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Bromine in PDB 1ijv: Human Beta-Defensin-1

Protein crystallography data

The structure of Human Beta-Defensin-1, PDB code: 1ijv was solved by D.M.Hoover, J.Lubkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.121, 47.243, 53.853, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.3

Other elements in 1ijv:

The structure of Human Beta-Defensin-1 also contains other interesting chemical elements:

Potassium (K) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Human Beta-Defensin-1 (pdb code 1ijv). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Human Beta-Defensin-1, PDB code: 1ijv:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 1ijv

Go back to Bromine Binding Sites List in 1ijv
Bromine binding site 1 out of 6 in the Human Beta-Defensin-1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Human Beta-Defensin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br105

b:19.6
occ:1.00
 O A:HOH235 3.0 33.2 1.0
O A:HOH236 3.1 18.0 1.0
N A:CYS12 3.3 7.7 1.0
CG2 A:VAL6 3.8 13.4 1.0
O A:HOH210 3.8 15.2 1.0
O A:HOH260 3.8 35.0 1.0
O A:HOH288 3.9 31.5 1.0
CB A:CYS12 3.9 7.8 1.0
CA A:GLN11 4.1 10.6 1.0
CA A:CYS12 4.1 6.5 1.0
C A:GLN11 4.2 8.2 1.0
CG A:GLN11 4.2 22.8 1.0
SG A:CYS12 4.2 7.2 1.0
O A:CYS12 4.2 9.5 1.0
OH A:TYR28 4.3 9.1 1.0
NE2 A:HIS2 4.4 7.7 1.0
CD2 A:HIS2 4.4 7.0 1.0
O A:HOH286 4.6 25.5 1.0
CB A:GLN11 4.7 17.2 1.0
C A:CYS12 4.7 7.5 1.0
O A:HOH308 4.8 35.5 1.0
O A:GLY10 4.9 10.0 1.0

Bromine binding site 2 out of 6 in 1ijv

Go back to Bromine Binding Sites List in 1ijv
Bromine binding site 2 out of 6 in the Human Beta-Defensin-1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Human Beta-Defensin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br106

b:42.0
occ:1.00
 O A:HOH330 2.0 49.8 1.0
O A:HOH346 2.5 27.0 0.5
O A:HOH231 3.4 14.9 1.0
N A:CYS17 3.4 10.8 1.0
CB A:CYS17 3.8 10.1 1.0
CE A:LYS33 3.8 13.6 1.0
CD A:LYS33 3.8 10.8 1.0
CA A:ALA16 4.0 16.5 1.0
SG A:CYS17 4.0 9.2 1.0
O A:HOH311 4.2 33.3 1.0
C A:ALA16 4.2 14.7 1.0
CA A:CYS17 4.2 8.7 1.0
CB A:ALA16 4.2 27.4 1.0
O A:HOH359 4.6 26.2 0.5
O A:CYS17 4.8 9.6 1.0

Bromine binding site 3 out of 6 in 1ijv

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Bromine binding site 3 out of 6 in the Human Beta-Defensin-1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Human Beta-Defensin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br108

b:11.4
occ:1.00
 O A:HOH267 3.3 21.5 1.0
O A:HOH276 3.3 27.3 1.0
OD1 A:ASN4 3.4 17.9 0.2
N A:ASP1 3.4 8.6 1.0
CA A:GLY25 3.7 7.6 1.0
N A:CYS5 3.7 7.0 1.0
O A:ASP1 3.7 6.7 1.0
O A:THR26 3.9 6.9 1.0
N A:THR26 3.9 7.1 1.0
CA A:CYS5 3.9 7.2 1.0
CB A:ASN4 3.9 7.5 0.2
CB A:CYS5 4.0 7.2 1.0
CG A:ASN4 4.1 9.3 0.2
CB A:ASN4 4.1 8.7 0.8
CB A:CYS34 4.1 6.6 1.0
C A:ASN4 4.2 7.0 0.2
C A:GLY25 4.2 6.5 1.0
C A:ASN4 4.3 7.6 0.8
SG A:CYS34 4.4 8.0 1.0
O A:GLN24 4.4 12.8 1.0
CG2 B:THR26 4.5 8.8 1.0
O A:HOH217 4.5 15.6 1.0
C A:ASP1 4.5 6.0 1.0
CA A:ASP1 4.6 6.1 1.0
O A:HOH287 4.6 28.9 1.0
CA A:ASN4 4.6 7.4 0.2
O A:ASN4 4.7 6.2 0.2
N A:GLY25 4.7 7.4 1.0
CA A:ASN4 4.8 8.7 0.8
C A:THR26 4.8 7.0 1.0
O A:HOH364 4.8 26.1 0.5
O A:ASN4 4.8 9.0 0.8
CA A:THR26 5.0 7.5 1.0

Bromine binding site 4 out of 6 in 1ijv

Go back to Bromine Binding Sites List in 1ijv
Bromine binding site 4 out of 6 in the Human Beta-Defensin-1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Human Beta-Defensin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br103

b:20.1
occ:1.00
 NE2 B:GLN24 1.8 48.3 0.5
CD B:GLN24 3.0 37.0 0.5
O B:HOH341 3.1 25.2 0.5
OD1 B:ASN4 3.3 19.7 0.5
OE1 B:GLN24 3.4 42.6 0.5
N B:ASP1 3.5 9.1 1.0
O B:GLN24 3.7 36.2 0.5
O B:ASP1 3.7 7.1 1.0
N B:CYS5 3.8 8.8 1.0
CA B:CYS5 3.9 8.4 1.0
CB B:CYS34 3.9 8.2 1.0
CB B:CYS5 3.9 9.5 1.0
O B:THR26 4.0 8.5 1.0
SG B:CYS34 4.0 8.9 1.0
CA B:GLY25 4.0 13.4 1.0
CB B:ASN4 4.1 9.0 0.5
O B:HOH224 4.1 21.8 1.0
CG B:ASN4 4.1 11.3 0.5
N B:THR26 4.1 9.1 1.0
C B:ASN4 4.3 8.3 0.5
C B:ASN4 4.3 8.4 0.5
CB B:ASN4 4.3 8.4 0.5
O B:HOH269 4.3 20.7 1.0
CG B:GLN24 4.4 35.6 0.5
C B:GLY25 4.4 8.1 1.0
C B:GLN24 4.4 25.9 0.5
N B:GLY25 4.6 17.7 1.0
C B:ASP1 4.6 6.0 1.0
CA B:ASP1 4.6 7.0 1.0
O B:GLN24 4.6 19.6 0.5
C B:GLN24 4.8 18.8 0.5
O B:ASN4 4.8 12.1 0.5
CA B:ASN4 4.8 8.8 0.5
O B:ASN4 4.8 10.2 0.5
CA B:ASN4 4.8 9.0 0.5
C B:THR26 4.9 7.9 1.0
SG B:CYS5 4.9 8.7 1.0

Bromine binding site 5 out of 6 in 1ijv

Go back to Bromine Binding Sites List in 1ijv
Bromine binding site 5 out of 6 in the Human Beta-Defensin-1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Human Beta-Defensin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br104

b:33.7
occ:0.25
 O B:HOH290 0.8 18.1 1.0
N B:CYS17 3.2 14.8 1.0
O B:HOH256 3.4 45.0 1.0
CA B:ALA16 3.6 17.2 1.0
CB B:ALA16 3.6 14.2 1.0
CE B:LYS33 3.9 25.0 1.0
C B:ALA16 3.9 16.2 1.0
CB B:CYS17 4.0 13.4 1.0
CD B:LYS33 4.0 17.9 1.0
O B:HOH249 4.0 26.8 1.0
SG B:CYS17 4.2 13.1 1.0
CA B:CYS17 4.2 13.9 1.0
O B:HOH303 4.5 30.7 1.0
O B:HOH362 4.5 23.3 0.5
O B:HOH334 4.6 38.8 0.5
O B:HOH333 4.9 29.9 0.5
O B:CYS17 4.9 14.5 1.0
N B:ALA16 4.9 19.9 1.0
O A:HOH284 4.9 36.1 1.0

Bromine binding site 6 out of 6 in 1ijv

Go back to Bromine Binding Sites List in 1ijv
Bromine binding site 6 out of 6 in the Human Beta-Defensin-1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Human Beta-Defensin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br107

b:41.0
occ:0.25
 O B:HOH289 1.6 15.2 1.0
O B:HOH350 1.9 38.7 0.5
O B:HOH242 2.0 30.2 1.0
O B:HOH258 2.3 29.8 1.0
O B:HOH211 2.9 27.0 1.0
O B:HOH219 3.0 26.2 1.0
O B:CYS12 3.8 11.1 1.0
OH B:TYR28 4.0 12.3 1.0
N B:CYS12 4.1 8.4 1.0
O B:HOH261 4.3 36.4 1.0
CB B:CYS12 4.3 8.2 1.0
CA B:CYS12 4.6 7.7 1.0
C B:CYS12 4.7 9.1 1.0
O B:HOH255 4.8 34.0 1.0

Reference:

D.M.Hoover, O.Chertov, J.Lubkowski. The Structure of Human Beta-Defensin-1: New Insights Into Structural Properties of Beta-Defensins. J.Biol.Chem. V. 276 39021 2001.
ISSN: ISSN 0021-9258
PubMed: 11486002
DOI: 10.1074/JBC.M103830200
Page generated: Mon Jul 7 03:19:03 2025

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