Bromine in PDB 2bvl: Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion

The structure of Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion, PDB code: 2bvl was solved by D.J.Reinert, T.Jank, K.Aktories, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.2
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.010, 95.797, 112.915, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.4

The structure of Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Tantalum	(Ta)	24 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion (pdb code 2bvl). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 48 binding sites of Bromine where determined in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion, PDB code: 2bvl:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:45.4 occ:0.25 BR1 A:TBR1548 0.0 45.4 0.2 TA1 A:TBR1548 2.6 45.5 0.2 TA2 A:TBR1548 2.7 44.5 0.2 BR2 A:TBR1548 3.5 47.9 0.2 BR3 A:TBR1548 3.7 47.0 0.2 BR6 A:TBR1548 3.7 46.3 0.2 BR5 A:TBR1548 3.7 46.4 0.2 TA3 A:TBR1548 4.1 49.0 0.2 TA5 A:TBR1548 4.3 47.7 0.2

Bromine binding site 2 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:47.9 occ:0.25 BR2 A:TBR1548 0.0 47.9 0.2 TA1 A:TBR1548 2.6 45.5 0.2 TA3 A:TBR1548 2.6 49.0 0.2 BR1 A:TBR1548 3.5 45.4 0.2 BRC A:TBR1548 3.7 48.6 0.2 BR5 A:TBR1548 3.7 46.4 0.2 BR4 A:TBR1548 3.8 46.4 0.2 TA2 A:TBR1548 4.1 44.5 0.2 TA6 A:TBR1548 4.3 46.9 0.2

Bromine binding site 3 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:47.0 occ:0.25 BR3 A:TBR1548 0.0 47.0 0.2 TA5 A:TBR1548 2.6 47.7 0.2 TA1 A:TBR1548 2.7 45.5 0.2 BR6 A:TBR1548 3.6 46.3 0.2 BR4 A:TBR1548 3.6 46.4 0.2 BRB A:TBR1548 3.6 47.5 0.2 BR1 A:TBR1548 3.7 45.4 0.2 TA2 A:TBR1548 4.2 44.5 0.2 TA6 A:TBR1548 4.2 46.9 0.2

Bromine binding site 4 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:46.4 occ:0.25 BR4 A:TBR1548 0.0 46.4 0.2 TA6 A:TBR1548 2.7 46.9 0.2 TA1 A:TBR1548 2.7 45.5 0.2 BRB A:TBR1548 3.6 47.5 0.2 BR3 A:TBR1548 3.6 47.0 0.2 BRC A:TBR1548 3.7 48.6 0.2 BR2 A:TBR1548 3.8 47.9 0.2 TA5 A:TBR1548 4.2 47.7 0.2 TA3 A:TBR1548 4.2 49.0 0.2

Bromine binding site 5 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:46.4 occ:0.25 BR5 A:TBR1548 0.0 46.4 0.2 TA2 A:TBR1548 2.7 44.5 0.2 TA3 A:TBR1548 2.7 49.0 0.2 O A:HOH2017 3.3 53.0 1.0 BRA A:TBR1548 3.6 45.6 0.2 BR9 A:TBR1548 3.6 49.2 0.2 BR2 A:TBR1548 3.7 47.9 0.2 BR1 A:TBR1548 3.7 45.4 0.2 TA4 A:TBR1548 4.1 50.0 0.2 TA1 A:TBR1548 4.3 45.5 0.2 OE2 A:GLU33 4.3 45.0 1.0 OD2 A:ASP29 4.9 33.2 1.0 CG A:ASP29 5.0 31.2 1.0

Bromine binding site 6 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:46.3 occ:0.25 BR6 A:TBR1548 0.0 46.3 0.2 TA5 A:TBR1548 2.7 47.7 0.2 TA2 A:TBR1548 2.7 44.5 0.2 BR3 A:TBR1548 3.6 47.0 0.2 BRA A:TBR1548 3.6 45.6 0.2 BR1 A:TBR1548 3.7 45.4 0.2 BR7 A:TBR1548 3.7 48.6 0.2 ND2 A:ASN36 3.8 47.1 1.0 CG A:GLU33 3.9 40.3 1.0 TA1 A:TBR1548 4.2 45.5 0.2 TA4 A:TBR1548 4.2 50.0 0.2 CA A:GLU33 4.7 38.8 1.0 OE2 A:GLU33 4.9 45.0 1.0 CB A:GLU33 4.9 38.5 1.0 CD A:GLU33 4.9 42.6 1.0 N A:GLU33 5.0 38.1 1.0

Bromine binding site 7 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:48.6 occ:0.25 BR7 A:TBR1548 0.0 48.6 0.2 TA4 A:TBR1548 2.6 50.0 0.2 TA5 A:TBR1548 2.6 47.7 0.2 CG A:GLU32 3.0 40.5 1.0 CB A:GLU32 3.5 37.6 1.0 BR8 A:TBR1548 3.6 48.3 0.2 BRB A:TBR1548 3.7 47.5 0.2 BR6 A:TBR1548 3.7 46.3 0.2 BRA A:TBR1548 3.7 45.6 0.2 TA6 A:TBR1548 4.2 46.9 0.2 ND2 A:ASN36 4.2 47.1 1.0 TA2 A:TBR1548 4.3 44.5 0.2 CD A:GLU32 4.3 43.9 1.0 OE2 A:GLU32 4.6 44.6 1.0 C A:GLU32 4.7 37.5 1.0 CA A:GLU32 4.7 37.2 1.0 N A:GLU33 4.8 38.1 1.0 O A:GLU32 5.0 37.4 1.0

Bromine binding site 8 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:48.3 occ:0.25 BR8 A:TBR1548 0.0 48.3 0.2 TA4 A:TBR1548 2.7 50.0 0.2 TA6 A:TBR1548 2.7 46.9 0.2 BR7 A:TBR1548 3.6 48.6 0.2 BR9 A:TBR1548 3.7 49.2 0.2 BRC A:TBR1548 3.7 48.6 0.2 BRB A:TBR1548 3.7 47.5 0.2 TA5 A:TBR1548 4.1 47.7 0.2 TA3 A:TBR1548 4.2 49.0 0.2 NH1 A:ARG6 4.6 38.5 1.0

Bromine binding site 9 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:49.2 occ:0.25 BR9 A:TBR1548 0.0 49.2 0.2 TA4 A:TBR1548 2.7 50.0 0.2 TA3 A:TBR1548 2.7 49.0 0.2 OD1 A:ASP29 3.1 32.6 1.0 CG A:ASP29 3.6 31.2 1.0 BRC A:TBR1548 3.6 48.6 0.2 BR5 A:TBR1548 3.6 46.4 0.2 BR8 A:TBR1548 3.7 48.3 0.2 BRA A:TBR1548 3.7 45.6 0.2 OD2 A:ASP29 3.9 33.2 1.0 TA2 A:TBR1548 4.2 44.5 0.2 TA6 A:TBR1548 4.2 46.9 0.2 NH1 A:ARG6 4.3 38.5 1.0 CB A:ASP29 4.4 30.4 1.0 CA A:ASP29 4.9 30.4 1.0

Bromine binding site 10 out of 48 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1548 b:45.6 occ:0.25 BRA A:TBR1548 0.0 45.6 0.2 TA4 A:TBR1548 2.7 50.0 0.2 TA2 A:TBR1548 2.7 44.5 0.2 O A:ASP29 3.2 30.8 1.0 OE2 A:GLU33 3.2 45.0 1.0 CG A:GLU33 3.5 40.3 1.0 BR5 A:TBR1548 3.6 46.4 0.2 BR6 A:TBR1548 3.6 46.3 0.2 CB A:ASP29 3.7 30.4 1.0 CA A:ASP29 3.7 30.4 1.0 C A:ASP29 3.7 31.0 1.0 BR7 A:TBR1548 3.7 48.6 0.2 BR9 A:TBR1548 3.7 49.2 0.2 CD A:GLU33 3.8 42.6 1.0 TA3 A:TBR1548 4.2 49.0 0.2 TA5 A:TBR1548 4.2 47.7 0.2 CG A:ASP29 4.3 31.2 1.0 O A:HOH2017 4.4 53.0 1.0 OD1 A:ASP29 4.4 32.6 1.0 N A:GLU33 4.5 38.1 1.0 CB A:GLU32 4.7 37.6 1.0 CB A:GLU33 4.7 38.5 1.0 N A:ALA30 4.9 31.5 1.0 OE1 A:GLU33 5.0 43.4 1.0 CA A:GLU33 5.0 38.8 1.0

D.J.Reinert, T.Jank, K.Aktories, G.E.Schulz. Structural Basis For the Function of Clostridium Difficile Toxin B. J.Mol.Biol. V. 351 973 2005.
ISSN: ISSN 0022-2836
PubMed: 16054646
DOI: 10.1016/J.JMB.2005.06.071