Bromine in PDB 2x40: Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol

All present enzymatic activity of Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol:
3.2.1.21;

The structure of Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol, PDB code: 2x40 was solved by T.Pozzo, E.N.Karlsson, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.453 / 2.31
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	74.946, 127.246, 175.209, 90.00, 90.00, 90.00
R / Rfree (%)	17.37 / 23.26

The binding sites of Bromine atom in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol (pdb code 2x40). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol, PDB code: 2x40:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1722 b:62.8 occ:1.00 OH A:TYR592 3.3 34.0 1.0 NH1 A:ARG340 3.5 44.0 1.0 CD A:ARG340 3.7 48.9 1.0 CG A:ARG340 3.7 47.4 1.0 CE1 A:TYR592 3.9 30.4 1.0 CB A:ARG340 4.0 43.6 1.0 CZ A:TYR592 4.0 35.2 1.0 CD A:ARG509 4.1 38.5 1.0 NH1 A:ARG509 4.3 43.9 1.0 O A:LEU339 4.4 45.8 1.0 NE A:ARG509 4.4 43.9 1.0 CZ A:ARG340 4.5 49.5 1.0 O A:HOH2097 4.5 58.3 1.0 NE A:ARG340 4.5 50.6 1.0 CZ A:ARG509 4.6 44.5 1.0 CG A:ARG509 4.8 39.4 1.0 CA A:ARG340 4.8 45.8 1.0

Bromine binding site 2 out of 4 in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1723 b:47.9 occ:1.00 O A:HOH2126 3.4 53.4 1.0 N A:GLY500 3.4 45.0 1.0 OG A:SER456 3.5 52.7 1.0 CA A:GLY500 3.7 43.8 1.0 N A:SER501 3.7 48.1 1.0 O A:HOH2121 3.8 60.8 1.0 C A:GLY500 3.8 46.3 1.0 CD A:ARG462 3.9 52.9 1.0 CB A:ARG454 3.9 39.7 1.0 CB A:SER456 4.0 49.5 1.0 CB A:SER501 4.0 46.8 1.0 N A:SER456 4.1 54.6 1.0 C A:ILE455 4.2 52.2 1.0 NE A:ARG462 4.2 52.1 1.0 NH1 A:ARG462 4.3 46.5 1.0 C A:ARG454 4.4 49.5 1.0 CZ A:ARG462 4.4 51.1 1.0 N A:ILE455 4.4 52.3 1.0 O A:HOH2137 4.4 44.6 1.0 CA A:SER501 4.4 43.8 1.0 CA A:ILE455 4.5 52.0 1.0 O A:ARG454 4.5 54.1 1.0 O A:ILE455 4.5 53.6 1.0 NE2 A:GLN520 4.5 45.5 1.0 C A:ILE499 4.6 42.5 1.0 O A:GLY500 4.6 45.0 1.0 CA A:SER456 4.7 56.1 1.0 O A:SER501 4.8 47.7 1.0 CA A:ARG454 4.8 45.1 1.0 CG A:ARG454 4.9 37.6 1.0 CA A:ILE499 5.0 37.7 1.0

Bromine binding site 3 out of 4 in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1724 b:37.9 occ:0.80 ND2 A:ASN121 3.0 32.8 1.0 N A:ALA167 3.4 37.0 1.0 N A:ILE122 3.5 27.8 1.0 ND2 A:ASN169 3.5 41.0 1.0 CA A:ALA167 3.6 37.8 1.0 CA A:ASN121 3.7 32.9 1.0 CD1 A:TYR190 3.7 36.1 1.0 CG2 A:VAL166 3.8 27.9 1.0 O A:TYR190 3.9 39.8 1.0 CB A:TYR190 3.9 36.3 1.0 CB A:ASN121 3.9 34.0 1.0 CG A:ASN121 3.9 37.2 1.0 CE2 A:PHE194 4.0 38.8 1.0 C A:ASN121 4.1 31.9 1.0 CA A:TYR190 4.2 36.5 1.0 OD1 A:ASN169 4.2 41.7 1.0 CG A:ASN169 4.3 36.2 1.0 CG A:TYR190 4.3 37.3 1.0 CG1 A:ILE122 4.3 30.3 1.0 CB A:ILE122 4.4 29.3 1.0 C A:TYR190 4.4 39.9 1.0 N A:ASN168 4.5 40.1 1.0 C A:ALA167 4.5 40.1 1.0 CA A:ILE122 4.5 32.9 1.0 C A:VAL166 4.5 40.2 1.0 CB A:ALA167 4.6 33.0 1.0 CZ A:PHE194 4.7 40.4 1.0 CE1 A:TYR190 4.7 38.4 1.0 N A:ASN121 4.9 37.6 1.0 CD2 A:PHE194 4.9 39.5 1.0 O A:MET120 4.9 39.9 1.0 CA A:VAL166 4.9 40.7 1.0 O A:HOH2055 4.9 39.9 1.0

Bromine binding site 4 out of 4 in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1725 b:48.2 occ:0.80 O A:HOH2160 3.5 52.9 1.0 N A:VAL571 3.6 33.8 1.0 CG1 A:VAL571 3.8 34.6 1.0 CB A:THR558 4.0 42.0 1.0 CA A:VAL570 4.0 37.3 1.0 O A:HOH2155 4.1 57.1 1.0 OE2 A:GLU562 4.1 88.7 1.0 CB A:GLU562 4.2 65.3 1.0 N A:GLU562 4.3 56.0 1.0 CG2 A:THR558 4.3 37.8 1.0 C A:VAL570 4.3 37.8 1.0 O A:LYS569 4.4 47.3 1.0 CA A:GLY561 4.5 51.5 1.0 C A:GLY561 4.6 54.3 1.0 OG1 A:THR558 4.6 39.2 1.0 CA A:VAL571 4.6 39.3 1.0 CB A:VAL571 4.7 39.4 1.0 N A:VAL570 4.7 38.2 1.0 O A:VAL571 4.7 39.7 1.0 C A:LYS569 4.8 46.1 1.0 O A:THR558 4.8 42.3 1.0 CA A:GLU562 4.9 59.1 1.0

T.Pozzo, J.Linares Pasten, E.N.Karlsson, D.T.Logan. Structural and Functional Analysis of Beta- Glucosidase 3B From Thermotoga Neapolitana: A Thermostable 3-Domain Representative of Glycoside Hydrolase Family 3 J.Mol.Biol. V. 397 724 2010.
ISSN: ISSN 0022-2836
PubMed: 20138890
DOI: 10.1016/J.JMB.2010.01.072