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Bromine in PDB 2vmf: 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: 2vmf 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) 37.45 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.051, 114.663, 99.090, 90.00, 113.19, 90.00
R / Rfree (%) 16.4 / 22.3

Other elements in 2vmf:

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

Chlorine (Cl) 11 atoms

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

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 2vmf). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 16 binding sites of Bromine where determined in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases, PDB code: 2vmf:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 16 in 2vmf

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Bromine binding site 1 out of 16 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:Br1881

b:24.2
occ:0.80
 O A:HOH2086 3.2 23.4 1.0
O A:HOH2140 3.3 20.6 1.0
N A:ILE107 3.5 24.1 1.0
CB A:LYS142 3.7 21.9 1.0
O A:ILE107 3.7 24.1 1.0
N A:LYS142 3.8 20.4 1.0
CB A:PRO140 3.8 24.5 1.0
CA A:GLY106 4.0 25.6 1.0
CG1 A:ILE249 4.0 24.3 1.0
N A:VAL141 4.1 21.2 1.0
CA A:PRO140 4.1 23.1 1.0
CD1 A:ILE249 4.2 25.5 1.0
C A:ILE107 4.3 23.8 1.0
C A:GLY106 4.3 25.2 1.0
C A:PRO140 4.3 22.1 1.0
CA A:LYS142 4.4 22.0 1.0
CA A:ILE107 4.4 23.6 1.0
O A:ASP105 4.8 25.9 1.0
C A:VAL141 4.9 19.5 1.0
OH A:TYR218 4.9 22.2 1.0
CG A:LYS142 4.9 21.7 1.0
CD A:LYS142 5.0 21.4 1.0

Bromine binding site 2 out of 16 in 2vmf

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Bromine binding site 2 out of 16 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:Br1882

b:20.8
occ:0.75
 N A:HIS284 3.2 23.1 1.0
CA A:ASN283 3.8 23.1 1.0
C A:ASN283 4.0 23.2 1.0
O A:HIS284 4.1 24.9 1.0
CD2 A:HIS284 4.2 26.6 1.0
CA A:HIS284 4.2 24.5 1.0
CB A:HIS284 4.3 24.4 1.0
O A:ILE282 4.3 21.7 1.0
CB A:ASN283 4.5 22.4 1.0
C A:HIS284 4.6 25.0 1.0
CG A:HIS284 4.6 26.4 1.0
OD1 A:ASN283 4.7 22.6 1.0
N A:ASN283 4.9 21.7 1.0
CG A:ASN283 5.0 24.8 1.0

Bromine binding site 3 out of 16 in 2vmf

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Bromine binding site 3 out of 16 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:Br1883

b:16.7
occ:0.50
 O A:HOH2465 3.3 12.0 1.0
O A:HOH2295 3.7 46.5 1.0
CE2 A:TYR509 3.9 15.4 1.0
CG A:PRO497 3.9 16.6 1.0
O A:PHE492 4.0 16.8 1.0
CB A:PRO497 4.0 14.7 1.0
CA A:ARG493 4.0 20.2 1.0
CB A:HIS511 4.1 15.6 1.0
CD2 A:TYR509 4.2 13.6 1.0
CB A:ARG493 4.4 19.9 1.0
O A:ARG493 4.4 19.8 1.0
C A:ARG493 4.6 20.4 1.0
CG A:ARG493 4.6 24.8 1.0
N A:HIS511 4.7 15.4 1.0
CG A:HIS511 4.8 19.4 1.0
CD2 A:HIS511 4.9 20.8 1.0
CA A:HIS511 4.9 15.9 1.0
C A:PHE492 4.9 18.7 1.0
CD A:PRO497 5.0 16.6 1.0
N A:ARG493 5.0 19.2 1.0

Bromine binding site 4 out of 16 in 2vmf

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Bromine binding site 4 out of 16 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:19.5
occ:0.50
 O A:HOH2140 3.2 20.6 1.0
OE1 A:GLN108 3.4 33.2 1.0
CB A:PRO140 3.8 24.5 1.0
CD A:PRO140 3.8 23.2 1.0
N A:PRO140 3.8 24.3 1.0
CA A:PRO140 4.0 23.1 1.0
CG A:PRO140 4.0 23.9 1.0
CB A:GLN108 4.1 25.9 1.0
CG2 A:THR138 4.1 24.6 1.0
ND2 A:ASN247 4.2 26.3 1.0
C A:LEU139 4.2 24.5 1.0
CD A:GLN108 4.4 29.4 1.0
O A:LEU139 4.5 23.5 1.0
O A:HOH2141 4.6 19.4 1.0
CG A:GLN108 4.6 27.2 1.0
O A:THR138 4.7 24.4 1.0
OH A:TYR218 4.7 22.2 1.0
C A:THR138 4.8 24.6 1.0
N A:LEU139 4.8 24.2 1.0
CA A:LEU139 4.9 24.3 1.0
CD1 A:ILE249 4.9 25.5 1.0

Bromine binding site 5 out of 16 in 2vmf

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Bromine binding site 5 out of 16 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:Br1885

b:22.3
occ:0.50
 N A:ASP688 3.3 37.3 1.0
NE2 A:GLN685 3.6 24.1 1.0
CG A:GLN685 3.8 29.9 1.0
CA A:ASP688 3.9 37.0 1.0
N A:ASN687 3.9 36.2 1.0
C A:GLN686 4.1 34.8 1.0
CA A:GLN686 4.2 33.8 1.0
CD A:GLN685 4.3 29.5 1.0
C A:ASN687 4.4 37.2 1.0
O A:GLN685 4.4 30.3 1.0
N A:GLN686 4.4 31.9 1.0
C A:GLN685 4.5 30.3 1.0
CA A:ASN687 4.5 37.7 1.0
O A:GLN686 4.7 34.4 1.0
C A:ASP688 4.9 36.4 1.0
CB A:ASP688 4.9 37.6 1.0
N A:SER689 4.9 35.8 1.0
OD1 A:ASP688 4.9 42.6 1.0

Bromine binding site 6 out of 16 in 2vmf

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Bromine binding site 6 out of 16 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
A:Br1886

b:26.8
occ:0.50
 N A:THR477 3.4 33.4 1.0
CG2 A:THR477 3.7 32.5 1.0
CA A:PHE476 3.7 35.0 1.0
CG2 A:VAL480 3.9 24.4 1.0
CD1 A:PHE476 4.0 27.7 1.0
CB A:PHE476 4.0 34.0 1.0
CB A:PHE172 4.0 22.0 1.0
CB A:VAL480 4.1 25.2 1.0
C A:PHE476 4.1 34.7 1.0
OG1 A:THR477 4.1 34.5 1.0
CG1 A:VAL480 4.3 24.0 1.0
CB A:THR477 4.3 33.7 1.0
CA A:THR477 4.4 33.3 1.0
CG A:PHE476 4.5 32.7 1.0
CG A:PHE172 4.7 21.4 1.0
O A:LYS475 4.8 38.4 1.0
O A:GLY171 4.8 24.9 1.0
CD2 A:PHE172 4.9 21.6 1.0
N A:PHE476 5.0 36.7 1.0

Bromine binding site 7 out of 16 in 2vmf

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Bromine binding site 7 out of 16 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
A:Br1889

b:58.4
occ:0.50
 N A:GLU579 3.1 25.0 1.0
O A:HOH2336 3.1 15.0 1.0
CB A:GLN577 3.5 25.9 1.0
N A:ILE578 3.5 24.6 1.0
CB A:GLU579 3.7 26.1 1.0
CA A:GLU579 3.9 25.4 1.0
CB A:ILE578 3.9 24.7 1.0
CG A:GLU579 3.9 29.8 1.0
CA A:ILE578 4.0 25.0 1.0
C A:ILE578 4.0 24.9 1.0
C A:GLN577 4.2 25.8 1.0
OE1 A:GLN577 4.4 28.3 1.0
CA A:GLN577 4.4 25.6 1.0
C A:GLU579 4.5 25.3 1.0
CG A:GLN577 4.5 24.6 1.0
CG1 A:ILE578 4.7 25.8 1.0
N A:SER580 4.7 24.8 1.0
CG2 A:ILE578 4.9 22.7 1.0
CD A:GLN577 4.9 27.6 1.0

Bromine binding site 8 out of 16 in 2vmf

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Bromine binding site 8 out of 16 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
A:Br1890

b:46.7
occ:0.50
 ND2 A:ASN402 3.5 26.9 1.0
O A:HOH2245 3.5 19.8 1.0
O A:HOH2242 3.5 21.0 1.0
CB A:ASN402 3.8 20.0 1.0
O A:HOH2134 3.9 19.7 1.0
CG A:ARG211 3.9 18.7 1.0
CD A:PRO212 4.0 17.3 1.0
CD A:ARG211 4.0 20.6 1.0
CG A:ASN402 4.2 24.8 1.0
NE A:ARG211 4.2 19.7 1.0
CB A:ARG211 4.4 18.5 1.0
O A:HOH2133 4.5 28.1 1.0
CG A:PRO212 4.6 18.5 1.0
OE1 A:GLU112 4.6 23.5 1.0
CA A:ASN402 4.9 19.6 1.0
CZ A:ARG211 5.0 18.3 1.0

Bromine binding site 9 out of 16 in 2vmf

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Bromine binding site 9 out of 16 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
A:Br1894

b:45.7
occ:0.50
 O A:HOH2420 3.4 25.0 1.0
O A:HOH2433 3.7 25.2 1.0
NH2 A:ARG626 3.7 21.0 1.0
O A:HOH2364 3.8 26.4 1.0
O A:HOH2422 3.8 18.9 1.0
O2 A:EDO1877 3.9 45.2 1.0
O A:HOH2366 4.1 28.8 1.0
N A:PHE775 4.4 24.5 1.0
OE1 A:GLN623 4.4 19.0 1.0
O A:PHE775 4.5 25.9 1.0
CZ A:ARG626 4.5 24.5 1.0
O A:HOH2423 4.7 20.1 1.0
C2 A:EDO1877 4.7 44.5 1.0
CB A:PHE775 4.7 24.3 1.0
ND1 A:HIS774 5.0 23.9 1.0
CA A:PHE775 5.0 25.3 1.0

Bromine binding site 10 out of 16 in 2vmf

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Bromine binding site 10 out of 16 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 10 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:Br1879

b:24.5
occ:0.80
 O B:HOH2084 3.1 25.2 1.0
O B:HOH2141 3.3 20.5 1.0
O B:HOH2048 3.4 33.8 1.0
N B:ILE107 3.5 21.4 1.0
O B:ILE107 3.5 21.1 1.0
CB B:LYS142 3.6 19.6 1.0
N B:LYS142 3.8 19.0 1.0
CB B:PRO140 3.9 18.5 1.0
N B:VAL141 4.0 19.2 1.0
CA B:GLY106 4.0 21.6 1.0
CA B:PRO140 4.1 19.1 1.0
CG1 B:ILE249 4.2 26.2 1.0
CD1 B:ILE249 4.2 29.7 1.0
C B:ILE107 4.3 21.8 1.0
C B:GLY106 4.3 21.1 1.0
C B:PRO140 4.3 18.8 1.0
CA B:LYS142 4.3 20.8 1.0
CA B:ILE107 4.4 20.6 1.0
C B:VAL141 4.9 19.4 1.0
CG B:LYS142 4.9 21.7 1.0
O B:ASP105 4.9 21.8 1.0
CD B:LYS142 4.9 20.7 1.0
OH B:TYR218 4.9 16.9 1.0
CA B:VAL141 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 18:38:55 2024

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