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Bromine in PDB 2vjx: Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases

Enzymatic activity of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases

All present enzymatic activity of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases:
3.2.1.25;

Protein crystallography data

The structure of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases, PDB code: 2vjx was solved by L.E.Tailford, W.A.Offen, N.L.Smith, C.Dumon, C.Moreland, J.Gratien, M.P.Heck, R.V.Stick, Y.Bleriot, A.Vasella, H.J.Gilbert, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.80 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.366, 114.396, 99.677, 90.00, 113.17, 90.00
R / Rfree (%) 16 / 20.1

Other elements in 2vjx:

The structure of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases (pdb code 2vjx). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases, PDB code: 2vjx:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 2vjx

Go back to Bromine Binding Sites List in 2vjx
Bromine binding site 1 out of 7 in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1891

b:18.2
occ:0.75
 O A:HOH2068 3.1 32.1 1.0
O A:HOH2177 3.2 18.4 1.0
O A:HOH2105 3.2 19.3 1.0
O A:ILE107 3.5 14.3 1.0
N A:ILE107 3.6 14.5 1.0
CB A:LYS142 3.7 15.8 1.0
N A:LYS142 3.7 14.2 1.0
CB A:PRO140 3.8 17.0 1.0
CA A:GLY106 3.9 15.8 1.0
CD1 A:ILE249 4.0 24.0 1.0
N A:VAL141 4.0 14.5 1.0
CG1 A:ILE249 4.0 19.9 1.0
CA A:PRO140 4.1 16.1 1.0
C A:ILE107 4.3 14.8 1.0
C A:PRO140 4.3 15.7 1.0
C A:GLY106 4.3 15.4 1.0
CA A:LYS142 4.3 16.1 1.0
CA A:ILE107 4.5 14.4 1.0
C A:VAL141 4.8 13.8 1.0
O A:ASP105 4.9 15.8 1.0
CG A:LYS142 4.9 15.6 1.0
OH A:TYR218 4.9 20.1 1.0
CD A:LYS142 5.0 16.0 1.0
CA A:VAL141 5.0 13.4 1.0

Bromine binding site 2 out of 7 in 2vjx

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Bromine binding site 2 out of 7 in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1892

b:19.6
occ:0.80
 N A:HIS284 3.3 17.5 1.0
CA A:ASN283 3.9 16.1 1.0
O A:HIS284 4.0 19.9 1.0
C A:ASN283 4.1 16.6 1.0
CA A:HIS284 4.2 19.1 1.0
CB A:HIS284 4.3 19.9 1.0
CD2 A:HIS284 4.3 24.1 1.0
O A:ILE282 4.4 15.6 1.0
C A:HIS284 4.5 19.9 1.0
CB A:ASN283 4.5 15.0 1.0
CG A:HIS284 4.6 22.3 1.0
OD1 A:ASN283 4.8 17.9 1.0
N A:ASN283 4.9 14.8 1.0
CG A:ASN283 5.0 15.6 1.0

Bromine binding site 3 out of 7 in 2vjx

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Bromine binding site 3 out of 7 in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1893

b:15.6
occ:0.50
 NZ A:LYS129 3.3 16.2 1.0
O1 A:EDO1876 3.4 30.9 1.0
NE2 A:HIS157 3.4 14.6 1.0
CE1 A:HIS157 3.5 15.0 1.0
NE2 A:GLN162 3.8 25.4 1.0
CE A:LYS129 3.9 18.1 1.0
OD2 A:ASP119 4.1 15.9 1.0
CD2 A:HIS157 4.1 13.8 1.0
ND1 A:HIS157 4.3 13.1 1.0
CG A:HIS157 4.6 13.6 1.0
OD1 A:ASP119 4.7 17.1 1.0
O2 A:EDO1880 4.8 29.4 1.0
C1 A:EDO1876 4.8 29.9 1.0
CG A:ASP119 4.8 15.6 1.0
CD A:GLN162 4.8 20.4 1.0
OE1 A:GLN162 4.9 22.4 1.0
O2 A:EDO1876 5.0 29.6 1.0

Bromine binding site 4 out of 7 in 2vjx

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Bromine binding site 4 out of 7 in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1894

b:15.8
occ:0.50
 O A:HOH2624 3.1 9.0 1.0
O A:HOH2378 3.4 29.7 1.0
CE2 A:TYR509 3.8 8.8 1.0
O A:HOH2159 4.0 33.1 1.0
O A:PHE492 4.0 9.7 1.0
CG A:PRO497 4.0 9.9 1.0
CA A:ARG493 4.1 12.2 1.0
CB A:HIS511 4.1 10.6 1.0
CB A:PRO497 4.1 10.1 1.0
CD2 A:TYR509 4.2 8.3 1.0
O A:ARG493 4.4 13.3 1.0
CB A:ARG493 4.6 12.1 1.0
C A:ARG493 4.6 13.1 1.0
CG A:ARG493 4.7 15.6 1.0
N A:HIS511 4.7 9.4 1.0
CD2 A:HIS511 4.7 12.6 1.0
CG A:HIS511 4.8 11.5 1.0
CA A:HIS511 4.8 9.3 1.0
CD A:PRO497 4.9 8.3 1.0
C A:PHE492 4.9 11.1 1.0

Bromine binding site 5 out of 7 in 2vjx

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Bromine binding site 5 out of 7 in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1899

b:43.3
occ:0.50
 O A:ASN300 2.8 16.2 1.0
ND2 A:ASN390 3.1 10.2 1.0
O A:HOH2284 3.1 17.1 1.0
O A:HOH2283 3.1 25.3 1.0
CB A:ASN390 3.8 10.3 1.0
CG A:ASN390 3.9 10.0 1.0
O A:HOH2307 4.0 21.8 1.0
C A:ASN300 4.0 14.8 1.0
CA A:GLY301 4.1 15.7 1.0
CD1 A:TRP302 4.2 16.1 1.0
O A:HOH2526 4.3 17.2 1.0
NE1 A:TRP302 4.3 14.4 1.0
CE A:LYS358 4.5 13.2 1.0
C A:GLY301 4.5 16.5 1.0
N A:GLY301 4.5 14.4 1.0
CG A:MET355 4.6 12.2 1.0
CG A:TRP302 4.6 15.6 1.0
CE2 A:TRP302 4.7 15.7 1.0
N A:TRP302 4.7 15.9 1.0
NZ A:LYS358 4.7 14.6 1.0
SD A:MET355 4.8 13.8 1.0
CD2 A:TRP302 4.9 15.0 1.0
CB A:ASP697 4.9 19.2 1.0
O A:PHE356 5.0 11.0 1.0

Bromine binding site 6 out of 7 in 2vjx

Go back to Bromine Binding Sites List in 2vjx
Bromine binding site 6 out of 7 in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1886

b:18.5
occ:0.80
 O B:HOH2194 3.1 14.6 1.0
O B:HOH2073 3.1 24.9 1.0
O B:HOH2115 3.2 20.8 1.0
N B:ILE107 3.5 11.8 1.0
O B:ILE107 3.6 11.5 1.0
CB B:LYS142 3.6 14.4 1.0
N B:LYS142 3.8 11.9 1.0
CB B:PRO140 3.9 13.4 1.0
CD1 B:ILE249 3.9 23.7 1.0
CA B:GLY106 3.9 12.7 1.0
N B:VAL141 4.1 12.6 1.0
CA B:PRO140 4.1 12.4 1.0
CG1 B:ILE249 4.2 20.4 1.0
C B:GLY106 4.2 12.4 1.0
C B:ILE107 4.3 12.8 1.0
CA B:LYS142 4.3 14.0 1.0
C B:PRO140 4.4 13.0 1.0
CA B:ILE107 4.5 11.4 1.0
O B:ASP105 4.8 11.7 1.0
O B:HOH2049 4.9 34.1 1.0
C B:VAL141 4.9 12.3 1.0
CG B:LYS142 4.9 15.2 1.0
CD B:LYS142 5.0 15.9 1.0

Bromine binding site 7 out of 7 in 2vjx

Go back to Bromine Binding Sites List in 2vjx
Bromine binding site 7 out of 7 in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1887

b:23.9
occ:0.50
 N B:ASP688 3.3 30.4 1.0
NE2 B:GLN685 3.4 20.6 1.0
OD1 B:ASP688 3.5 39.2 1.0
N B:ASN687 3.7 28.5 1.0
CA B:ASP688 3.8 30.5 1.0
CG B:GLN685 3.9 20.8 1.0
C B:GLN686 4.0 26.4 1.0
CD B:GLN685 4.1 19.2 1.0
CA B:GLN686 4.2 24.6 1.0
C B:ASN687 4.3 30.7 1.0
N B:GLN686 4.4 22.8 1.0
CA B:ASN687 4.4 30.6 1.0
O B:HOH2251 4.4 45.9 1.0
CG B:ASP688 4.4 34.1 1.0
O B:GLN685 4.5 19.8 1.0
C B:GLN685 4.5 20.9 1.0
CB B:ASP688 4.5 31.8 1.0
O B:HOH2533 4.7 37.3 1.0
O B:GLN686 4.8 26.8 1.0
CB B:GLN685 4.9 20.3 1.0
C B:ASP688 4.9 29.9 1.0
N B:SER689 5.0 28.5 1.0

Reference:

L.E.Tailford, W.A.Offen, N.L.Smith, C.Dumon, C.Moreland, J.Gratien, M.P.Heck, R.V.Stick, Y.Bleriot, A.Vasella, H.J.Gilbert, G.J.Davies. Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases. Nat.Chem.Biol. V. 4 306 2008.
ISSN: ISSN 1552-4450
PubMed: 18408714
DOI: 10.1038/NCHEMBIO.81
Page generated: Wed Jul 10 18:38:30 2024

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