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Bromine in PDB 7op6: Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine

Protein crystallography data

The structure of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine, PDB code: 7op6 was solved by N.G.S.Mcgregor, T.J.M.Beenakker, C.Kuo, C.Wong, W.A.Offen, Z.Armstrong, J.D.C.Codee, J.M.F.G.Aerts, B.I.Florea, H.S.Overkleeft, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.19 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.92, 116.858, 100.844, 90, 114.15, 90
R / Rfree (%) 18.5 / 23.3

Other elements in 7op6:

The structure of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine also contains other interesting chemical elements:

Chlorine (Cl) 14 atoms
Sodium (Na) 3 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine (pdb code 7op6). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 10 binding sites of Bromine where determined in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine, PDB code: 7op6:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 10 in 7op6

Go back to Bromine Binding Sites List in 7op6
Bromine binding site 1 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br901

b:42.0
occ:0.75
 O A:HOH1412 3.1 51.6 1.0
O A:HOH1091 3.3 28.1 1.0
NE2 A:GLN108 3.4 35.7 1.0
CG A:GLN108 3.7 36.3 1.0
CB A:PRO140 3.8 34.9 1.0
N A:PRO140 3.8 32.9 1.0
CD A:PRO140 3.9 34.6 1.0
CD A:GLN108 4.1 36.4 1.0
CA A:PRO140 4.1 31.7 1.0
CG A:PRO140 4.2 37.7 1.0
CG2 A:THR138 4.2 34.2 1.0
C A:LEU139 4.3 31.0 1.0
ND2 A:ASN247 4.4 33.7 1.0
O A:LEU139 4.6 27.3 1.0
O A:HOH1191 4.7 29.5 1.0
CB A:GLN108 4.8 34.9 1.0
OH A:TYR218 4.8 30.0 1.0
O A:THR138 4.8 25.5 1.0
C A:THR138 4.9 28.5 1.0
N A:LEU139 4.9 25.6 1.0
CA A:LEU139 5.0 27.5 1.0

Bromine binding site 2 out of 10 in 7op6

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Bromine binding site 2 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br902

b:39.7
occ:0.50
 O A:HOH1278 3.3 23.8 1.0
O A:HOH1083 3.4 39.1 1.0
O A:HOH1367 3.5 27.9 1.0
CB A:ASN402 3.7 29.2 1.0
CG A:ARG211 3.9 28.1 1.0
O A:HOH1368 4.0 28.9 1.0
CD A:ARG211 4.0 27.2 1.0
CD A:PRO212 4.0 27.7 1.0
NE A:ARG211 4.2 28.7 1.0
ND2 A:ASN402 4.2 42.7 1.0
OE1 A:GLU112 4.4 29.9 1.0
CG A:ASN402 4.5 34.0 1.0
O A:HOH1341 4.5 39.0 1.0
CB A:ARG211 4.6 26.7 1.0
CG A:PRO212 4.6 30.0 1.0
CA A:ASN402 4.8 25.6 1.0
NA A:NA928 5.0 33.3 1.0

Bromine binding site 3 out of 10 in 7op6

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Bromine binding site 3 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br903

b:32.1
occ:0.80
 O A:HOH1091 3.1 28.1 1.0
O A:HOH1357 3.3 36.1 1.0
O A:ILE107 3.6 27.3 1.0
N A:ILE107 3.6 29.3 1.0
CB A:LYS142 3.7 35.0 1.0
CB A:PRO140 3.9 34.9 1.0
N A:LYS142 4.0 29.6 1.0
CA A:GLY106 4.0 30.9 1.0
CG1 A:ILE249 4.1 39.2 1.0
CA A:PRO140 4.3 31.7 1.0
N A:VAL141 4.3 30.4 1.0
CD1 A:ILE249 4.3 41.4 1.0
C A:GLY106 4.3 30.2 1.0
C A:ILE107 4.3 30.0 1.0
CA A:LYS142 4.5 34.0 1.0
CA A:ILE107 4.6 29.6 1.0
C A:PRO140 4.6 31.5 1.0
OH A:TYR218 4.9 30.0 1.0
O A:ASP105 5.0 30.5 1.0
CG A:LYS142 5.0 33.9 1.0

Bromine binding site 4 out of 10 in 7op6

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Bromine binding site 4 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br904

b:32.3
occ:0.70
 O A:HOH1017 3.2 45.1 1.0
O A:HOH1123 3.2 22.2 1.0
O A:HOH1355 3.3 43.5 1.0
O A:HOH1488 3.8 45.3 1.0
CE2 A:TYR509 3.9 21.8 1.0
CB A:HIS511 4.1 29.8 1.0
CG A:PRO497 4.2 27.7 1.0
O A:PHE492 4.2 28.0 1.0
CA A:ARG493 4.2 28.0 1.0
CD2 A:TYR509 4.2 23.3 1.0
CB A:PRO497 4.3 27.1 1.0
O A:ARG493 4.6 27.7 1.0
CB A:ARG493 4.6 29.2 1.0
CG A:ARG493 4.6 35.1 1.0
CD2 A:HIS511 4.6 34.2 1.0
N A:HIS511 4.7 26.0 1.0
CG A:HIS511 4.7 34.0 1.0
C A:ARG493 4.8 27.8 1.0
CA A:HIS511 4.9 27.7 1.0
O1 A:EDO911 5.0 39.5 1.0

Bromine binding site 5 out of 10 in 7op6

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Bromine binding site 5 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br905

b:34.6
occ:1.00
 N A:HIS284 3.4 28.6 1.0
O A:HOH1348 3.5 46.2 1.0
CA A:ASN283 3.8 27.0 1.0
C A:ASN283 4.1 29.2 1.0
O A:HIS284 4.1 34.8 1.0
CA A:HIS284 4.3 32.9 1.0
CB A:HIS284 4.3 36.1 1.0
CD2 A:HIS284 4.4 47.2 1.0
CB A:ASN283 4.5 29.2 1.0
O A:ILE282 4.5 27.6 1.0
C A:HIS284 4.7 34.8 1.0
CG A:HIS284 4.8 41.5 1.0
OD1 A:ASN283 4.9 26.3 1.0
N A:ASN283 4.9 24.7 1.0
CG A:ASN283 5.0 29.0 1.0

Bromine binding site 6 out of 10 in 7op6

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Bromine binding site 6 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br906

b:54.5
occ:0.50
 N A:ASP688 3.5 62.9 1.0
NE2 A:GLN685 3.6 45.4 1.0
CG A:GLN685 3.8 50.2 1.0
CA A:ASP688 3.9 63.7 1.0
N A:ASN687 4.0 59.1 1.0
CD A:GLN685 4.2 48.9 1.0
C A:GLN686 4.3 52.6 1.0
OD1 A:ASP688 4.3 56.0 0.5
N A:GLN686 4.4 45.1 1.0
CA A:GLN686 4.4 48.1 1.0
C A:GLN685 4.5 42.5 1.0
O A:GLN685 4.5 40.6 1.0
CG A:ASP688 4.5 58.5 0.5
C A:ASN687 4.6 62.1 1.0
CA A:ASN687 4.8 60.8 1.0
CB A:GLN685 4.8 50.9 1.0
CB A:ASP688 4.9 58.4 0.5
OD2 A:ASP688 5.0 57.9 0.5
C A:ASP688 5.0 60.0 1.0

Bromine binding site 7 out of 10 in 7op6

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Bromine binding site 7 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br902

b:44.1
occ:1.00
 O B:HOH1099 3.2 29.9 1.0
O B:HOH1282 3.3 47.0 1.0
O B:ILE107 3.5 31.9 1.0
N B:ILE107 3.5 34.1 1.0
CB B:LYS142 3.7 35.0 1.0
N B:LYS142 3.8 31.4 1.0
CB B:PRO140 3.9 34.8 1.0
CA B:GLY106 4.0 37.1 1.0
N B:VAL141 4.1 32.4 1.0
CA B:PRO140 4.1 31.6 1.0
C B:ILE107 4.2 33.7 1.0
C B:GLY106 4.2 37.1 1.0
CA B:LYS142 4.3 34.1 1.0
CD1 B:ILE249 4.3 48.7 1.0
C B:PRO140 4.4 30.7 1.0
CG1 B:ILE249 4.4 46.2 1.0
CA B:ILE107 4.4 32.7 1.0
C B:VAL141 4.8 30.8 1.0
CG B:LYS142 4.9 37.4 1.0
OH B:TYR218 5.0 37.1 1.0

Bromine binding site 8 out of 10 in 7op6

Go back to Bromine Binding Sites List in 7op6
Bromine binding site 8 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br903

b:39.9
occ:0.80
 O B:HOH1327 3.1 34.7 1.0
CE2 B:TYR509 4.0 29.5 1.0
CB B:HIS511 4.1 30.9 1.0
CG B:PRO497 4.2 31.6 1.0
CA B:ARG493 4.2 35.0 1.0
CG B:ARG493 4.2 41.2 1.0
CB B:PRO497 4.3 32.4 1.0
CD2 B:TYR509 4.3 30.5 1.0
O B:HOH1401 4.3 47.4 1.0
O B:PHE492 4.3 27.0 1.0
O B:ARG493 4.5 31.9 1.0
CB B:ARG493 4.5 39.5 1.0
CD B:ARG493 4.6 49.5 1.0
CD2 B:HIS511 4.7 35.0 1.0
CG B:HIS511 4.8 31.8 1.0
N B:HIS511 4.8 27.8 1.0
C B:ARG493 4.8 34.2 1.0
CA B:HIS511 4.9 27.7 1.0

Bromine binding site 9 out of 10 in 7op6

Go back to Bromine Binding Sites List in 7op6
Bromine binding site 9 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br904

b:58.8
occ:0.50
 N B:ASP688 3.4 56.4 1.0
NE2 B:GLN685 3.5 37.9 1.0
CA B:ASP688 3.8 54.9 1.0
CG B:GLN685 3.9 44.3 1.0
N B:ASN687 3.9 56.8 1.0
C B:GLN686 4.1 51.0 1.0
CA B:GLN686 4.2 51.5 1.0
CD B:GLN685 4.3 41.5 1.0
O B:HOH1019 4.4 27.5 0.5
N B:GLN686 4.4 45.0 1.0
C B:ASN687 4.5 55.9 1.0
O B:GLN685 4.5 42.4 1.0
C B:GLN685 4.5 42.2 1.0
CA B:ASN687 4.6 55.9 1.0
O B:GLN686 4.7 53.5 1.0
CB B:ASP688 4.7 53.6 0.5
C B:ASP688 4.9 55.0 1.0
CB B:GLN685 4.9 43.8 1.0
N B:SER689 5.0 51.1 1.0

Bromine binding site 10 out of 10 in 7op6

Go back to Bromine Binding Sites List in 7op6
Bromine binding site 10 out of 10 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br905

b:41.6
occ:0.50
 O B:HOH1031 3.1 39.5 1.0
O B:HOH1341 3.4 33.9 1.0
O B:HOH1266 3.4 32.5 1.0
CB B:ASN402 3.8 31.6 1.0
CD B:PRO212 4.0 27.4 1.0
O B:HOH1285 4.0 24.9 1.0
CD B:ARG211 4.0 28.1 1.0
CG B:ARG211 4.2 28.7 1.0
NE B:ARG211 4.3 26.8 1.0
ND2 B:ASN402 4.3 42.6 1.0
OE1 B:GLU112 4.4 34.3 1.0
O B:HOH1391 4.5 47.4 1.0
CB B:ARG211 4.5 27.0 1.0
CG B:ASN402 4.6 34.0 1.0
CG B:PRO212 4.6 30.2 1.0
O B:HOH1289 4.7 43.8 1.0
CA B:ASN402 5.0 28.9 1.0

Reference:

N.G.S.Mcgregor, C.L.Kuo, T.J.M.Beenakker, C.S.Wong, W.A.Offen, Z.Armstrong, B.I.Florea, J.D.C.Codee, H.S.Overkleeft, J.M.F.G.Aerts, G.J.Davies. Synthesis of Broad-Specificity Activity-Based Probes For Exo -Beta-Mannosidases. Org.Biomol.Chem. V. 20 877 2022.
ISSN: ESSN 1477-0539
PubMed: 35015006
DOI: 10.1039/D1OB02287C
Page generated: Thu Jul 11 04:16:56 2024

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