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Bromine in PDB 2vot: 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: 2vot was solved by L.N.Tailford, W.A.Offen, N.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) 20.03 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.315, 115.289, 99.400, 90.00, 113.14, 90.00
R / Rfree (%) 16.6 / 22.1

Other elements in 2vot:

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

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

Bromine binding site 1 out of 8 in 2vot

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Bromine binding site 1 out of 8 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:Br1886

b:26.7
occ:0.80
 O A:HOH2145 3.2 27.5 1.0
O A:HOH2081 3.3 25.6 1.0
O A:ILE107 3.4 24.0 1.0
N A:ILE107 3.6 23.6 1.0
CB A:LYS142 3.7 24.9 1.0
N A:LYS142 3.8 20.9 1.0
CB A:PRO140 3.8 25.9 1.0
CA A:GLY106 4.0 24.6 1.0
N A:VAL141 4.0 23.4 1.0
CA A:PRO140 4.1 25.0 1.0
CG1 A:ILE249 4.1 26.9 1.0
CD1 A:ILE249 4.2 29.2 1.0
C A:ILE107 4.2 24.7 1.0
C A:PRO140 4.3 24.2 1.0
C A:GLY106 4.3 24.4 1.0
CA A:LYS142 4.4 24.8 1.0
CA A:ILE107 4.5 22.4 1.0
C A:VAL141 4.8 21.3 1.0
O A:ASP105 4.9 25.3 1.0
OH A:TYR218 5.0 25.2 1.0

Bromine binding site 2 out of 8 in 2vot

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Bromine binding site 2 out of 8 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:Br1887

b:22.4
occ:0.75
 N A:HIS284 3.2 24.0 1.0
CA A:ASN283 3.8 23.0 1.0
C A:ASN283 4.0 23.7 1.0
O A:HIS284 4.1 25.9 1.0
CA A:HIS284 4.2 25.8 1.0
CD2 A:HIS284 4.2 31.1 1.0
CB A:HIS284 4.3 26.0 1.0
O A:ILE282 4.4 21.1 1.0
CB A:ASN283 4.5 23.5 1.0
C A:HIS284 4.6 26.9 1.0
CG A:HIS284 4.6 28.2 1.0
OD1 A:ASN283 4.7 22.8 1.0
N A:ASN283 4.9 20.6 1.0
CG A:ASN283 4.9 24.6 1.0

Bromine binding site 3 out of 8 in 2vot

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Bromine binding site 3 out of 8 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:Br1888

b:28.0
occ:0.60
 O A:HOH2175 3.0 33.8 1.0
O A:HOH2145 3.2 27.5 1.0
NE2 A:GLN108 3.4 29.0 1.0
N A:PRO140 3.8 24.6 1.0
CB A:PRO140 3.9 25.9 1.0
CD A:PRO140 3.9 24.3 1.0
CG A:GLN108 4.0 30.1 1.0
CA A:PRO140 4.0 25.0 1.0
ND2 A:ASN247 4.0 29.7 1.0
CG2 A:THR138 4.1 26.8 1.0
CD A:GLN108 4.2 29.8 1.0
CG A:PRO140 4.2 26.7 1.0
C A:LEU139 4.3 24.8 1.0
O A:HOH2146 4.5 28.7 1.0
CB A:GLN108 4.5 27.2 1.0
O A:LEU139 4.7 24.1 1.0
OH A:TYR218 4.7 25.2 1.0
CD1 A:ILE249 4.8 29.2 1.0
N A:LEU139 4.9 23.9 1.0
O A:THR138 4.9 22.1 1.0
C A:THR138 4.9 24.0 1.0
CA A:LEU139 5.0 24.3 1.0

Bromine binding site 4 out of 8 in 2vot

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Bromine binding site 4 out of 8 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:Br1889

b:28.2
occ:0.50
 N A:ASP688 3.3 37.5 1.0
O A:HOH2455 3.5 40.0 1.0
NE2 A:GLN685 3.7 33.6 1.0
N A:ASN687 3.8 37.4 1.0
CG A:GLN685 3.8 30.9 1.0
CA A:ASP688 3.8 38.4 1.0
C A:GLN686 4.0 35.5 1.0
CA A:GLN686 4.1 34.4 1.0
CD A:GLN685 4.2 34.9 1.0
N A:GLN686 4.4 32.8 1.0
C A:ASN687 4.4 38.1 1.0
C A:GLN685 4.5 31.1 1.0
O A:GLN685 4.5 29.6 1.0
CA A:ASN687 4.5 38.6 1.0
O A:GLN686 4.8 35.1 1.0
CB A:ASP688 4.8 38.6 1.0
C A:ASP688 4.9 38.0 1.0
N A:SER689 4.9 37.1 1.0
CB A:GLN685 4.9 31.1 1.0

Bromine binding site 5 out of 8 in 2vot

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Bromine binding site 5 out of 8 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:Br1900

b:21.8
occ:0.50
 O A:HOH2538 3.2 16.1 1.0
O A:HOH2342 3.4 36.1 1.0
CE2 A:TYR509 3.8 18.8 1.0
O A:HOH2125 4.0 41.8 1.0
O A:PHE492 4.0 20.1 1.0
CB A:PRO497 4.1 16.9 1.0
CG A:PRO497 4.1 16.7 1.0
CB A:HIS511 4.1 18.8 1.0
CD2 A:TYR509 4.1 20.0 1.0
CA A:ARG493 4.2 23.0 1.0
O A:ARG493 4.5 21.8 1.0
N A:HIS511 4.6 16.9 1.0
CB A:ARG493 4.7 23.7 1.0
CD2 A:HIS511 4.7 24.5 1.0
C A:ARG493 4.7 22.3 1.0
CG A:HIS511 4.7 20.7 1.0
CA A:HIS511 4.8 18.0 1.0
CG A:ARG493 4.8 27.3 1.0
CD A:PRO497 4.9 14.6 1.0
C A:PHE492 5.0 21.3 1.0

Bromine binding site 6 out of 8 in 2vot

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Bromine binding site 6 out of 8 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:Br1890

b:28.4
occ:0.80
 O B:HOH2066 3.1 37.7 1.0
O B:HOH2107 3.1 30.6 1.0
O B:HOH2173 3.2 22.1 1.0
N B:ILE107 3.5 23.2 1.0
O B:ILE107 3.5 25.1 1.0
CB B:LYS142 3.6 24.6 1.0
N B:LYS142 3.8 21.8 1.0
CB B:PRO140 3.8 25.1 1.0
CA B:GLY106 4.0 23.4 1.0
CD1 B:ILE249 4.0 34.6 1.0
N B:VAL141 4.1 22.7 1.0
CA B:PRO140 4.1 23.9 1.0
CG1 B:ILE249 4.2 31.8 1.0
C B:GLY106 4.3 22.5 1.0
C B:ILE107 4.3 23.7 1.0
CA B:LYS142 4.3 24.3 1.0
C B:PRO140 4.3 24.3 1.0
CA B:ILE107 4.5 23.2 1.0
C B:VAL141 4.8 21.5 1.0
O B:ASP105 4.9 24.5 1.0
CG B:LYS142 4.9 24.5 1.0
OH B:TYR218 4.9 24.2 1.0
CD B:LYS142 4.9 24.0 1.0
O B:HOH2033 4.9 44.3 1.0

Bromine binding site 7 out of 8 in 2vot

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Bromine binding site 7 out of 8 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:Br1891

b:23.9
occ:0.50
 N B:ASP688 3.3 31.9 1.0
NE2 B:GLN685 3.5 26.7 1.0
CG B:GLN685 3.7 24.9 1.0
CA B:ASP688 3.9 34.1 1.0
N B:ASN687 3.9 29.5 1.0
C B:GLN686 4.1 28.0 1.0
CD B:GLN685 4.1 25.6 1.0
CA B:GLN686 4.2 26.4 1.0
O B:HOH2493 4.2 38.1 1.0
N B:GLN686 4.4 24.7 1.0
C B:ASN687 4.4 31.8 1.0
O B:GLN685 4.4 21.4 1.0
C B:GLN685 4.5 23.7 1.0
CA B:ASN687 4.6 31.7 1.0
O B:GLN686 4.7 27.7 1.0
CB B:ASP688 4.8 36.2 1.0
CB B:GLN685 4.9 24.0 1.0
O B:HOH2595 4.9 50.2 1.0
N B:SER689 4.9 33.0 1.0
C B:ASP688 4.9 34.4 1.0

Bromine binding site 8 out of 8 in 2vot

Go back to Bromine Binding Sites List in 2vot
Bromine binding site 8 out of 8 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:Br1892

b:20.3
occ:0.50
 O B:HOH2378 3.0 39.6 1.0
O B:HOH2593 3.1 19.7 1.0
O B:HOH2377 3.3 32.1 1.0
CE2 B:TYR509 3.8 18.3 1.0
CG B:PRO497 4.0 18.4 1.0
CB B:HIS511 4.0 18.0 1.0
O B:HOH2155 4.1 35.1 1.0
CD2 B:TYR509 4.1 17.1 1.0
O B:PHE492 4.1 17.7 1.0
CB B:PRO497 4.2 17.3 1.0
CA B:ARG493 4.2 19.9 1.0
O B:ARG493 4.5 21.1 1.0
N B:HIS511 4.6 16.9 1.0
CB B:ARG493 4.7 20.6 1.0
CG B:HIS511 4.7 18.9 1.0
CD2 B:HIS511 4.7 21.7 1.0
C B:ARG493 4.8 19.9 1.0
CA B:HIS511 4.8 18.0 1.0
CG B:ARG493 4.8 24.1 1.0
CD B:PRO497 5.0 18.2 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 18:45:32 2024

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