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Bromine 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
Chlorine (Cl) 7 atoms

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Bromine 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 Bromine atom.
In total 12 binding sites of Bromine 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 Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 1 out of 12 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 Bromine with other atoms in the Br 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:Br1881

b:25.8
occ:1.00
 O A:HOH2199 3.2 13.7 1.0
O A:HOH2085 3.2 28.8 1.0
O A:HOH2119 3.3 14.8 1.0
N A:ILE107 3.4 17.0 1.0
CB A:LYS142 3.5 16.6 1.0
O A:ILE107 3.5 16.7 1.0
N A:LYS142 3.7 15.8 1.0
CB A:PRO140 3.8 16.1 1.0
CA A:GLY106 3.9 17.8 1.0
N A:VAL141 4.0 14.2 1.0
CD1 A:ILE249 4.1 21.5 1.0
CG1 A:ILE249 4.1 21.4 1.0
CA A:PRO140 4.2 15.7 1.0
C A:GLY106 4.2 17.9 1.0
CA A:LYS142 4.2 16.7 1.0
C A:ILE107 4.3 16.8 1.0
C A:PRO140 4.3 15.4 1.0
CA A:ILE107 4.5 16.4 1.0
CG A:LYS142 4.7 18.9 1.0
C A:VAL141 4.8 15.2 1.0
O A:ASP105 4.9 20.6 1.0
CD A:LYS142 4.9 20.0 1.0
OH A:TYR218 5.0 23.7 1.0

Bromine binding site 2 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 2 out of 12 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 Bromine with other atoms in the Br 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:Br1882

b:29.7
occ:0.60
 O A:HOH2199 3.3 13.7 1.0
NE2 A:GLN108 3.3 26.2 1.0
CG A:GLN108 3.5 21.7 1.0
O A:HOH2225 3.5 25.4 1.0
CB A:PRO140 3.8 16.1 1.0
N A:PRO140 3.9 15.0 1.0
CD A:PRO140 3.9 15.3 1.0
CD A:GLN108 3.9 23.8 1.0
CA A:PRO140 4.0 15.7 1.0
CG2 A:THR138 4.1 16.3 1.0
CG A:PRO140 4.1 17.1 1.0
C A:LEU139 4.3 15.1 1.0
O A:THR138 4.5 15.8 1.0
ND2 A:ASN247 4.5 29.4 1.0
CB A:GLN108 4.6 17.6 1.0
O A:HOH2198 4.7 17.4 1.0
O A:LEU139 4.7 15.4 1.0
C A:THR138 4.8 14.3 1.0
OH A:TYR218 4.8 23.7 1.0
O A:HOH2086 4.9 25.6 1.0
N A:LEU139 5.0 15.2 1.0

Bromine binding site 3 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 3 out of 12 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 Bromine with other atoms in the Br 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:Br1883

b:42.2
occ:0.80
 N A:ASP688 3.3 37.8 1.0
NE2 A:GLN685 3.5 24.3 1.0
CG A:GLN685 3.6 27.5 1.0
CA A:ASP688 3.8 38.0 1.0
N A:ASN687 3.9 36.1 1.0
C A:GLN686 4.0 34.5 1.0
CD A:GLN685 4.1 27.8 1.0
CA A:GLN686 4.1 33.3 1.0
O A:GLN685 4.3 30.2 1.0
N A:GLN686 4.3 32.2 1.0
C A:GLN685 4.3 30.6 1.0
C A:ASN687 4.4 38.0 1.0
CA A:ASN687 4.6 37.3 1.0
O A:GLN686 4.6 33.9 1.0
N A:SER689 4.6 35.2 1.0
C A:ASP688 4.7 37.3 1.0
CB A:GLN685 4.7 28.6 1.0
CB A:ASP688 4.9 39.1 1.0

Bromine binding site 4 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 4 out of 12 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 Bromine with other atoms in the Br 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:Br1884

b:35.9
occ:0.50
 N A:THR477 3.2 26.1 1.0
CG2 A:VAL480 3.6 20.1 1.0
CA A:PHE476 3.6 27.4 1.0
OG1 A:THR477 3.7 25.4 1.0
CB A:VAL480 3.7 20.3 1.0
CG2 A:THR477 3.7 26.6 1.0
CB A:PHE476 3.8 26.9 1.0
CD1 A:PHE476 3.8 21.7 1.0
CG1 A:VAL480 3.9 19.8 1.0
C A:PHE476 4.0 27.0 1.0
CB A:THR477 4.1 26.3 1.0
CB A:PHE172 4.2 13.6 1.0
CA A:THR477 4.2 26.3 1.0
CG A:PHE476 4.3 25.8 1.0
O A:HOH2363 4.7 26.4 1.0
CG A:PHE172 4.8 14.1 1.0
O A:LYS475 4.8 29.8 1.0
N A:PHE476 5.0 29.1 1.0
CE1 A:PHE476 5.0 21.7 1.0

Bromine binding site 5 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 5 out of 12 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 Bromine with other atoms in the Br 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
A:Br1885

b:10.6
occ:0.50
 O A:HOH2574 3.3 17.5 1.0
O A:HOH2375 3.3 36.3 1.0
CE2 A:TYR509 3.7 12.1 1.0
O A:PHE492 4.0 15.3 1.0
CA A:ARG493 4.0 18.3 1.0
CG A:PRO497 4.1 12.8 1.0
CD2 A:TYR509 4.1 11.0 1.0
CB A:PRO497 4.1 11.8 1.0
CB A:HIS511 4.2 12.2 1.0
O A:ARG493 4.4 18.0 1.0
CB A:ARG493 4.5 18.7 1.0
CG A:ARG493 4.6 22.6 1.0
C A:ARG493 4.6 17.9 1.0
N A:HIS511 4.6 12.2 1.0
O1 A:EDO1874 4.8 18.7 1.0
CA A:HIS511 4.8 12.6 1.0
CD2 A:HIS511 4.9 16.2 1.0
CG A:HIS511 4.9 14.2 1.0
C A:PHE492 4.9 15.8 1.0
CD A:PRO497 4.9 13.2 1.0
CZ A:TYR509 5.0 10.9 1.0
N A:ARG493 5.0 17.6 1.0

Bromine binding site 6 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 6 out of 12 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 Bromine with other atoms in the Br 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
A:Br1890

b:35.5
occ:0.50
 O A:HOH2078 3.1 10.9 0.5
O A:HOH2320 3.4 8.1 1.0
O A:HOH2088 3.4 14.5 1.0
O A:HOH2321 3.5 12.8 1.0
CB A:ASN402 3.7 14.1 1.0
CG A:ARG211 3.9 11.3 1.0
ND2 A:ASN402 3.9 17.8 1.0
CD A:ARG211 3.9 8.5 1.0
O A:HOH2192 4.0 9.6 1.0
CD A:PRO212 4.0 13.2 1.0
NE A:ARG211 4.0 11.3 1.0
CG A:ASN402 4.3 17.5 1.0
OE1 A:GLU112 4.4 15.2 1.0
O A:HOH2191 4.4 26.3 1.0
CB A:ARG211 4.5 10.9 1.0
O2 A:EDO1866 4.6 32.8 1.0
CG A:PRO212 4.7 13.3 1.0
O A:HOH2041 4.8 11.0 0.5
O A:HOH2087 4.9 10.6 1.0
CA A:ASN402 4.9 13.3 1.0
CZ A:ARG211 5.0 12.0 1.0
O A:HOH2039 5.0 17.9 0.5

Bromine binding site 7 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 7 out of 12 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 Bromine with other atoms in the Br 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:Br1881

b:21.2
occ:0.90
 O B:HOH2114 3.1 14.6 1.0
O B:HOH2083 3.2 27.6 1.0
O B:HOH2181 3.2 13.5 1.0
N B:ILE107 3.4 16.4 1.0
O B:ILE107 3.4 17.8 1.0
CB B:LYS142 3.6 13.8 1.0
N B:LYS142 3.9 14.6 1.0
CB B:PRO140 4.0 16.6 1.0
CA B:GLY106 4.0 16.9 1.0
CD1 B:ILE249 4.2 25.9 1.0
C B:ILE107 4.2 17.4 1.0
N B:VAL141 4.2 13.2 1.0
CA B:PRO140 4.2 16.0 1.0
CG1 B:ILE249 4.2 24.9 1.0
C B:GLY106 4.2 17.5 1.0
CA B:LYS142 4.3 14.7 1.0
CA B:ILE107 4.4 16.7 1.0
C B:PRO140 4.4 15.6 1.0
O1 B:EDO1894 4.6 32.5 1.0
CG B:LYS142 4.9 16.8 1.0
O B:ASP105 4.9 17.2 1.0
C B:VAL141 5.0 14.3 1.0
CB B:ILE107 5.0 16.1 1.0

Bromine binding site 8 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 8 out of 12 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 Bromine with other atoms in the Br binding site number 8 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:Br1882

b:42.1
occ:0.70
 N B:ASP688 3.3 35.6 1.0
O B:HOH2466 3.4 30.9 1.0
NE2 B:GLN685 3.5 27.9 1.0
N B:ASN687 3.6 33.2 1.0
CG B:GLN685 3.7 27.5 1.0
CA B:ASP688 3.9 35.6 1.0
C B:GLN686 3.9 31.4 1.0
CA B:GLN686 4.1 29.9 1.0
CD B:GLN685 4.1 26.9 1.0
C B:ASN687 4.3 34.9 1.0
N B:GLN686 4.3 28.2 1.0
CA B:ASN687 4.4 34.7 1.0
C B:GLN685 4.5 27.9 1.0
O B:GLN685 4.5 26.4 1.0
O B:GLN686 4.7 32.1 1.0
C B:ASP688 4.7 35.6 1.0
N B:SER689 4.7 34.9 1.0
CB B:GLN685 4.9 26.3 1.0

Bromine binding site 9 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 9 out of 12 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 Bromine with other atoms in the Br binding site number 9 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:Br1883

b:25.3
occ:0.80
 O B:HOH2356 3.3 18.1 1.0
CE2 B:TYR509 3.9 15.8 1.0
CG B:PRO497 4.0 15.3 1.0
O B:HOH2343 4.0 32.9 1.0
CB B:HIS511 4.1 13.3 1.0
O B:PHE492 4.1 16.7 1.0
CA B:ARG493 4.1 16.6 1.0
CB B:PRO497 4.2 15.6 1.0
CD2 B:TYR509 4.2 15.7 1.0
O B:HOH2165 4.3 34.7 1.0
O B:ARG493 4.4 16.2 1.0
CB B:ARG493 4.6 16.6 1.0
CG B:ARG493 4.6 20.2 1.0
C B:ARG493 4.7 16.3 1.0
CD2 B:HIS511 4.7 16.7 1.0
N B:HIS511 4.7 14.9 1.0
CG B:HIS511 4.7 14.0 1.0
CA B:HIS511 4.9 13.4 1.0
CD B:PRO497 4.9 14.7 1.0
C B:PHE492 5.0 16.1 1.0

Bromine binding site 10 out of 12 in 2wbk

Go back to Bromine Binding Sites List in 2wbk
Bromine binding site 10 out of 12 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 Bromine with other atoms in the Br binding site number 10 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:Br1884

b:56.5
occ:1.00
 O B:HOH2181 3.3 13.5 1.0
NE2 B:GLN108 3.3 25.7 1.0
CD B:PRO140 3.7 17.2 1.0
CG B:GLN108 3.8 19.9 1.0
N B:PRO140 3.9 17.0 1.0
CG2 B:THR138 4.0 14.4 1.0
CD B:GLN108 4.0 21.4 1.0
CB B:PRO140 4.0 16.6 1.0
CA B:PRO140 4.1 16.0 1.0
CG B:PRO140 4.3 17.8 1.0
C B:LEU139 4.3 16.7 1.0
ND2 B:ASN247 4.5 29.6 1.0
CB B:GLN108 4.6 17.8 1.0
O B:LEU139 4.7 17.6 1.0
O B:HOH2200 4.8 27.6 1.0
OH B:TYR218 4.9 18.8 1.0
O B:THR138 4.9 15.2 1.0
N B:LEU139 4.9 14.2 1.0
C B:THR138 4.9 14.7 1.0
CA B:LEU139 5.0 15.6 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: Wed Jul 10 18:50:44 2024

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