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Chlorine in PDB 2wbk: Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis

Enzymatic activity of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis

All present enzymatic activity of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis:
3.2.1.25;

Protein crystallography data

The structure of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis, PDB code: 2wbk was solved by W.A.Offen, D.L.Zechel, S.G.Withers, 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) 47.84 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.447, 115.504, 97.705, 90.00, 115.99, 90.00
R / Rfree (%) 16.9 / 23.2

Other elements in 2wbk:

The structure of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Bromine (Br) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis (pdb code 2wbk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis, PDB code: 2wbk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 2wbk

Go back to Chlorine Binding Sites List in 2wbk
Chlorine binding site 1 out of 7 in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1867

b:18.9
occ:0.50
 O A:HOH2390 2.0 5.2 0.5
O A:ALA517 3.0 19.9 1.0
O A:HOH2392 3.2 20.2 1.0
O A:LEU516 3.3 16.3 1.0
CB A:GLU465 3.4 17.9 1.0
CG A:GLU465 3.6 22.4 1.0
CE2 A:TYR469 3.6 19.7 1.0
C A:ALA517 3.7 19.4 1.0
CD A:GLU465 3.7 27.4 1.0
CB A:ASN518 3.8 20.1 1.0
CA A:GLU465 3.8 18.1 1.0
OE2 A:GLU465 3.8 32.2 1.0
CD2 A:TYR469 3.9 21.4 1.0
CG A:PRO514 3.9 15.3 1.0
C A:LEU516 3.9 18.0 1.0
CA A:ASN518 4.0 20.7 1.0
N A:ASN518 4.1 19.8 1.0
OE1 A:GLU465 4.2 28.9 1.0
ND2 A:ASN518 4.3 19.0 1.0
O A:PRO514 4.4 16.1 1.0
N A:GLU465 4.4 17.2 1.0
N A:ALA517 4.4 18.7 1.0
CG A:ASN518 4.6 19.8 1.0
CA A:ALA517 4.7 18.4 1.0
CA A:LEU516 4.7 18.6 1.0
O A:HOH2393 4.8 16.0 1.0
O A:HOH2388 4.9 12.5 1.0
CZ A:TYR469 4.9 20.2 1.0
CD A:PRO514 4.9 15.8 1.0
CB A:PRO514 4.9 14.9 1.0
O A:HOH2356 4.9 18.8 1.0
N A:LEU516 5.0 18.4 1.0

Chlorine binding site 2 out of 7 in 2wbk

Go back to Chlorine Binding Sites List in 2wbk
Chlorine binding site 2 out of 7 in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1880

b:37.9
occ:1.00
 N B:ILE578 3.2 20.5 1.0
C1 B:EDO1878 3.3 36.2 1.0
O1 B:EDO1878 3.5 35.8 1.0
CA B:GLN577 3.7 21.7 1.0
O B:HOH2396 3.7 23.5 1.0
CG1 B:ILE578 3.9 20.8 1.0
C B:GLN577 3.9 21.3 1.0
CB B:GLN577 4.0 21.9 1.0
CB B:ILE578 4.1 22.4 1.0
CA B:ILE578 4.2 21.2 1.0
CD1 B:PHE610 4.2 23.0 1.0
CD1 B:ILE578 4.3 21.8 1.0
CB B:PHE610 4.4 20.0 1.0
O B:TYR576 4.6 22.1 1.0
CG B:GLN577 4.6 22.9 1.0
CA B:PHE610 4.7 19.9 1.0
C2 B:EDO1878 4.7 37.5 1.0
CG B:PHE610 4.8 23.8 1.0
N B:PHE610 4.9 21.1 1.0
N B:GLN577 5.0 20.7 1.0

Chlorine binding site 3 out of 7 in 2wbk

Go back to Chlorine Binding Sites List in 2wbk
Chlorine binding site 3 out of 7 in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1893

b:31.1
occ:1.00
 O A:HOH2289 2.7 11.2 1.0
O A:HOH2315 2.8 10.5 1.0
O A:THR399 2.9 9.7 1.0
N A:THR399 3.1 8.5 1.0
CG2 A:ILE394 3.4 5.5 1.0
CE2 A:TYR362 3.7 10.1 1.0
C A:THR399 3.8 10.1 1.0
CA A:GLY398 3.8 8.9 1.0
OG1 A:THR399 4.0 10.1 1.0
C A:GLY398 4.0 9.9 1.0
CA A:THR399 4.0 9.7 1.0
CD2 A:TYR362 4.0 8.0 1.0
CG A:GLU401 4.0 10.3 1.0
CD A:PRO364 4.2 11.2 1.0
N A:PRO364 4.2 10.2 1.0
CG A:PRO364 4.3 8.7 1.0
OE1 A:GLU401 4.4 9.8 1.0
O A:TRP395 4.4 11.7 1.0
C A:ILE363 4.5 10.6 1.0
CB A:THR399 4.6 9.4 1.0
CD A:GLU401 4.6 12.4 1.0
CA A:PRO364 4.6 9.6 1.0
N A:GLY398 4.7 10.5 1.0
O A:TYR362 4.7 10.2 1.0
CB A:ILE394 4.8 8.3 1.0
CZ A:TYR362 4.9 11.1 1.0
CB A:PRO364 4.9 9.1 1.0
CA A:ILE363 5.0 9.2 1.0
O A:ILE363 5.0 11.1 1.0

Chlorine binding site 4 out of 7 in 2wbk

Go back to Chlorine Binding Sites List in 2wbk
Chlorine binding site 4 out of 7 in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1894

b:33.6
occ:0.50
 O A:HOH2056 2.2 3.5 0.5
O A:HOH2156 3.8 9.8 1.0
OE2 A:GLU78 3.9 12.7 1.0
O A:HIS180 4.1 11.8 1.0
CD A:GLN82 4.1 16.2 1.0
OE1 A:GLN82 4.2 16.4 1.0
CG A:GLN82 4.3 12.7 1.0
CD A:ARG203 4.4 12.2 1.0
CD A:GLU78 4.4 14.6 1.0
CG A:GLU78 4.5 13.7 1.0
NE2 A:GLN82 4.6 16.9 1.0
CB A:HIS180 4.6 12.0 1.0
CB A:ARG203 4.6 13.8 1.0
O A:HOH2058 4.7 10.2 1.0
O A:HOH2157 5.0 32.2 1.0

Chlorine binding site 5 out of 7 in 2wbk

Go back to Chlorine Binding Sites List in 2wbk
Chlorine binding site 5 out of 7 in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1885

b:22.3
occ:0.50
 O B:HOH2462 2.6 28.8 1.0
O B:HOH2464 2.7 27.8 1.0
N B:GLN685 3.4 25.4 1.0
CE1 B:HIS774 3.7 33.5 1.0
O B:GLN685 3.7 26.4 1.0
CD1 B:ILE684 3.8 21.6 1.0
CE1 B:HIS627 3.9 27.0 1.0
CB B:GLN685 3.9 26.3 1.0
CA B:GLN685 4.1 26.6 1.0
CA B:ILE684 4.2 25.7 1.0
C B:ILE684 4.3 25.4 1.0
O B:PRO683 4.3 24.4 1.0
C B:GLN685 4.4 27.9 1.0
O B:HOH2497 4.4 26.5 1.0
ND1 B:HIS774 4.4 32.9 1.0
ND1 B:HIS627 4.5 24.3 1.0
CG1 B:ILE684 4.7 25.9 1.0
NE2 B:HIS774 4.8 33.3 1.0
O B:HOH2432 4.8 19.2 1.0
NE2 B:HIS627 4.9 27.6 1.0
O B:HOH2434 5.0 28.6 1.0

Chlorine binding site 6 out of 7 in 2wbk

Go back to Chlorine Binding Sites List in 2wbk
Chlorine binding site 6 out of 7 in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1886

b:37.4
occ:0.70
 O2 A:EDO1873 2.6 36.7 1.0
N A:ILE578 3.2 23.8 1.0
CA A:GLN577 3.3 23.5 1.0
O A:HOH2422 3.7 21.4 1.0
C A:GLN577 3.7 23.9 1.0
CB A:GLN577 3.8 23.1 0.7
C2 A:EDO1873 3.9 33.4 1.0
CD1 A:PHE610 4.0 24.1 1.0
CG1 A:ILE578 4.0 24.6 1.0
CA A:ILE578 4.3 24.4 1.0
CB A:PHE610 4.3 22.3 1.0
CB A:ILE578 4.3 25.4 1.0
O A:TYR576 4.3 23.9 1.0
CG A:GLN577 4.4 25.1 0.3
C1 A:EDO1873 4.4 31.4 1.0
CD1 A:ILE578 4.5 24.3 1.0
N A:GLN577 4.5 24.8 1.0
CG A:PHE610 4.6 23.9 1.0
C A:TYR576 4.8 24.9 1.0
CA A:PHE610 4.9 22.3 1.0
O A:GLN577 4.9 22.5 1.0
CE1 A:PHE610 4.9 26.8 1.0

Chlorine binding site 7 out of 7 in 2wbk

Go back to Chlorine Binding Sites List in 2wbk
Chlorine binding site 7 out of 7 in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1893

b:8.4
occ:0.50
 O B:HOH2078 2.0 16.6 0.5
O B:HOH2296 3.2 13.8 1.0
O B:HOH2085 3.3 18.5 1.0
O B:HOH2297 3.4 19.5 1.0
CB B:ASN402 3.6 12.8 1.0
CD B:ARG211 3.9 10.3 1.0
O B:HOH2176 4.0 10.6 1.0
ND2 B:ASN402 4.0 19.1 1.0
NE B:ARG211 4.1 8.6 1.0
CG B:ARG211 4.1 9.7 1.0
CD B:PRO212 4.1 10.6 1.0
CG B:ASN402 4.3 15.8 1.0
OE1 B:GLU112 4.4 12.5 1.0
O B:HOH2175 4.4 28.8 1.0
CB B:ARG211 4.7 10.7 1.0
CA B:ASN402 4.7 12.8 1.0
CG B:PRO212 4.8 12.0 1.0
O B:HOH2086 4.9 14.1 1.0
N B:ASN403 4.9 11.7 1.0
CZ B:ARG211 4.9 13.6 1.0

Reference:

W.A.Offen, D.L.Zechel, S.G.Withers, H.J.Gilbert, G.J.Davies. Structure of the Michaelis Complex of Beta- Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis. Cell(Cambridge,Mass.) V. 18 2484 2009.
ISSN: ISSN 0092-8674
PubMed: 19532864
DOI: 10.1039/B902240F
Page generated: Sat Jul 20 12:39:56 2024

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