Atomistry » Chlorine » PDB 2vo5-2vv7 » 2vr4
Atomistry »
  Chlorine »
    PDB 2vo5-2vv7 »
      2vr4 »

Chlorine in PDB 2vr4: Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure

Enzymatic activity of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure

All present enzymatic activity of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure:
3.2.1.25;

Protein crystallography data

The structure of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure, PDB code: 2vr4 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) 65.37 / 1.8
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.195, 114.738, 99.173, 90.00, 113.03, 90.00
R / Rfree (%) 17.7 / 22.2

Other elements in 2vr4:

The structure of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure also contains other interesting chemical elements:

Bromine (Br) 8 atoms

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure (pdb code 2vr4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure, PDB code: 2vr4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 1 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1880

b:33.5
occ:1.00
 N A:THR477 3.3 40.0 1.0
CA A:PHE476 3.6 42.8 1.0
CG2 A:VAL480 3.8 29.9 1.0
CD1 A:PHE476 3.8 39.9 1.0
CG2 A:THR477 3.8 38.8 1.0
CB A:PHE476 3.9 42.5 1.0
CB A:VAL480 3.9 30.1 1.0
C A:PHE476 4.0 41.5 1.0
CG1 A:VAL480 4.1 26.9 1.0
OG1 A:THR477 4.1 38.5 1.0
CB A:PHE172 4.2 23.5 1.0
CB A:THR477 4.3 38.8 1.0
CG A:PHE476 4.3 42.2 1.0
CA A:THR477 4.4 39.0 1.0
O A:LYS475 4.7 45.7 1.0
CG A:PHE172 4.8 22.7 1.0
CE1 A:PHE476 4.9 42.0 1.0
N A:PHE476 4.9 43.8 1.0

Chlorine binding site 2 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 2 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1887

b:23.6
occ:0.60
 O A:HOH2464 2.5 25.1 1.0
N A:GLN685 3.2 24.5 1.0
O2 A:EDO1894 3.2 59.6 1.0
CD1 A:ILE684 3.6 17.4 1.0
CA A:ILE684 3.7 22.7 1.0
CE1 A:HIS774 3.7 28.0 1.0
CE1 A:HIS627 3.8 21.7 1.0
C A:ILE684 3.9 23.6 1.0
O A:GLN685 4.0 25.2 1.0
O A:PRO683 4.0 23.7 1.0
CB A:GLN685 4.0 25.2 1.0
CA A:GLN685 4.1 24.8 1.0
O A:HOH2505 4.2 26.5 1.0
C2 A:EDO1894 4.4 59.9 1.0
ND1 A:HIS774 4.4 25.3 1.0
ND1 A:HIS627 4.4 21.9 1.0
C A:GLN685 4.5 26.2 1.0
CG1 A:ILE684 4.5 23.1 1.0
CB A:ILE684 4.6 21.2 1.0
N A:ILE684 4.6 22.7 1.0
C A:PRO683 4.7 22.9 1.0
O A:HOH2434 4.7 23.0 1.0
NE2 A:HIS774 4.8 28.4 1.0
O A:HOH2433 4.9 25.8 1.0
NE2 A:HIS627 4.9 19.4 1.0

Chlorine binding site 3 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 3 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1890

b:18.6
occ:0.50
 OG A:SER589 0.6 22.9 0.5
CB A:SER589 2.0 23.6 0.5
OG A:SER589 2.7 13.8 0.5
CA A:SER589 2.7 23.4 0.5
OH A:TYR537 2.8 26.5 1.0
N A:SER590 2.8 24.7 0.5
CE1 A:TYR537 2.9 24.8 1.0
C A:SER589 2.9 24.2 0.5
CZ A:TYR537 3.2 23.3 1.0
N A:ILE591 3.3 24.8 0.5
O A:ILE591 3.3 25.1 0.5
NE1 A:TRP536 3.3 20.3 1.0
CB A:SER589 3.7 13.2 0.5
O A:SER589 3.8 24.9 0.5
CG1 A:ILE591 3.9 15.9 0.5
CA A:SER590 3.9 24.8 0.5
CD1 A:TYR537 4.0 24.8 1.0
CZ2 A:TRP656 4.0 20.5 1.0
C A:ILE591 4.0 24.7 0.5
N A:SER589 4.1 22.9 0.5
C A:SER590 4.1 25.0 0.5
OG A:SER590 4.1 24.8 0.5
CA A:ILE591 4.1 25.0 0.5
CD1 A:TRP536 4.2 19.1 1.0
CD1 A:ILE591 4.2 16.4 0.5
CE2 A:TRP536 4.2 19.7 1.0
CE2 A:TYR537 4.4 22.0 1.0
CH2 A:TRP656 4.4 23.3 1.0
CB A:ILE591 4.4 24.8 0.5
CZ2 A:TRP536 4.5 21.4 1.0
CB A:SER590 4.6 25.5 0.5
CA A:SER589 4.6 13.2 0.5
OE1 A:GLN587 4.7 19.5 0.5
O6 A:17B1865 5.0 17.6 1.0

Chlorine binding site 4 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 4 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1892

b:63.4
occ:1.00
 O A:ASN337 3.7 23.2 1.0
O A:HOH2254 3.9 31.6 1.0
CD A:GLU344 4.1 27.1 1.0
OE1 A:GLU344 4.1 22.3 1.0
O1 A:EDO1871 4.1 28.6 1.0
O A:HOH2085 4.1 41.9 1.0
OE2 A:GLU344 4.2 24.4 1.0
O A:HOH2247 4.3 32.3 1.0
OD1 A:ASN337 4.3 20.5 1.0
C A:ASN337 4.5 23.1 1.0
N A:LYS339 4.6 26.4 1.0
CG A:GLU344 4.6 21.2 1.0
CG A:LYS339 4.6 28.8 1.0
CA A:GLU338 4.7 26.1 1.0
CG A:ASN337 4.7 21.2 1.0
CE A:LYS339 4.8 37.5 1.0
N A:GLU338 4.9 24.0 1.0
O A:HOH2245 4.9 24.3 1.0
ND2 A:ASN337 4.9 16.6 1.0
C A:GLU338 4.9 25.6 1.0

Chlorine binding site 5 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 5 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1897

b:28.4
occ:0.50
 O A:HOH2418 2.3 19.6 0.5
OD1 A:ASP603 3.0 30.8 1.0
N A:THR779 3.1 22.6 1.0
CA A:LYS778 3.3 23.3 1.0
CB A:LYS778 3.7 23.0 1.0
C A:LYS778 3.7 23.1 1.0
CG A:ASP603 3.7 27.6 1.0
CB A:ASP603 3.7 22.8 1.0
OG1 A:THR779 3.7 20.0 1.0
O A:ASP603 3.8 20.2 1.0
O A:HOH2508 3.9 23.4 1.0
CB A:THR779 4.0 21.8 1.0
CA A:THR779 4.1 22.1 1.0
CG A:LYS778 4.2 24.4 1.0
CA A:ASP603 4.4 21.6 1.0
C A:ASP603 4.5 20.6 1.0
N A:LYS778 4.6 22.2 1.0
OH A:TYR604 4.6 20.3 1.0
O A:HOH2373 4.6 39.2 1.0
CZ A:TYR604 4.7 20.3 1.0
O A:ARG777 4.7 21.3 1.0
O A:HOH2431 4.7 37.8 1.0
CE2 A:TYR604 4.8 21.1 1.0
OD2 A:ASP603 4.8 31.1 1.0
C1 A:EDO1894 4.9 59.9 1.0
O A:HOH2519 4.9 22.0 1.0
O A:LYS778 4.9 23.4 1.0

Chlorine binding site 6 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 6 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1883

b:31.3
occ:1.00
 O B:HOH2165 3.2 21.3 1.0
NE2 B:GLN108 3.4 29.1 1.0
CG B:GLN108 3.7 25.3 1.0
CB B:PRO140 3.9 20.3 1.0
N B:PRO140 4.0 18.6 1.0
CD B:GLN108 4.1 26.2 1.0
CD B:PRO140 4.1 19.2 1.0
CA B:PRO140 4.1 19.2 1.0
ND2 B:ASN247 4.2 32.6 1.0
CG2 B:THR138 4.2 19.3 1.0
CG B:PRO140 4.4 21.4 1.0
C B:LEU139 4.6 17.7 1.0
O B:HOH2191 4.6 24.6 1.0
O B:THR138 4.8 17.8 1.0
OH B:TYR218 4.8 20.4 1.0
CB B:GLN108 4.9 20.1 1.0

Chlorine binding site 7 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 7 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1891

b:54.7
occ:1.00
 O B:HOH2268 2.6 28.1 1.0
ND2 B:ASN390 3.1 12.1 1.0
O B:ASN300 3.1 16.1 1.0
O B:HOH2295 3.9 28.7 1.0
CD1 B:TRP302 4.0 22.8 1.0
NE1 B:TRP302 4.0 18.2 1.0
CG B:ASN390 4.1 12.2 1.0
CB B:ASN390 4.1 11.2 1.0
O B:HOH2474 4.1 24.6 1.0
C B:ASN300 4.3 15.8 1.0
CG B:TRP302 4.3 17.0 1.0
CE2 B:TRP302 4.3 18.3 1.0
CA B:GLY301 4.4 18.3 1.0
CG B:MET355 4.5 16.8 1.0
CD2 B:TRP302 4.5 18.0 1.0
CE B:LYS358 4.6 15.9 1.0
SD B:MET355 4.6 17.2 1.0
NZ B:LYS358 4.7 13.5 1.0
C B:GLY301 4.7 19.5 1.0
N B:GLY301 4.8 17.1 1.0
CB B:ASP697 4.9 21.9 1.0
N B:TRP302 4.9 17.8 1.0
O B:ASP697 4.9 22.6 1.0
O B:PHE356 5.0 11.6 1.0

Chlorine binding site 8 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 8 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1894

b:43.5
occ:0.70
 CE B:MET298 1.3 2.0 0.3
SD B:MET298 2.9 16.9 0.3
ND2 B:ASN351 3.2 12.7 1.0
SD B:MET298 3.3 31.7 0.7
CE3 B:TRP302 3.5 17.1 1.0
CB B:ASN351 3.8 15.9 1.0
CD B:PRO299 3.9 15.4 1.0
CG B:ASN351 4.0 14.5 1.0
CG B:MET298 4.1 14.5 0.3
CB B:MET298 4.1 15.4 0.7
CZ3 B:TRP302 4.2 19.7 1.0
O B:VAL350 4.3 16.1 1.0
CA B:MET298 4.3 15.0 0.7
CG B:MET298 4.4 21.1 0.7
CB B:TRP302 4.4 17.1 1.0
CA B:MET298 4.4 13.9 0.3
CD2 B:TRP302 4.5 18.0 1.0
CD1 B:ILE353 4.5 25.9 1.0
CB B:MET298 4.5 13.5 0.3
CG1 B:VAL350 4.8 16.1 1.0
C B:VAL350 4.8 15.7 1.0
CE B:MET298 4.8 26.6 0.7
O B:TRP297 4.9 12.5 1.0
CG B:TRP302 4.9 17.0 1.0
CG B:PRO299 4.9 16.0 1.0
O B:TRP302 4.9 20.8 1.0
CD1 B:LEU699 5.0 21.7 1.0
N B:PRO299 5.0 14.5 1.0

Chlorine binding site 9 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 9 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1901

b:36.6
occ:0.50
 O A:HOH2499 2.2 29.2 0.5
NE2 A:GLN768 3.2 37.8 1.0
CA A:ALA770 3.6 27.9 1.0
O A:HOH2500 3.7 23.1 1.0
N A:ALA770 3.7 28.5 1.0
C A:ALA770 3.8 28.2 1.0
CG A:GLN768 3.9 36.6 1.0
C A:VAL769 3.9 30.3 1.0
N A:GLU771 4.0 26.7 1.0
CD A:GLN768 4.0 39.4 1.0
O A:VAL769 4.1 30.7 1.0
O A:ALA770 4.3 27.3 1.0
CG A:GLU771 4.3 32.8 1.0
O A:GLN768 4.6 34.9 1.0
CB A:GLU771 4.6 27.8 1.0
CD A:GLU771 4.6 39.3 1.0
CB A:GLN768 4.7 35.8 1.0
C A:GLN768 4.7 34.5 1.0
OE2 A:GLU771 4.7 39.8 1.0
CA A:VAL769 4.7 31.6 1.0
N A:VAL769 4.8 32.4 1.0
O A:HOH2497 4.8 40.2 1.0
CA A:GLU771 4.9 27.5 1.0

Chlorine binding site 10 out of 11 in 2vr4

Go back to Chlorine Binding Sites List in 2vr4
Chlorine binding site 10 out of 11 in the Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Transition-State Mimicry in Mannoside Hydrolysis: Characterisation of Twenty Six Inhibitors and Insight Into Binding From Linear Free Energy Relationships and 3-D Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1902

b:47.6
occ:0.70
 O B:HOH2332 3.1 20.6 1.0
O B:HOH2564 3.2 45.0 1.0
O B:ARG447 3.7 13.0 1.0
O B:HOH2305 3.8 22.3 1.0
CE1 B:HIS326 3.9 18.6 1.0
O B:HOH2241 4.2 29.2 1.0
O B:HOH2333 4.4 17.2 1.0
O B:HOH2330 4.5 20.9 0.5
O1 B:EDO1882 4.5 18.1 1.0
ND1 B:HIS326 4.5 17.3 1.0
CG B:ARG447 4.5 10.8 1.0
C B:ARG447 4.6 12.2 1.0
CA B:ARG447 4.6 13.1 1.0
O B:HOH2175 4.7 23.9 1.0
O B:HOH2055 4.7 27.3 0.5
OD1 B:ASN403 4.7 13.4 1.0
ND2 B:ASN403 4.7 14.8 1.0
O B:HOH2306 4.8 21.4 1.0
CG B:ASN403 4.9 15.1 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 12:10:55 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy