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Chlorine in PDB 3zoa: The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose

Enzymatic activity of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose

All present enzymatic activity of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose:
3.2.1.1; 5.4.99.16;

Protein crystallography data

The structure of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose, PDB code: 3zoa was solved by S.Caner, N.Nguyen, A.Aguda, R.Zhang, Y.T.Pan, S.G.Withers, G.D.Brayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.816 / 1.85
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 127.180, 127.180, 216.950, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.81

Other elements in 3zoa:

The structure of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose (pdb code 3zoa). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose, PDB code: 3zoa:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3zoa

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Chlorine binding site 1 out of 7 in the The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1589

b:24.8
occ:1.00
 O A:HOH2326 3.1 25.1 1.0
N A:ASN340 3.2 24.0 1.0
NH1 A:ARG374 3.2 26.4 1.0
ND1 A:HIS341 3.4 26.4 1.0
N A:ARG375 3.6 21.0 1.0
N A:HIS341 3.6 24.0 1.0
CA A:ARG374 3.8 21.3 1.0
CD A:ARG374 3.8 24.3 1.0
CA A:ASN340 3.9 25.1 1.0
O A:ARG375 4.0 22.7 1.0
CB A:ARG339 4.0 26.8 1.0
O A:ILE373 4.0 23.8 1.0
CB A:ASN340 4.0 24.1 1.0
CA A:ARG339 4.1 25.5 1.0
C A:ARG339 4.1 26.5 1.0
C A:ASN340 4.1 28.3 1.0
CB A:HIS341 4.2 23.8 1.0
CG A:HIS341 4.2 29.2 1.0
C A:ARG374 4.2 22.2 1.0
CZ A:ARG374 4.3 25.7 1.0
CE1 A:HIS341 4.3 30.1 1.0
CA A:HIS341 4.5 23.1 1.0
CB A:ARG374 4.5 23.1 1.0
NE A:ARG374 4.5 27.2 1.0
CG A:ARG374 4.6 23.0 1.0
CD1 A:LEU380 4.6 29.6 1.0
CA A:ARG375 4.6 21.9 1.0
N A:ARG374 4.7 23.2 1.0
C A:ARG375 4.8 22.4 1.0
O A:HIS341 4.8 27.2 1.0
C A:ILE373 4.8 26.6 1.0
O A:HOH2323 4.8 26.7 0.8
CB A:ARG375 4.9 20.8 1.0

Chlorine binding site 2 out of 7 in 3zoa

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Chlorine binding site 2 out of 7 in the The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1590

b:30.0
occ:1.00
 NH1 A:ARG228 3.1 38.8 1.0
N A:GLU343 3.2 27.2 1.0
NH1 A:ARG339 3.4 24.8 1.0
NH2 A:ARG228 3.4 35.1 1.0
CZ A:ARG228 3.7 37.4 1.0
CG A:GLU343 3.8 30.7 1.0
CA A:ASP342 3.8 27.3 1.0
CB A:GLU343 3.9 30.8 1.0
C A:ASP342 4.0 27.6 1.0
CE1 A:PHE300 4.0 30.4 1.0
CZ A:PHE337 4.1 28.8 1.0
CE2 A:PHE337 4.1 25.9 1.0
CD A:ARG339 4.1 26.1 1.0
CA A:GLU343 4.1 30.2 1.0
CZ A:PHE300 4.3 33.1 1.0
OD2 A:ASP342 4.4 45.1 1.0
CH2 A:TRP79 4.4 33.7 1.0
O A:HIS341 4.5 27.2 1.0
CZ A:ARG339 4.5 25.6 1.0
CG A:ASP342 4.5 39.0 1.0
OE1 A:GLU343 4.5 32.7 1.0
CD A:GLU343 4.6 36.4 1.0
CB A:ASP342 4.7 28.1 1.0
NE A:ARG339 4.8 26.6 1.0
N A:ASP342 4.9 25.3 1.0
CZ2 A:TRP79 4.9 31.8 1.0

Chlorine binding site 3 out of 7 in 3zoa

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Chlorine binding site 3 out of 7 in the The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1591

b:30.4
occ:1.00
 O A:HOH2011 3.1 24.8 1.0
NE A:ARG47 3.2 38.6 1.0
O A:HOH2018 3.2 35.5 1.0
N A:ARG47 3.3 20.1 1.0
O A:HOH2013 3.4 38.8 0.9
CZ A:PHE105 3.6 28.6 1.0
N A:VAL46 3.6 20.5 1.0
CG A:ARG47 3.7 28.7 1.0
CB A:ARG47 3.7 20.9 1.0
NH2 A:ARG47 3.8 40.2 1.0
CE2 A:PHE105 3.8 28.9 1.0
CZ A:ARG47 3.9 45.9 1.0
CB A:LEU45 3.9 23.6 1.0
CD A:ARG47 4.0 31.9 1.0
CD2 A:LEU45 4.0 35.0 1.0
CG A:LEU45 4.0 28.9 1.0
CA A:ARG47 4.1 16.6 1.0
C A:LEU45 4.1 21.3 1.0
CB A:VAL46 4.2 21.8 1.0
CA A:VAL46 4.2 20.4 1.0
CA A:LEU45 4.2 21.0 1.0
C A:VAL46 4.2 20.4 1.0
O A:PRO82 4.3 27.6 1.0
O A:HOH2014 4.5 41.3 0.7
CE1 A:PHE105 4.6 22.1 1.0
CD2 A:PHE105 5.0 25.1 1.0
CG2 A:VAL46 5.0 20.8 1.0

Chlorine binding site 4 out of 7 in 3zoa

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Chlorine binding site 4 out of 7 in the The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1592

b:35.7
occ:1.00
 N A:VAL108 3.2 24.8 1.0
N A:VAL101 3.4 25.1 1.0
O A:HOH2099 3.5 31.5 0.9
CG1 A:VAL108 3.7 33.6 1.0
CA A:THR107 3.7 25.5 1.0
C A:THR107 3.8 26.2 1.0
CA A:LYS100 3.9 26.8 1.0
CB A:THR107 3.9 30.5 1.0
CG A:LYS100 4.0 33.0 1.0
CG2 A:VAL108 4.0 34.1 1.0
CB A:VAL101 4.1 21.7 1.0
CB A:VAL108 4.2 29.9 1.0
CA A:VAL108 4.2 22.2 1.0
C A:LYS100 4.2 24.3 1.0
CG2 A:VAL101 4.2 25.0 1.0
CA A:VAL101 4.3 21.4 1.0
CB A:LYS100 4.5 30.8 1.0
O A:VAL101 4.5 24.9 1.0
O A:TYR99 4.5 30.6 1.0
CG2 A:THR107 4.7 27.0 1.0
C A:VAL101 4.9 24.1 1.0
O A:GLY106 4.9 23.3 1.0
O A:THR107 5.0 22.9 1.0

Chlorine binding site 5 out of 7 in 3zoa

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Chlorine binding site 5 out of 7 in the The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1588

b:30.2
occ:1.00
 NH1 B:ARG228 3.2 32.2 1.0
N B:GLU343 3.2 26.9 1.0
NH2 B:ARG228 3.4 37.5 1.0
NH1 B:ARG339 3.4 27.1 1.0
CZ B:ARG228 3.7 36.2 1.0
CA B:ASP342 3.8 27.3 1.0
CG B:GLU343 3.8 31.7 1.0
CB B:GLU343 4.0 31.6 1.0
CZ B:PHE337 4.0 28.4 1.0
CE2 B:PHE337 4.0 30.1 1.0
CE1 B:PHE300 4.0 30.1 1.0
C B:ASP342 4.0 27.6 1.0
CD B:ARG339 4.1 27.7 1.0
CZ B:PHE300 4.1 30.5 1.0
CA B:GLU343 4.2 29.3 1.0
OD2 B:ASP342 4.4 43.0 1.0
O B:HIS341 4.4 27.6 1.0
CG B:ASP342 4.5 38.0 1.0
CZ B:ARG339 4.5 27.2 1.0
CH2 B:TRP79 4.5 34.9 1.0
OE1 B:GLU343 4.6 29.1 1.0
CD B:GLU343 4.6 33.4 1.0
CB B:ASP342 4.6 30.9 1.0
NE B:ARG339 4.8 27.7 1.0
N B:ASP342 4.9 24.2 1.0

Chlorine binding site 6 out of 7 in 3zoa

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Chlorine binding site 6 out of 7 in the The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1589

b:24.7
occ:1.00
 O B:HOH2299 3.1 25.6 1.0
N B:ASN340 3.2 22.3 1.0
NH1 B:ARG374 3.3 21.2 1.0
ND1 B:HIS341 3.5 29.1 1.0
N B:HIS341 3.6 21.5 1.0
N B:ARG375 3.6 21.6 1.0
CD B:ARG374 3.7 24.5 1.0
CA B:ARG374 3.8 22.8 1.0
CB B:ARG339 3.9 22.4 1.0
CA B:ASN340 4.0 24.1 1.0
O B:ILE373 4.0 24.3 1.0
O B:ARG375 4.0 24.0 1.0
CA B:ARG339 4.0 23.4 1.0
C B:ARG339 4.1 28.2 1.0
CB B:ASN340 4.1 24.9 1.0
C B:ASN340 4.2 27.0 1.0
CB B:HIS341 4.2 24.7 1.0
C B:ARG374 4.2 23.5 1.0
CG B:HIS341 4.3 27.2 1.0
CZ B:ARG374 4.3 25.3 1.0
CA B:HIS341 4.4 22.9 1.0
CE1 B:HIS341 4.5 28.5 1.0
NE B:ARG374 4.5 24.6 1.0
CG B:ARG374 4.5 21.1 1.0
CB B:ARG374 4.5 21.8 1.0
CD1 B:LEU380 4.6 28.6 1.0
CA B:ARG375 4.6 23.0 1.0
N B:ARG374 4.7 21.7 1.0
O B:HIS341 4.8 27.6 1.0
C B:ILE373 4.8 26.7 1.0
C B:ARG375 4.8 25.4 1.0
O B:HOH2296 4.8 26.5 0.8
CB B:ARG375 4.9 22.2 1.0

Chlorine binding site 7 out of 7 in 3zoa

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Chlorine binding site 7 out of 7 in the The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Structure of Trehalose Synthase (Tres) of Mycobacterium Smegmatis in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1591

b:33.8
occ:1.00
 O B:HOH2017 3.1 24.5 1.0
NE B:ARG47 3.2 39.0 1.0
O B:HOH2021 3.2 32.0 0.9
N B:ARG47 3.2 19.9 1.0
CZ B:PHE105 3.5 32.5 1.0
N B:VAL46 3.6 22.1 1.0
CB B:ARG47 3.6 21.7 1.0
CG B:ARG47 3.7 28.3 1.0
CE2 B:PHE105 3.8 31.9 1.0
NH2 B:ARG47 3.9 41.2 1.0
CB B:LEU45 3.9 24.0 1.0
CD2 B:LEU45 4.0 34.8 1.0
CZ B:ARG47 4.0 45.8 1.0
CD B:ARG47 4.0 33.3 1.0
CA B:ARG47 4.1 18.9 1.0
CG B:LEU45 4.1 29.6 1.0
CB B:VAL46 4.1 22.1 1.0
CA B:VAL46 4.2 23.1 1.0
C B:VAL46 4.2 23.1 1.0
C B:LEU45 4.2 20.5 1.0
O B:PRO82 4.2 29.2 1.0
CA B:LEU45 4.3 23.7 1.0
CE1 B:PHE105 4.4 28.0 1.0
CD2 B:PHE105 4.8 29.1 1.0
CG2 B:VAL46 5.0 23.1 1.0

Reference:

S.Caner, N.Nguyen, A.Aguda, R.Zhang, Y.T.Pan, S.G.Withers, G.D.Brayer. The Structure of the Mycobacterium Smegmatis Trehalose Synthase Reveals An Unusual Active Site Configuration and Acarbose-Binding Mode. Glycobiology V. 23 1075 2013.
ISSN: ISSN 0959-6658
PubMed: 23735230
DOI: 10.1093/GLYCOB/CWT044
Page generated: Sun Jul 21 08:16:41 2024

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