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Chlorine in PDB 5n6s: Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic

Enzymatic activity of Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic

All present enzymatic activity of Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic:
3.2.1.21;

Protein crystallography data

The structure of Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic, PDB code: 5n6s was solved by W.Offen, G.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.91 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.626, 76.674, 95.257, 72.34, 86.39, 85.54
R / Rfree (%) 23.9 / 31

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic (pdb code 5n6s). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic, PDB code: 5n6s:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5n6s

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Chlorine binding site 1 out of 6 in the Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:49.7
occ:1.00
 O A:HOH727 2.3 17.8 0.5
N A:MET32 2.9 19.5 1.0
CA A:GLY31 3.4 17.9 1.0
C A:GLY31 3.6 18.2 1.0
CB A:MET32 3.9 21.0 1.0
CA A:MET32 4.0 19.9 1.0
CG A:MET32 4.0 22.4 1.0
O A:HOH690 4.1 21.5 1.0
CE A:MET32 4.3 25.8 1.0
O A:PRO87 4.5 18.7 1.0
O A:MET32 4.6 17.4 1.0
N A:GLY31 4.7 17.4 1.0
C A:MET32 4.8 17.3 1.0
O A:ALA30 4.8 17.4 1.0
O A:GLY31 4.9 15.8 1.0

Chlorine binding site 2 out of 6 in 5n6s

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Chlorine binding site 2 out of 6 in the Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:46.9
occ:1.00
 N A:ARG137 3.6 25.5 1.0
OD1 A:ASN136 3.8 25.4 1.0
CG A:ARG137 4.0 29.3 1.0
CB C:LEU130 4.0 24.1 1.0
CA A:ASN136 4.1 25.9 1.0
CD1 C:LEU130 4.2 24.2 1.0
CB A:ARG137 4.2 28.5 1.0
O A:ALA135 4.2 23.1 1.0
C A:ASN136 4.4 23.3 1.0
CD A:ARG137 4.5 30.4 1.0
CA A:ARG137 4.5 27.3 1.0
CG A:ASN136 4.6 24.6 1.0
CG C:LEU130 4.8 25.4 1.0
O C:LEU130 4.9 20.9 1.0
CB A:ASN136 4.9 22.5 1.0

Chlorine binding site 3 out of 6 in 5n6s

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Chlorine binding site 3 out of 6 in the Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl509

b:58.9
occ:1.00
 O B:HOH620 3.0 31.9 1.0
N B:GLY9 3.2 33.3 1.0
O B:HOH727 3.6 37.5 1.0
CA B:GLY9 4.0 31.4 1.0
CA B:GLU8 4.1 42.8 1.0
C B:GLU8 4.1 36.9 1.0
CG B:GLU8 4.2 42.8 0.5
ND2 B:ASN442 4.2 35.5 1.0
OE1 B:GLU8 4.4 42.4 0.5
CD B:GLU8 4.6 43.4 0.5
CG B:ASN442 4.6 39.5 1.0
CB B:GLU8 4.7 43.0 1.0
O B:HOH699 4.7 36.2 1.0
N B:PHE10 4.8 26.0 1.0
C B:GLY9 4.8 30.6 1.0
O B:PRO7 4.8 30.2 1.0

Chlorine binding site 4 out of 6 in 5n6s

Go back to Chlorine Binding Sites List in 5n6s
Chlorine binding site 4 out of 6 in the Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl510

b:44.8
occ:1.00
 N B:MET32 3.1 19.4 1.0
CA B:GLY31 3.5 18.3 1.0
C B:GLY31 3.8 19.1 1.0
O B:HOH675 4.0 10.2 1.0
CB B:MET32 4.1 22.8 1.0
CA B:MET32 4.2 20.6 1.0
CG B:MET32 4.4 23.2 1.0
CE B:MET32 4.5 26.2 1.0
O B:HOH725 4.5 44.1 1.0
O B:PRO87 4.6 23.6 1.0
N B:GLY31 4.8 19.1 1.0
O B:ALA30 4.8 18.7 1.0
OE1 B:GLU88 4.8 38.6 0.5
O B:MET32 4.9 18.6 1.0

Chlorine binding site 5 out of 6 in 5n6s

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Chlorine binding site 5 out of 6 in the Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:58.6
occ:1.00
 O A:HOH638 3.3 25.9 1.0
N C:ARG137 3.4 24.9 1.0
CB C:ARG137 3.5 27.6 1.0
OD1 C:ASN136 3.7 22.6 1.0
CA C:ASN136 4.1 21.6 1.0
CA C:ARG137 4.1 26.3 1.0
C C:ASN136 4.2 23.3 1.0
CG C:ASN136 4.2 23.4 1.0
CB A:LEU130 4.3 20.2 1.0
O2 C:EDO501 4.4 33.2 1.0
O C:ALA135 4.4 17.4 1.0
CG A:LYS131 4.5 22.8 1.0
C1 C:EDO501 4.5 33.7 1.0
CD A:LYS131 4.7 28.2 1.0
CB C:ASN136 4.7 22.4 1.0
CD1 A:LEU130 4.8 22.6 1.0
O A:LEU130 4.8 19.3 1.0
CG C:ARG137 4.9 30.1 1.0
N C:GLU138 5.0 23.3 1.0
C A:LEU130 5.0 20.6 1.0

Chlorine binding site 6 out of 6 in 5n6s

Go back to Chlorine Binding Sites List in 5n6s
Chlorine binding site 6 out of 6 in the Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Thermotoga Maritima Family 1 Glycoside Hydrolase Complexed with Carba- Cyclophellitol Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl505

b:60.0
occ:1.00
 O D:HOH616 3.0 31.6 1.0
N D:ARG137 3.3 21.2 1.0
CB D:ARG137 3.6 22.8 1.0
OD1 D:ASN136 4.0 22.2 1.0
CA D:ASN136 4.0 20.0 1.0
CA D:ARG137 4.1 22.2 1.0
CG D:ARG137 4.1 23.6 1.0
C D:ASN136 4.2 20.1 1.0
O1 D:EDO504 4.2 20.9 0.5
C2 D:EDO504 4.4 21.2 0.5
O D:ALA135 4.4 20.7 1.0
CG D:ASN136 4.5 24.1 1.0
CD D:ARG137 4.8 23.7 1.0
CB D:ASN136 4.8 21.7 1.0
C1 D:EDO504 4.9 20.0 0.5

Reference:

T.J.M.Beenakker, D.P.A.Wander, W.A.Offen, M.Artola, L.Raich, M.J.Ferraz, K.Y.Li, J.H.P.M.Houben, E.R.Van Rijssel, T.Hansen, G.A.Van Der Marel, J.D.C.Codee, J.M.F.G.Aerts, C.Rovira, G.J.Davies, H.S.Overkleeft. Carba-Cyclophellitols Are Neutral Retaining-Glucosidase Inhibitors. J. Am. Chem. Soc. V. 139 6534 2017.
ISSN: ESSN 1520-5126
PubMed: 28463498
DOI: 10.1021/JACS.7B01773
Page generated: Sat Dec 12 12:08:38 2020

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