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Bromine in PDB 2x42: Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Alpha-D-Glucose

Enzymatic activity of Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Alpha-D-Glucose

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

Protein crystallography data

The structure of Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Alpha-D-Glucose, PDB code: 2x42 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) 29.28 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 74.550, 128.160, 175.650, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.4

Bromine Binding Sites:

The binding sites of Bromine atom in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Alpha-D-Glucose (pdb code 2x42). 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 Alpha-D-Glucose, PDB code: 2x42:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 2x42

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


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 Alpha-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1723

b:42.9
occ:0.69
 OH A:TYR592 2.9 28.8 1.0
NH1 A:ARG340 3.2 34.1 1.0
CD A:ARG340 3.6 36.7 1.0
CE1 A:TYR592 3.7 28.3 1.0
CZ A:TYR592 3.7 28.6 1.0
CG A:ARG340 3.9 33.2 1.0
CB A:ARG340 4.0 30.5 1.0
CD A:ARG509 4.0 30.3 1.0
O A:HOH2293 4.0 52.5 1.0
CZ A:ARG340 4.2 38.2 1.0
O A:LEU339 4.2 30.0 1.0
NE A:ARG340 4.3 38.0 1.0
NE A:ARG509 4.4 34.5 1.0
NH1 A:ARG509 4.5 32.2 1.0
CZ A:ARG509 4.6 35.8 1.0
CG A:ARG509 4.7 31.6 1.0
CA A:ARG340 4.8 31.2 1.0
CB A:ARG509 4.8 30.3 1.0

Bromine binding site 2 out of 4 in 2x42

Go back to Bromine Binding Sites List in 2x42
Bromine binding site 2 out of 4 in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Alpha-D-Glucose


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 Alpha-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1724

b:45.4
occ:1.00
 N A:GLY500 3.3 31.4 1.0
OG A:SER456 3.4 41.6 1.0
O A:HOH2276 3.4 43.7 1.0
CA A:GLY500 3.6 28.1 1.0
OG A:SER501 3.6 42.4 1.0
CB A:SER456 3.7 36.1 1.0
C A:GLY500 3.9 29.9 1.0
CB A:ARG454 3.9 26.3 1.0
N A:SER501 3.9 32.7 1.0
N A:SER456 4.0 28.4 1.0
C A:ILE455 4.0 32.6 1.0
O A:HOH2266 4.0 35.6 1.0
CD A:ARG462 4.1 29.4 1.0
O A:HOH2265 4.2 43.2 1.0
NE2 A:GLN520 4.2 26.4 1.0
C A:ARG454 4.2 31.3 1.0
CA A:ILE455 4.2 30.5 1.0
N A:ILE455 4.2 27.9 1.0
O A:ARG454 4.3 33.5 1.0
O A:ILE455 4.4 38.6 1.0
C A:ILE499 4.4 28.4 1.0
NE A:ARG462 4.5 32.9 1.0
CA A:SER456 4.5 34.1 1.0
CB A:SER501 4.6 35.4 1.0
O A:GLY500 4.6 26.6 1.0
NH1 A:ARG462 4.7 34.5 1.0
CZ A:ARG462 4.7 33.7 1.0
CA A:ARG454 4.8 28.6 1.0
CA A:ILE499 4.8 23.2 1.0
CA A:SER501 4.8 30.8 1.0
CG A:ARG454 4.9 28.4 1.0
CB A:ILE499 5.0 23.8 1.0
O A:SER501 5.0 28.4 1.0

Bromine binding site 3 out of 4 in 2x42

Go back to Bromine Binding Sites List in 2x42
Bromine binding site 3 out of 4 in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Alpha-D-Glucose


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 Alpha-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1725

b:28.1
occ:0.61
 ND2 A:ASN121 3.2 23.1 1.0
N A:ALA167 3.3 25.3 1.0
N A:ILE122 3.4 26.9 1.0
ND2 A:ASN169 3.4 23.1 1.0
CD1 A:TYR190 3.6 19.2 1.0
CA A:ASN121 3.6 24.1 1.0
CA A:ALA167 3.6 21.5 1.0
CB A:TYR190 3.8 21.5 1.0
CB A:ASN121 3.9 18.8 1.0
O A:TYR190 3.9 26.2 1.0
CE2 A:PHE194 4.0 20.0 1.0
CG2 A:VAL166 4.0 18.9 1.0
C A:ASN121 4.0 25.8 1.0
CG A:ASN121 4.0 23.8 1.0
CA A:TYR190 4.1 25.4 1.0
OD1 A:ASN169 4.1 23.3 1.0
CG A:TYR190 4.2 22.0 1.0
CG A:ASN169 4.2 25.5 1.0
CG1 A:ILE122 4.2 22.0 1.0
CB A:ILE122 4.2 24.9 1.0
N A:ASN168 4.4 28.1 1.0
C A:TYR190 4.4 23.6 1.0
CA A:ILE122 4.4 25.6 1.0
C A:ALA167 4.5 26.9 1.0
C A:VAL166 4.5 26.7 1.0
CE1 A:TYR190 4.6 16.7 1.0
CZ A:PHE194 4.7 25.9 1.0
CB A:ALA167 4.8 22.7 1.0
N A:ASN121 4.8 22.5 1.0
O A:MET120 4.9 25.6 1.0
CA A:VAL166 4.9 22.0 1.0
O A:HOH2109 4.9 20.8 1.0
CD2 A:PHE194 5.0 20.9 1.0
O A:HIS164 5.0 28.3 1.0

Bromine binding site 4 out of 4 in 2x42

Go back to Bromine Binding Sites List in 2x42
Bromine binding site 4 out of 4 in the Structure of Beta-Glucosidase 3B From Thermotoga Neapolitana in Complex with Alpha-D-Glucose


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 Alpha-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1726

b:34.2
occ:0.45
 O A:HOH2320 2.9 51.2 1.0
N A:VAL571 3.2 25.3 1.0
CB A:THR558 3.6 23.4 1.0
O A:HOH2330 3.7 28.7 1.0
CA A:VAL570 3.8 25.2 1.0
CG2 A:THR558 3.8 21.9 1.0
CB A:VAL571 3.9 25.0 1.0
CG2 A:VAL571 4.0 25.6 1.0
C A:VAL570 4.0 29.1 1.0
CA A:VAL571 4.1 27.4 1.0
O A:HOH2127 4.2 34.9 1.0
O A:LYS569 4.2 29.2 1.0
CA A:GLY561 4.3 26.8 1.0
OE2 A:GLU562 4.4 73.0 1.0
OG1 A:THR558 4.4 21.7 1.0
O A:VAL571 4.5 24.8 1.0
CB A:GLU562 4.5 40.8 1.0
N A:GLU562 4.5 30.7 1.0
O A:THR558 4.6 26.8 1.0
C A:GLY561 4.6 30.7 1.0
CG2 A:VAL570 4.7 23.6 1.0
N A:VAL570 4.7 26.6 1.0
CA A:THR558 4.7 25.9 1.0
C A:LYS569 4.8 29.9 1.0
CB A:VAL570 4.8 27.4 1.0
C A:VAL571 4.8 25.7 1.0
C A:THR558 5.0 22.8 1.0

Reference:

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
Page generated: Wed Jul 10 18:55:47 2024

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