Chlorine 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:

Bromine (Br) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases, PDB code: 2vo5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 2vo5

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Chlorine binding site 1 out of 6 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 Chlorine with other atoms in the Cl 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:Cl1876

b:21.7
occ:1.00
 N A:ASP688 3.3 34.9 1.0
O A:HOH2394 3.5 17.4 1.0
NE2 A:GLN685 3.6 31.6 1.0
CG A:GLN685 3.7 28.8 1.0
N A:ASN687 3.8 34.6 1.0
CA A:ASP688 3.9 34.8 1.0
C A:GLN686 4.1 33.1 1.0
O A:GLN685 4.1 28.9 1.0
CD A:GLN685 4.2 31.4 1.0
CA A:GLN686 4.2 32.0 1.0
C A:ASN687 4.3 35.1 1.0
C A:GLN685 4.4 28.7 1.0
N A:GLN686 4.4 30.0 1.0
CA A:ASN687 4.5 35.6 1.0
O A:GLN686 4.7 33.1 1.0
N A:SER689 4.8 32.5 1.0
C A:ASP688 4.9 33.9 1.0
CB A:GLN685 5.0 27.7 1.0

Chlorine binding site 2 out of 6 in 2vo5

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Chlorine binding site 2 out of 6 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 Chlorine with other atoms in the Cl 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:Cl1877

b:36.6
occ:1.00
 O A:HOH2392 2.7 25.4 1.0
N A:GLN685 3.2 25.1 1.0
CE1 A:HIS774 3.7 27.7 1.0
CD1 A:ILE684 3.7 13.8 1.0
CA A:ILE684 3.8 21.5 1.0
O A:PRO683 4.0 20.6 1.0
CE1 A:HIS627 4.0 16.4 1.0
C A:ILE684 4.0 23.0 1.0
CB A:GLN685 4.0 27.7 1.0
O A:GLN685 4.1 28.9 1.0
CA A:GLN685 4.1 27.3 1.0
O A:HOH2422 4.2 16.4 1.0
ND1 A:HIS774 4.3 26.5 1.0
ND1 A:HIS627 4.5 12.5 1.0
C A:GLN685 4.5 28.7 1.0
CG1 A:ILE684 4.6 19.9 1.0
CB A:ILE684 4.6 20.4 1.0
O A:HOH2462 4.7 33.8 1.0
N A:ILE684 4.7 20.6 1.0
C A:PRO683 4.7 19.3 1.0
NE2 A:HIS774 4.8 29.0 1.0
O A:HOH2370 4.8 17.9 1.0

Chlorine binding site 3 out of 6 in 2vo5

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Chlorine binding site 3 out of 6 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 Chlorine with other atoms in the Cl 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
B:Cl1886

b:20.0
occ:1.00
 O B:HOH2140 3.1 14.0 1.0
NE2 B:GLN108 3.5 24.2 1.0
CG B:GLN108 3.9 22.4 1.0
CB B:PRO140 4.0 16.4 1.0
CD B:PRO140 4.1 15.6 1.0
N B:PRO140 4.1 15.8 1.0
CA B:PRO140 4.1 16.4 1.0
ND2 B:ASN247 4.2 28.2 1.0
O B:HOH2154 4.2 30.4 1.0
CD B:GLN108 4.2 24.9 1.0
CG2 B:THR138 4.3 17.5 1.0
CG B:PRO140 4.5 15.6 1.0
C B:LEU139 4.6 15.9 1.0
OH B:TYR218 4.7 13.9 1.0
O B:HOH2155 4.7 12.3 1.0
O B:THR138 4.9 16.8 1.0
CB B:GLN108 5.0 19.6 1.0

Chlorine binding site 4 out of 6 in 2vo5

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Chlorine binding site 4 out of 6 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 Chlorine with other atoms in the Cl 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
B:Cl1887

b:32.0
occ:1.00
 O B:HOH2384 2.8 25.0 1.0
N B:GLN685 3.2 21.6 1.0
O B:HOH2386 3.3 27.9 1.0
CE1 B:HIS774 3.7 15.5 1.0
CD1 B:ILE684 3.7 14.5 1.0
O2 B:EDO1882 3.8 25.4 1.0
CB B:GLN685 3.8 22.8 1.0
O B:HOH2426 3.9 5.9 0.5
CA B:ILE684 4.0 18.8 1.0
CE1 B:HIS627 4.0 13.2 1.0
CA B:GLN685 4.0 22.8 1.0
O B:GLN685 4.0 23.3 1.0
O B:PRO683 4.0 18.3 1.0
C B:ILE684 4.1 20.5 1.0
ND1 B:HIS774 4.2 12.0 1.0
C B:GLN685 4.5 23.9 1.0
ND1 B:HIS627 4.7 16.0 1.0
CG1 B:ILE684 4.7 16.7 1.0
O B:HOH2362 4.7 10.9 1.0
C B:PRO683 4.8 17.0 1.0
N B:ILE684 4.8 18.8 1.0
CB B:ILE684 4.8 18.3 1.0
NE2 B:HIS774 4.8 15.4 1.0
O B:HOH2360 4.8 15.8 1.0

Chlorine binding site 5 out of 6 in 2vo5

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Chlorine binding site 5 out of 6 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 Chlorine with other atoms in the Cl 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
B:Cl1888

b:30.8
occ:1.00
 N B:THR477 3.4 30.4 1.0
CG2 B:VAL480 3.6 23.9 1.0
CG2 B:THR477 3.6 27.5 1.0
O B:HOH2286 3.7 32.0 1.0
CA B:PHE476 3.7 30.9 1.0
OG1 B:THR477 3.9 29.0 1.0
CB B:VAL480 3.9 26.2 1.0
CD1 B:PHE476 3.9 28.9 1.0
CB B:PHE476 3.9 30.4 1.0
C B:PHE476 4.0 30.8 1.0
CB B:THR477 4.2 29.8 1.0
CB B:PHE172 4.2 16.3 1.0
CG1 B:VAL480 4.2 26.1 1.0
CA B:THR477 4.4 30.1 1.0
CG B:PHE476 4.4 30.7 1.0
O B:LYS475 4.6 32.1 1.0
CG B:PHE172 4.8 13.0 1.0
N B:PHE476 4.9 31.1 1.0
O B:GLY171 4.9 21.1 1.0
CE1 B:PHE476 5.0 29.5 1.0
CD2 B:PHE172 5.0 10.0 1.0

Chlorine binding site 6 out of 6 in 2vo5

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Chlorine binding site 6 out of 6 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 Chlorine with other atoms in the Cl 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:Cl1896

b:24.8
occ:0.70
 O B:HOH2275 2.9 14.9 1.0
O B:ARG447 4.0 11.5 1.0
O B:HOH2253 4.1 13.0 1.0
O B:HOH2028 4.1 14.4 1.0
CE1 B:HIS326 4.2 10.6 1.0
O B:HOH2119 4.2 27.4 1.0
CA B:ARG447 4.6 11.1 1.0
O B:HOH2201 4.6 18.9 1.0
CG B:ARG447 4.6 12.3 1.0
ND2 B:ASN403 4.6 11.4 1.0
ND1 B:HIS326 4.7 13.6 1.0
C B:ARG447 4.8 11.4 1.0
OD1 B:ASN403 4.8 9.4 1.0
O B:HOH2277 4.9 12.5 1.0
CG B:ASN403 5.0 11.6 1.0
NE2 B:GLN324 5.0 29.2 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: Sat Jul 20 12:04:06 2024

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