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Chlorine 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:

Bromine (Br) 16 atoms

Chlorine Binding Sites:

Pages:

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

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 2vmf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Structural and Biochemical Evidence For A Boat-Like Transition State in Beta-Mannosidases, PDB code: 2vmf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 2vmf

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Chlorine binding site 1 out of 11 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:Cl1887

b:16.7
occ:1.00
 O A:HOH2392 2.7 17.8 1.0
N A:GLN685 3.4 27.8 1.0
CD1 A:ILE684 3.6 21.7 1.0
CA A:ILE684 3.7 25.1 1.0
CE1 A:HIS627 3.7 20.4 1.0
CE1 A:HIS774 3.7 27.3 1.0
O A:PRO683 3.8 25.4 1.0
C2 A:EDO1877 3.8 44.5 1.0
O A:HOH2422 3.9 18.9 1.0
C A:ILE684 4.1 27.2 1.0
ND1 A:HIS627 4.2 18.8 1.0
O A:GLN685 4.2 30.3 1.0
O A:HOH2368 4.3 28.0 1.0
O A:HOH2366 4.3 28.8 1.0
ND1 A:HIS774 4.3 23.9 1.0
CB A:GLN685 4.3 28.9 1.0
CA A:GLN685 4.3 29.0 1.0
CG1 A:ILE684 4.5 25.2 1.0
CB A:ILE684 4.5 23.9 1.0
N A:ILE684 4.5 24.5 1.0
C A:PRO683 4.5 24.5 1.0
O2 A:EDO1877 4.6 45.2 1.0
C1 A:EDO1877 4.6 45.1 1.0
C A:GLN685 4.8 30.3 1.0
NE2 A:HIS774 4.9 29.1 1.0
NE2 A:HIS627 4.9 17.3 1.0

Chlorine binding site 2 out of 11 in 2vmf

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Chlorine binding site 2 out of 11 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:Cl1891

b:36.8
occ:0.50
 O A:HOH2269 2.6 14.3 0.5
O A:HOH2246 3.4 22.0 1.0
CG A:ARG447 3.6 16.1 1.0
CB A:ARG447 3.7 15.7 1.0
CA A:ARG447 4.0 17.0 1.0
OH A:TYR443 4.0 18.3 1.0
CD A:ARG447 4.0 12.3 1.0
CE1 A:TYR443 4.1 19.0 1.0
CZ A:TYR443 4.2 21.3 1.0
O A:HOH2276 4.4 35.2 1.0
N A:ARG447 4.6 17.4 1.0
O A:HOH2268 4.6 23.8 1.0
O A:HOH2272 4.8 30.1 1.0
O A:TYR443 4.9 15.7 1.0
CD1 A:TYR443 4.9 16.3 1.0

Chlorine binding site 3 out of 11 in 2vmf

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Chlorine binding site 3 out of 11 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:Cl1897

b:38.0
occ:0.60
 O A:HOH2018 2.6 42.1 1.0
O A:HOH2032 2.9 30.7 1.0
ND2 A:ASN77 3.1 18.8 1.0
CB A:PRO70 3.9 27.3 1.0
CG A:ASN77 4.1 25.0 1.0
CD2 A:TYR74 4.1 26.4 1.0
N A:ASN71 4.3 27.6 1.0
OD1 A:ASN77 4.3 24.7 1.0
CB A:TYR74 4.4 26.8 1.0
CG A:TYR74 4.6 27.5 1.0
CB A:ASN71 4.6 26.1 1.0
CA A:PRO70 4.7 26.5 1.0
O A:ASN71 4.8 22.2 1.0
O A:HOH2014 4.8 50.3 1.0
C A:PRO70 4.9 27.4 1.0
CA A:ASN71 5.0 26.0 1.0
CE2 A:TYR74 5.0 26.9 1.0

Chlorine binding site 4 out of 11 in 2vmf

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Chlorine binding site 4 out of 11 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:44.8
occ:1.00
 CA A:PRO786 3.7 37.0 1.0
CG A:GLU861 3.8 33.8 1.0
CG A:ARG860 3.8 31.7 1.0
N A:THR787 3.8 38.4 1.0
O A:THR787 4.0 38.0 1.0
N A:GLU861 4.1 28.7 1.0
CA A:GLU861 4.1 29.0 1.0
CE1 A:HIS858 4.2 30.7 1.0
CB A:PRO786 4.2 37.7 1.0
C A:ARG860 4.2 28.4 1.0
O A:ARG860 4.2 27.9 1.0
CB A:ARG860 4.3 28.8 1.0
C A:PRO786 4.3 37.7 1.0
CB A:GLU861 4.5 30.2 1.0
NE2 A:HIS858 4.5 31.7 1.0
CG A:PRO786 4.6 36.4 1.0
N A:PRO786 4.8 36.1 1.0
C A:THR787 4.8 38.5 1.0
NH1 A:ARG860 4.9 38.2 1.0
CD A:GLU861 4.9 39.7 1.0
CA A:THR787 4.9 38.5 1.0
OE2 A:GLU861 4.9 40.4 1.0
CA A:ARG860 4.9 27.7 1.0

Chlorine binding site 5 out of 11 in 2vmf

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Chlorine binding site 5 out of 11 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:Cl1883

b:31.7
occ:0.70
 NH1 B:ARG446 3.4 29.8 1.0
O B:HOH2283 3.5 26.0 1.0
CA B:TYR443 3.6 17.0 1.0
N B:TYR443 3.9 16.6 1.0
CB B:TYR443 4.0 17.0 1.0
CD1 B:TYR443 4.1 16.7 1.0
CG1 B:VAL442 4.1 16.6 1.0
CD B:ARG446 4.1 22.1 1.0
O B:HOH2286 4.1 32.0 1.0
C B:VAL442 4.4 17.0 1.0
O B:VAL442 4.5 17.5 1.0
CZ B:ARG446 4.5 31.0 1.0
CG B:TYR443 4.5 18.8 1.0
C B:TYR443 4.8 16.8 1.0
NE B:ARG446 4.8 28.6 1.0
O B:TYR443 4.9 17.6 1.0
CB B:VAL442 4.9 16.1 1.0

Chlorine binding site 6 out of 11 in 2vmf

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Chlorine binding site 6 out of 11 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:Cl1884

b:27.0
occ:0.50
 O B:HOH2116 1.9 11.1 0.5
NE2 B:HIS181 3.6 28.1 1.0
CE1 B:HIS181 3.7 28.4 1.0
O B:HOH2034 3.7 35.0 1.0
O B:HOH2032 3.9 26.0 1.0
CD2 B:LEU164 4.1 18.0 1.0
NZ B:LYS183 4.2 38.0 1.0
CD1 B:LEU164 4.3 17.5 1.0
CG2 B:ILE160 4.5 23.1 1.0
CG B:LEU164 4.8 19.7 1.0
CD B:LYS183 4.9 30.2 1.0
CD2 B:HIS181 5.0 29.2 1.0
ND1 B:HIS181 5.0 29.1 1.0

Chlorine binding site 7 out of 11 in 2vmf

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Chlorine binding site 7 out of 11 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:Cl1885

b:26.1
occ:1.00
 O B:HOH2141 3.2 20.5 1.0
NE2 B:GLN108 3.3 24.8 1.0
CG B:GLN108 3.7 23.1 1.0
CB B:PRO140 4.0 18.5 1.0
CD B:GLN108 4.0 24.0 1.0
N B:PRO140 4.0 19.5 1.0
CD B:PRO140 4.0 19.2 1.0
CA B:PRO140 4.1 19.1 1.0
CG2 B:THR138 4.1 20.1 1.0
ND2 B:ASN247 4.4 35.9 1.0
CG B:PRO140 4.5 21.3 1.0
O B:HOH2140 4.5 29.9 1.0
C B:LEU139 4.5 19.7 1.0
OH B:TYR218 4.7 16.9 1.0
O B:THR138 4.8 19.7 1.0
CB B:GLN108 4.9 21.4 1.0
CD1 B:ILE249 5.0 29.7 1.0

Chlorine binding site 8 out of 11 in 2vmf

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Chlorine binding site 8 out of 11 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:Cl1886

b:16.8
occ:1.00
 O B:HOH2404 2.6 23.5 1.0
N B:GLN685 3.4 25.1 1.0
CE1 B:HIS774 3.7 27.4 1.0
CE1 B:HIS627 3.8 18.8 1.0
CA B:ILE684 3.8 23.3 1.0
O1 B:EDO1877 3.8 40.9 1.0
O B:PRO683 3.9 23.1 1.0
CD1 B:ILE684 3.9 23.3 1.0
O B:HOH2435 4.0 19.4 1.0
C B:ILE684 4.1 24.2 1.0
O B:HOH2380 4.2 17.7 1.0
CB B:GLN685 4.2 26.3 1.0
ND1 B:HIS774 4.2 24.0 1.0
O B:GLN685 4.2 27.9 1.0
ND1 B:HIS627 4.2 19.8 1.0
CA B:GLN685 4.3 26.4 1.0
O B:HOH2379 4.4 24.9 1.0
O B:HOH2473 4.4 13.7 0.5
C B:PRO683 4.6 22.1 1.0
N B:ILE684 4.7 22.2 1.0
CB B:ILE684 4.7 22.2 1.0
CG1 B:ILE684 4.7 23.6 1.0
C B:GLN685 4.7 27.5 1.0
NE2 B:HIS774 4.9 26.1 1.0

Chlorine binding site 9 out of 11 in 2vmf

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Chlorine binding site 9 out of 11 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 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
B:Cl1892

b:29.9
occ:0.50
 CE B:MET298 1.2 20.4 0.5
SD B:MET298 2.6 29.1 0.5
SD B:MET298 2.9 26.8 0.5
ND2 B:ASN351 3.2 17.8 1.0
CE3 B:TRP302 3.5 17.7 1.0
CE B:MET298 3.7 29.3 0.5
CD B:PRO299 3.8 15.3 1.0
CB B:MET298 3.8 17.3 0.5
CB B:ASN351 4.0 16.7 1.0
CG B:MET298 4.0 19.9 0.5
CA B:MET298 4.0 17.2 0.5
CG B:ASN351 4.1 15.9 1.0
CG B:MET298 4.1 21.9 0.5
CA B:MET298 4.2 17.9 0.5
CB B:TRP302 4.2 22.1 1.0
CB B:MET298 4.2 18.4 0.5
CZ3 B:TRP302 4.3 18.7 1.0
CD2 B:TRP302 4.4 20.9 1.0
O B:VAL350 4.6 16.8 1.0
O B:TRP297 4.6 17.0 1.0
CG1 B:VAL350 4.7 15.6 1.0
CG B:TRP302 4.7 21.0 1.0
CG B:PRO299 4.8 18.2 1.0
O B:TRP302 4.8 22.6 1.0
N B:PRO299 4.9 17.1 1.0
CD1 B:ILE353 4.9 28.1 1.0
CD1 B:LEU699 4.9 25.8 1.0

Chlorine binding site 10 out of 11 in 2vmf

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Chlorine binding site 10 out of 11 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 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:Cl1893

b:28.3
occ:0.50
 O B:HOH2209 2.2 19.4 0.5
NE2 B:GLN324 2.8 33.0 1.0
N B:SER325 3.0 20.4 1.0
CD B:GLN324 3.6 28.4 1.0
CB B:SER325 3.7 19.7 1.0
O B:SER325 3.7 19.7 1.0
CA B:GLN324 3.7 20.3 1.0
CA B:SER325 3.8 20.6 1.0
C B:GLN324 3.9 20.4 1.0
CA B:GLY27 4.1 36.1 1.0
OE1 B:GLU323 4.1 23.8 1.0
OE1 B:GLN324 4.2 30.3 1.0
C B:SER325 4.2 19.6 1.0
CG B:GLN324 4.3 24.0 1.0
N B:GLY27 4.4 37.2 1.0
O B:GLU323 4.5 20.0 1.0
CB B:GLN324 4.5 19.7 1.0
OG B:SER325 4.6 26.3 1.0
N B:GLN324 4.7 19.8 1.0
CD B:GLU323 4.9 27.2 1.0
C B:GLU323 5.0 19.4 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 Dec 12 09:21:01 2020

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