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Chlorine in PDB 2vqu: 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: 2vqu 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) 91.29 / 1.9
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.100, 115.100, 99.500, 90.00, 113.40, 90.00
R / Rfree (%) 17.7 / 23.1

Other elements in 2vqu:

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

Bromine (Br) 12 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 2vqu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases, PDB code: 2vqu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 2vqu

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Chlorine 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 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:Cl1888

b:34.8
occ:1.00
 O A:HOH2487 2.5 21.4 1.0
N A:GLN685 3.2 23.0 1.0
CD1 A:ILE684 3.6 18.0 1.0
CE1 A:HIS627 3.6 19.0 1.0
CA A:ILE684 3.7 21.7 1.0
CE1 A:HIS774 3.8 29.2 1.0
C A:ILE684 3.9 21.9 1.0
O A:PRO683 4.0 24.9 1.0
CB A:GLN685 4.1 24.9 1.0
O A:GLN685 4.1 24.6 1.0
CA A:GLN685 4.1 24.6 1.0
O A:HOH2533 4.2 24.6 1.0
O A:HOH2406 4.3 36.5 1.0
ND1 A:HIS627 4.4 18.1 1.0
ND1 A:HIS774 4.4 27.0 1.0
CG1 A:ILE684 4.5 21.4 1.0
CB A:ILE684 4.5 20.6 1.0
N A:ILE684 4.5 22.3 1.0
C A:GLN685 4.6 25.7 1.0
C A:PRO683 4.6 23.0 1.0
O A:HOH2461 4.6 22.3 1.0
NE2 A:HIS627 4.7 19.1 1.0
O A:HOH2459 4.8 27.1 1.0
O A:HOH2488 4.8 45.6 1.0
NE2 A:HIS774 4.9 27.4 1.0
C1 A:EDO1875 5.0 40.9 1.0

Chlorine binding site 2 out of 8 in 2vqu

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Chlorine 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 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:Cl1892

b:23.5
occ:0.75
 N A:THR477 3.3 33.3 1.0
CG2 A:THR477 3.6 33.4 1.0
CA A:PHE476 3.7 33.2 1.0
CD1 A:PHE476 3.8 26.5 1.0
CB A:PHE476 3.9 32.9 1.0
CG2 A:VAL480 3.9 27.0 1.0
C A:PHE476 4.0 33.6 1.0
CB A:VAL480 4.0 25.9 1.0
CG1 A:VAL480 4.1 24.8 1.0
CB A:PHE172 4.2 22.5 1.0
OG1 A:THR477 4.2 33.6 1.0
CB A:THR477 4.3 33.1 1.0
CG A:PHE476 4.3 30.1 1.0
CA A:THR477 4.4 33.3 1.0
O A:LYS475 4.8 34.4 1.0
O A:HOH2365 4.8 27.6 1.0
CG A:PHE172 4.8 19.8 1.0
CE1 A:PHE476 4.9 28.6 1.0
N A:PHE476 4.9 33.6 1.0

Chlorine binding site 3 out of 8 in 2vqu

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Chlorine 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 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
A:Cl1893

b:32.2
occ:0.50
 CE B:MET298 1.7 2.0 0.5
ND2 B:ASN351 3.1 17.1 1.0
SD B:MET298 3.2 27.4 0.5
SD B:MET298 3.3 16.9 0.5
CE3 B:TRP302 3.5 19.9 1.0
CB B:ASN351 3.6 17.0 1.0
CD B:PRO299 3.7 15.2 1.0
CG B:ASN351 3.8 16.7 1.0
CB B:MET298 3.9 16.0 0.5
O B:VAL350 4.1 15.4 1.0
CG B:MET298 4.2 20.3 0.5
CZ3 B:TRP302 4.2 18.7 1.0
CA B:MET298 4.2 15.4 0.5
CA B:MET298 4.3 14.4 0.5
CB B:MET298 4.4 14.6 0.5
CB B:TRP302 4.4 19.5 1.0
CG1 B:VAL350 4.4 16.4 1.0
CG B:MET298 4.4 15.4 0.5
CD2 B:TRP302 4.4 19.4 1.0
C B:VAL350 4.6 15.4 1.0
CD1 B:ILE353 4.6 25.8 1.0
CG B:PRO299 4.6 17.5 1.0
O B:HOH2066 4.7 43.5 1.0
CE B:MET298 4.7 24.2 0.5
O B:TRP297 4.7 14.3 1.0
CA B:ASN351 4.8 16.5 1.0
CG B:TRP302 4.8 21.2 1.0
N B:ASN351 4.9 15.7 1.0
N B:PRO299 4.9 15.3 1.0

Chlorine binding site 4 out of 8 in 2vqu

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Chlorine 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 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
A:Cl1898

b:18.8
occ:0.50
 O A:HOH2264 2.2 15.3 0.5
O A:HOH2351 3.0 19.0 1.0
O A:HOH2324 3.1 32.2 1.0
ND1 A:HIS326 3.2 21.2 1.0
O A:HOH2260 3.4 23.1 1.0
NE2 A:HIS451 3.5 15.7 1.0
CE1 A:HIS451 3.5 14.3 1.0
O A:HOH2263 3.6 25.6 1.0
CB A:ASN450 3.8 14.5 1.0
CE1 A:HIS326 3.8 22.5 1.0
CD2 A:HIS451 3.9 12.2 1.0
ND1 A:HIS451 4.0 11.8 1.0
O A:HOH2352 4.0 33.5 1.0
O A:HOH2320 4.0 18.5 1.0
CG A:HIS326 4.1 20.0 1.0
CG A:HIS451 4.3 13.4 1.0
C A:ASN450 4.3 13.8 1.0
CB A:HIS326 4.4 17.1 1.0
CA A:ASN450 4.5 13.4 1.0
O A:ASN450 4.5 13.7 1.0
N A:HIS451 4.6 13.6 1.0
O A:ARG447 4.6 15.5 1.0
ND2 A:ASN450 4.7 10.3 1.0
CG A:ASN450 4.8 13.7 1.0
NE2 A:HIS326 4.9 21.5 1.0
OD1 A:ASP407 4.9 16.3 1.0
CA A:HIS326 4.9 17.4 1.0
N A:ASN450 4.9 14.4 1.0
O A:ARG327 4.9 16.2 1.0

Chlorine binding site 5 out of 8 in 2vqu

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Chlorine 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 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:Cl1890

b:33.2
occ:1.00
 O B:HOH2503 2.7 25.4 1.0
O2 B:EDO1883 2.9 44.6 1.0
N B:GLN685 3.1 21.4 1.0
CE1 B:HIS774 3.6 21.0 1.0
CD1 B:ILE684 3.6 14.6 1.0
CB B:GLN685 3.8 23.1 1.0
O B:GLN685 3.8 22.5 1.0
CA B:ILE684 3.9 19.4 1.0
CA B:GLN685 3.9 22.2 1.0
C B:ILE684 4.0 20.1 1.0
CE1 B:HIS627 4.0 18.1 1.0
O B:PRO683 4.1 20.1 1.0
ND1 B:HIS774 4.2 18.9 1.0
O B:HOH2609 4.3 18.2 1.0
C2 B:EDO1883 4.3 43.5 1.0
C B:GLN685 4.4 23.5 1.0
C2 B:EDO1880 4.6 37.7 1.0
CG1 B:ILE684 4.6 16.5 1.0
ND1 B:HIS627 4.7 17.2 1.0
NE2 B:HIS774 4.7 17.8 1.0
N B:ILE684 4.7 19.1 1.0
O B:HOH2475 4.8 21.5 1.0
CB B:ILE684 4.8 18.8 1.0
C B:PRO683 4.8 19.3 1.0
O B:HOH2473 4.9 23.1 1.0

Chlorine binding site 6 out of 8 in 2vqu

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Chlorine 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 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:Cl1891

b:30.7
occ:0.50
 O B:HOH2562 2.2 13.8 0.5
O B:HOH2561 3.0 36.5 1.0
CG B:GLU816 3.8 22.4 1.0
CD B:GLU816 3.9 23.9 1.0
N B:PRO818 3.9 26.6 1.0
C B:THR817 4.0 25.8 1.0
CG B:PRO818 4.0 27.7 1.0
OE1 B:GLU816 4.1 28.0 1.0
O B:GLU816 4.2 22.1 1.0
CD B:PRO818 4.2 26.7 1.0
CB B:PRO818 4.3 28.1 1.0
O B:THR817 4.3 25.3 1.0
CA B:PRO818 4.3 27.4 1.0
CA B:THR817 4.3 25.1 1.0
C B:GLU816 4.3 22.4 1.0
OE2 B:GLU816 4.4 20.4 1.0
O B:HOH2176 4.5 28.1 1.0
CB B:ASN855 4.5 26.8 1.0
N B:THR817 4.5 23.4 1.0
CB B:GLU816 4.6 21.4 1.0
O B:HOH2432 5.0 17.9 1.0

Chlorine binding site 7 out of 8 in 2vqu

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1892

b:31.8
occ:0.70
 O B:HOH2425 2.7 23.6 1.0
O3 B:NOY1869 2.9 18.5 1.0
NE1 B:TRP200 3.1 17.6 1.0
CE2 B:TRP395 3.3 11.3 1.0
O B:HOH2485 3.3 15.0 1.0
C3 B:NOY1869 3.4 17.8 1.0
CD2 B:TRP395 3.4 11.9 1.0
CG2 B:ILE363 3.5 12.4 1.0
NE1 B:TRP395 3.5 13.9 1.0
CZ2 B:TRP395 3.7 12.5 1.0
O4 B:NOY1869 3.7 16.6 1.0
CG B:TRP395 3.8 13.4 1.0
CD1 B:TRP395 3.8 12.2 1.0
CE3 B:TRP395 3.9 9.6 1.0
CE2 B:TRP200 3.9 16.6 1.0
CH2 B:TRP395 4.1 13.5 1.0
CD1 B:TRP200 4.1 14.2 1.0
C4 B:NOY1869 4.1 17.7 1.0
CZ2 B:TRP200 4.1 16.3 1.0
CZ3 B:TRP395 4.2 10.2 1.0
NE1 B:TRP198 4.5 16.5 1.0
OE1 B:GLN646 4.6 16.1 1.0
C2 B:NOY1869 4.6 17.6 1.0
CB B:TRP395 4.7 12.1 1.0
O2 B:NOY1869 4.7 16.4 1.0
OE2 B:GLU555 4.9 16.2 1.0
CD1 B:TRP198 4.9 15.1 1.0
CB B:ILE363 5.0 14.4 1.0

Chlorine binding site 8 out of 8 in 2vqu

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1897

b:34.0
occ:0.75
 O B:HOH2500 3.3 22.9 1.0
NH1 B:ARG698 3.4 38.9 1.0
O B:HOH2543 3.7 30.3 1.0
CD B:ARG698 3.7 30.5 1.0
CB B:PRO678 3.8 17.3 1.0
CG2 B:VAL679 3.9 19.7 1.0
CB B:VAL679 4.3 18.2 1.0
CZ B:ARG698 4.3 37.8 1.0
CG B:ARG698 4.3 26.6 1.0
N B:VAL679 4.3 16.5 1.0
NE B:ARG698 4.4 33.0 1.0
CG B:PRO678 4.5 17.4 1.0
C B:PRO678 4.9 16.4 1.0
CA B:VAL679 5.0 17.9 1.0
CA B:PRO678 5.0 16.3 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 12:09:37 2024

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