.3 19.9 1.0
CA A:HIS123 3.8 23.3 1.0
CG A:ARG124 3.9 22.0 1.0
C A:HIS123 4.0 21.3 1.0
CB A:ARG124 4.0 19.8 1.0
CB A:HIS123 4.0 26.5 1.0
CA A:ARG124 4.3 19.7 1.0
CD2 A:HIS123 4.3 33.3 1.0
O A:HOH593 4.3 29.0 1.0
O A:HOH680 4.4 49.8 1.0
CD A:ARG124 4.4 23.0 1.0
CG A:HIS123 4.4 30.8 1.0
O A:LYS122 4.8 24.2 1.0
NE A:ARG124 4.9 24.2 1.0

Reference:

D.Nesic, Y.Hsu, C.E.Stebbins. Assembly and Function of A Bacterial Genotoxin Nature V. 429 429 2004.
ISSN: ISSN 0028-0836
PubMed: 15164065
DOI: 10.1038/NATURE02532
Page generated: Wed Jul 10 17:20:48 2024

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