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Chlorine in PDB 2vl4: 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: 2vl4 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) 48.91 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.559, 115.038, 98.697, 90.00, 112.59, 90.00
R / Rfree (%) 16.2 / 21.5

Other elements in 2vl4:

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

Bromine (Br) 11 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 2vl4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases, PDB code: 2vl4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 2vl4

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Chlorine binding site 1 out of 5 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:Cl1885

b:28.0
occ:0.50
 O A:HOH2041 1.8 17.4 0.5
O A:HOH2376 3.1 16.6 1.0
O A:HOH2088 3.3 26.4 1.0
O A:HOH2380 3.5 25.8 1.0
CB A:ASN402 3.6 15.1 1.0
ND2 A:ASN402 3.8 29.9 1.0
CD A:ARG211 3.9 17.1 1.0
O A:HOH2192 3.9 15.9 1.0
CG A:ARG211 4.0 13.6 1.0
CD A:PRO212 4.0 14.5 1.0
NE A:ARG211 4.0 17.6 1.0
CG A:ASN402 4.2 19.8 1.0
OE1 A:GLU112 4.3 17.1 1.0
CB A:ARG211 4.5 13.1 1.0
CA A:ASN402 4.7 13.9 1.0
CG A:PRO212 4.7 16.8 1.0
O A:HOH2086 4.8 12.4 1.0
CZ A:ARG211 4.8 17.3 1.0
O A:HOH2191 5.0 39.6 1.0

Chlorine binding site 2 out of 5 in 2vl4

Go back to Chlorine Binding Sites List in 2vl4
Chlorine binding site 2 out of 5 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:Cl1889

b:60.5
occ:1.00
 O A:HOH2044 3.1 38.3 1.0
ND2 A:ASN77 3.3 27.4 1.0
O A:HOH2050 3.7 45.1 1.0
O A:HOH2045 4.0 36.1 1.0
N A:ASN71 4.2 27.1 1.0
CD2 A:TYR74 4.2 35.4 1.0
CB A:TYR74 4.3 30.7 1.0
CB A:PRO70 4.3 25.6 1.0
CG A:ASN77 4.4 30.8 1.0
CG A:TYR74 4.4 33.8 1.0
CB A:ASN71 4.5 27.7 1.0
OD1 A:ASN77 4.7 33.8 1.0
CA A:PRO70 4.8 26.1 1.0
O A:ASN71 4.9 23.4 1.0
CA A:ASN71 4.9 27.0 1.0
C A:PRO70 5.0 26.8 1.0

Chlorine binding site 3 out of 5 in 2vl4

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Chlorine binding site 3 out of 5 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:Cl1889

b:23.3
occ:1.00
 O B:HOH2609 2.5 25.6 1.0
N B:GLN685 3.2 18.5 1.0
O B:HOH2611 3.5 42.6 1.0
C2 B:EDO1891 3.6 43.9 1.0
CD1 B:ILE684 3.7 19.2 1.0
CE1 B:HIS774 3.7 20.6 1.0
O2 B:EDO1891 3.7 45.3 1.0
CE1 B:HIS627 3.8 16.3 1.0
CA B:ILE684 3.8 18.0 1.0
O B:PRO683 4.0 17.1 1.0
O B:HOH2669 4.0 24.1 1.0
C B:ILE684 4.0 18.5 1.0
O B:GLN685 4.1 20.1 1.0
CB B:GLN685 4.2 20.5 1.0
CA B:GLN685 4.2 20.1 1.0
ND1 B:HIS774 4.2 16.9 1.0
ND1 B:HIS627 4.3 18.3 1.0
O B:HOH2579 4.4 19.8 1.0
O B:HOH2578 4.5 22.1 1.0
CG1 B:ILE684 4.6 19.1 1.0
C B:GLN685 4.6 20.9 1.0
CB B:ILE684 4.6 18.1 1.0
C B:PRO683 4.7 16.7 1.0
N B:ILE684 4.7 17.4 1.0
NE2 B:HIS627 4.9 17.2 1.0
NE2 B:HIS774 4.9 18.4 1.0

Chlorine binding site 4 out of 5 in 2vl4

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Chlorine binding site 4 out of 5 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:Cl1894

b:43.8
occ:0.60
 O B:HOH2239 2.5 44.0 1.0
O B:HOH2243 3.0 37.3 1.0
NE2 B:GLN230 3.3 17.9 1.0
CG2 B:THR332 3.9 16.9 1.0
CA B:SER232 4.0 23.5 1.0
CG B:GLN230 4.1 22.5 1.0
O B:LEU231 4.2 25.2 1.0
CD B:GLN230 4.2 22.8 1.0
N B:LEU233 4.3 21.5 1.0
C B:SER232 4.4 22.5 1.0
N B:SER232 4.4 23.3 1.0
C B:LEU231 4.4 24.6 1.0
O B:GLN230 4.4 20.6 1.0
O B:HOH2340 4.6 21.5 1.0
O B:HOH2336 4.7 30.0 1.0
CB B:LEU233 4.7 19.3 1.0
C B:GLN230 4.9 21.6 1.0
CB B:GLN230 4.9 20.2 1.0

Chlorine binding site 5 out of 5 in 2vl4

Go back to Chlorine Binding Sites List in 2vl4
Chlorine binding site 5 out of 5 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:Cl1896

b:29.8
occ:0.50
 OD2 B:ASP797 2.0 39.3 0.5
CG B:ASP797 2.5 38.1 0.5
OD1 B:ASP797 2.8 36.9 0.5
O A:HOH2353 2.9 40.7 1.0
N B:ASP797 3.4 39.8 1.0
CB B:ASP797 3.6 38.2 0.5
CA B:ASP797 4.0 38.7 1.0
NH2 A:ARG376 4.0 24.2 1.0
CD A:ARG376 4.1 22.2 1.0
CG2 A:THR373 4.1 25.3 1.0
O A:ASN371 4.2 19.8 1.0
CB B:LYS848 4.2 46.6 1.0
C B:THR796 4.4 40.0 1.0
O A:HOH2349 4.5 32.8 1.0
CA B:THR796 4.6 40.0 1.0
CB B:THR796 4.7 39.8 1.0
OG1 A:THR373 4.7 23.0 1.0
O B:ASP797 4.9 37.4 1.0
CZ A:ARG376 4.9 22.9 1.0
NE A:ARG376 4.9 25.2 1.0
C B:ASP797 5.0 36.8 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: Sat Jul 20 11:59:38 2024

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