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Bromine in PDB 2vo5: 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: 2vo5 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) 52.49 / 2.3
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.118, 115.692, 99.643, 90.00, 113.17, 90.00
R / Rfree (%) 16.9 / 24.7

Other elements in 2vo5:

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

Chlorine (Cl) 6 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 2vo5). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases, PDB code: 2vo5:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 2vo5

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Bromine binding site 1 out of 9 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:Br1874

b:14.5
occ:0.80
 O A:HOH2144 3.3 11.8 1.0
N A:ILE107 3.5 15.3 1.0
O A:ILE107 3.6 16.7 1.0
CB A:LYS142 3.7 14.2 1.0
O A:HOH2087 3.8 24.9 1.0
CB A:PRO140 3.8 17.0 1.0
CA A:GLY106 3.9 17.2 1.0
N A:LYS142 4.0 14.1 1.0
CG1 A:ILE249 4.1 19.1 1.0
CA A:PRO140 4.1 16.2 1.0
CD1 A:ILE249 4.2 17.4 1.0
N A:VAL141 4.2 15.0 1.0
C A:GLY106 4.3 16.5 1.0
C A:ILE107 4.3 16.5 1.0
C A:PRO140 4.4 15.7 1.0
CA A:ILE107 4.5 15.4 1.0
CA A:LYS142 4.5 15.6 1.0
O A:ASP105 4.8 17.2 1.0
OH A:TYR218 4.8 18.6 1.0
CD A:LYS142 4.9 9.6 1.0
CG A:LYS142 4.9 14.0 1.0

Bromine binding site 2 out of 9 in 2vo5

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Bromine binding site 2 out of 9 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:Br1875

b:12.9
occ:0.80
 N A:HIS284 3.3 19.4 1.0
CA A:ASN283 3.9 17.7 1.0
O A:HIS284 4.0 21.9 1.0
C A:ASN283 4.0 18.4 1.0
CD2 A:HIS284 4.1 29.3 1.0
CA A:HIS284 4.2 21.5 1.0
CB A:HIS284 4.2 21.7 1.0
O A:ILE282 4.4 16.6 1.0
CG A:HIS284 4.5 25.7 1.0
C A:HIS284 4.6 21.3 1.0
CB A:ASN283 4.6 16.4 1.0
OD1 A:ASN283 4.8 14.0 1.0
N A:ASN283 4.9 16.3 1.0
CG A:ASN283 5.0 17.4 1.0

Bromine binding site 3 out of 9 in 2vo5

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Bromine binding site 3 out of 9 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:Br1882

b:32.6
occ:0.50
 N A:THR477 3.4 30.0 1.0
CA A:PHE476 3.7 30.8 1.0
CG2 A:VAL480 3.8 22.6 1.0
CD1 A:PHE476 3.8 27.1 1.0
CB A:VAL480 3.9 23.4 1.0
CG2 A:THR477 4.0 27.5 1.0
CB A:PHE476 4.0 30.5 1.0
CG1 A:VAL480 4.0 22.0 1.0
C A:PHE476 4.0 30.8 1.0
CB A:PHE172 4.1 19.8 1.0
OG1 A:THR477 4.2 30.5 1.0
CG A:PHE476 4.4 29.4 1.0
CB A:THR477 4.4 29.7 1.0
CA A:THR477 4.5 29.4 1.0
O A:LYS475 4.7 32.3 1.0
CG A:PHE172 4.7 16.9 1.0
O A:GLY171 4.7 21.5 1.0
CE1 A:PHE476 4.8 29.2 1.0
O A:HOH2289 4.9 21.0 1.0
N A:PHE476 4.9 31.4 1.0
CD2 A:PHE172 5.0 18.4 1.0

Bromine binding site 4 out of 9 in 2vo5

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Bromine binding site 4 out of 9 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:Br1884

b:8.9
occ:0.50
 O A:HOH2144 3.2 11.8 1.0
CG A:GLN108 3.6 19.5 1.0
NE2 A:GLN108 3.7 20.4 1.0
CG A:PRO140 3.9 16.3 1.0
CB A:PRO140 3.9 17.0 1.0
N A:PRO140 3.9 16.5 1.0
ND2 A:ASN247 4.0 21.5 1.0
CA A:PRO140 4.1 16.2 1.0
CD A:PRO140 4.1 16.6 1.0
CD A:GLN108 4.2 19.5 1.0
CG2 A:THR138 4.2 15.3 1.0
C A:LEU139 4.4 16.1 1.0
O A:HOH2143 4.5 2.2 1.0
OH A:TYR218 4.6 18.6 1.0
O A:LEU139 4.7 15.2 1.0
O A:THR138 4.8 14.7 1.0
CD1 A:ILE249 4.9 17.4 1.0
CB A:GLN108 4.9 18.1 1.0
N A:LEU139 4.9 15.3 1.0
C A:THR138 5.0 15.1 1.0
CA A:LEU139 5.0 15.6 1.0

Bromine binding site 5 out of 9 in 2vo5

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Bromine binding site 5 out of 9 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:Br1895

b:9.1
occ:0.60
 O B:HOH2294 3.1 11.8 1.0
O B:HOH2480 3.2 12.3 1.0
CE2 B:TYR509 3.9 7.2 1.0
CB B:HIS511 4.1 8.1 1.0
O B:PHE492 4.1 12.1 1.0
CG B:PRO497 4.1 11.3 1.0
CA B:ARG493 4.1 12.4 1.0
CD2 B:TYR509 4.2 9.1 1.0
CB B:PRO497 4.3 11.1 1.0
O B:ARG493 4.5 12.1 1.0
CG B:ARG493 4.5 15.8 1.0
CB B:ARG493 4.5 13.2 1.0
N B:HIS511 4.6 8.8 1.0
CD2 B:HIS511 4.7 13.8 1.0
C B:ARG493 4.7 12.9 1.0
CG B:HIS511 4.7 10.2 1.0
CA B:HIS511 4.8 8.3 1.0
O B:HOH2301 4.9 8.0 1.0
O1 B:EDO1883 4.9 18.8 1.0

Bromine binding site 6 out of 9 in 2vo5

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Bromine binding site 6 out of 9 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:Br1884

b:20.4
occ:0.80
 O B:HOH2140 3.3 14.0 1.0
N B:ILE107 3.5 19.2 1.0
CB B:LYS142 3.6 16.4 1.0
O B:ILE107 3.6 19.6 1.0
O B:HOH2088 3.7 28.1 1.0
N B:LYS142 3.9 16.6 1.0
CB B:PRO140 4.0 16.4 1.0
CA B:GLY106 4.1 20.4 1.0
N B:VAL141 4.1 17.1 1.0
CG1 B:ILE249 4.1 26.4 1.0
CA B:PRO140 4.2 16.4 1.0
CD1 B:ILE249 4.2 29.3 1.0
C B:ILE107 4.3 19.5 1.0
C B:GLY106 4.3 19.2 1.0
C B:PRO140 4.3 16.7 1.0
CA B:LYS142 4.4 16.6 1.0
CA B:ILE107 4.5 18.8 1.0
CG B:LYS142 4.7 17.6 1.0
O B:ASP105 4.7 22.1 1.0
OH B:TYR218 4.9 13.9 1.0
CD B:LYS142 4.9 18.4 1.0
C B:VAL141 5.0 16.7 1.0

Bromine binding site 7 out of 9 in 2vo5

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Bromine binding site 7 out of 9 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:Br1885

b:15.6
occ:0.50
 NE2 B:GLN685 3.2 17.2 1.0
N B:ASP688 3.3 30.4 1.0
CA B:ASP688 3.8 31.0 1.0
N B:ASN687 3.9 29.5 1.0
CG B:GLN685 3.9 22.8 1.0
CD B:GLN685 4.1 22.2 1.0
C B:GLN686 4.2 28.2 1.0
CA B:GLN686 4.3 26.5 1.0
C B:ASN687 4.4 30.6 1.0
O B:GLN685 4.5 23.3 1.0
N B:GLN686 4.5 25.2 1.0
C B:GLN685 4.5 23.9 1.0
CA B:ASN687 4.6 30.4 1.0
CB B:ASP688 4.7 31.9 1.0
CB B:GLN685 4.8 22.8 1.0
O B:GLN686 4.8 29.0 1.0
OD1 B:ASP688 4.8 33.5 1.0
C B:ASP688 4.9 30.4 1.0
N B:SER689 5.0 28.9 1.0

Bromine binding site 8 out of 9 in 2vo5

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Bromine binding site 8 out of 9 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 8 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:Br1893

b:43.8
occ:0.50
 O B:ASN300 3.1 16.4 1.0
O B:HOH2220 3.2 23.9 1.0
ND2 B:ASN390 3.4 5.7 1.0
NE1 B:TRP302 3.8 14.3 1.0
CD1 B:TRP302 3.9 17.0 1.0
CE2 B:TRP302 4.1 13.2 1.0
O B:HOH2244 4.2 25.5 1.0
O B:HOH2389 4.2 31.2 1.0
CB B:ASN390 4.2 8.9 1.0
CG B:TRP302 4.2 16.6 1.0
C B:ASN300 4.3 16.2 1.0
CG B:ASN390 4.3 9.6 1.0
CG B:MET355 4.3 12.6 1.0
CD2 B:TRP302 4.4 13.0 1.0
CA B:GLY301 4.5 16.9 1.0
SD B:MET355 4.6 13.8 1.0
C B:GLY301 4.6 17.5 1.0
N B:TRP302 4.7 17.2 1.0
NZ B:LYS358 4.8 10.1 1.0
O B:ASP697 4.8 22.1 1.0
CE B:LYS358 4.8 10.8 1.0
CZ2 B:TRP302 4.8 10.7 1.0
N B:GLY301 4.8 15.7 1.0
CB B:PRO299 4.9 12.6 1.0
CB B:ASP697 5.0 23.1 1.0

Bromine binding site 9 out of 9 in 2vo5

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Bromine binding site 9 out of 9 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 9 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:Br1895

b:17.7
occ:0.70
 O A:HOH2463 3.3 4.7 1.0
O A:HOH2298 3.4 22.4 1.0
CE2 A:TYR509 3.7 5.8 1.0
CB A:PRO497 4.0 15.1 1.0
CA A:ARG493 4.0 13.2 1.0
CG A:PRO497 4.0 12.7 1.0
CD2 A:TYR509 4.1 9.3 1.0
O A:PHE492 4.1 12.7 1.0
CB A:HIS511 4.2 10.7 1.0
CB A:ARG493 4.5 13.0 1.0
O A:ARG493 4.5 13.3 1.0
C A:ARG493 4.6 13.7 1.0
N A:HIS511 4.7 10.7 1.0
CD2 A:HIS511 4.8 17.7 1.0
CG A:HIS511 4.9 13.4 1.0
CA A:HIS511 4.9 10.7 1.0
O A:HOH2305 4.9 13.6 1.0
CG A:ARG493 4.9 16.0 1.0
CZ A:TYR509 4.9 6.8 1.0
CD A:PRO497 4.9 14.3 1.0
C A:PHE492 5.0 12.7 1.0
N A:ARG493 5.0 12.8 1.0

Reference:

L.E.Tailford, W.A.Offen, N.L.Smith, C.Dumon, C.Morland, 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 18:38:59 2024

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