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Cadmium in PDB 2bmy: Banana Lectin

Protein crystallography data

The structure of Banana Lectin, PDB code: 2bmy was solved by J.L.Meagher, H.C.Winter, P.Ezell, I.J.Goldstein, J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 2.5
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.500, 81.500, 147.200, 90.00, 90.00, 120.00
R / Rfree (%) 24.8 / 28.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Banana Lectin (pdb code 2bmy). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Banana Lectin, PDB code: 2bmy:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 2bmy

Go back to Cadmium Binding Sites List in 2bmy
Cadmium binding site 1 out of 3 in the Banana Lectin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Banana Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1143

b:34.3
occ:1.00
CE1 B:HIS84 1.9 7.1 1.0
NE2 B:HIS84 2.1 4.7 1.0
OD2 A:ASP41 2.2 28.5 1.0
ND1 A:HIS54 2.5 26.1 1.0
O A:HOH2024 2.6 34.3 1.0
O B:HOH2051 2.7 57.3 1.0
OD1 A:ASP41 2.8 23.4 1.0
CG A:ASP41 2.8 27.8 1.0
O B:HOH2023 3.2 24.9 1.0
ND1 B:HIS84 3.2 19.8 1.0
CE1 A:HIS54 3.3 25.5 1.0
CG A:HIS54 3.5 24.6 1.0
CD2 B:HIS84 3.5 14.5 1.0
CB A:HIS54 3.8 27.2 1.0
CG B:HIS84 4.0 18.1 1.0
CB A:ASP41 4.3 25.4 1.0
NE2 A:HIS54 4.5 26.0 1.0
CA A:HIS54 4.5 28.4 1.0
CD2 A:HIS54 4.5 25.0 1.0
OD2 B:ASP35 4.6 26.1 1.0
OH B:TYR83 4.7 41.8 1.0
CE1 A:PHE32 4.8 38.8 1.0
CE2 B:TYR83 4.8 40.6 1.0
O A:HOH2020 4.8 39.6 1.0
CZ A:PHE32 4.9 39.3 1.0
CZ B:TYR83 5.0 40.6 1.0

Cadmium binding site 2 out of 3 in 2bmy

Go back to Cadmium Binding Sites List in 2bmy
Cadmium binding site 2 out of 3 in the Banana Lectin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Banana Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1144

b:61.2
occ:1.00
ND1 A:HIS84 2.2 47.8 1.0
O A:HOH2037 2.4 29.7 1.0
CE1 A:HIS84 2.9 47.2 1.0
O A:HOH2023 3.1 51.5 1.0
CG A:HIS84 3.4 46.9 1.0
CA A:HIS84 3.9 45.3 1.0
CB A:HIS84 3.9 45.2 1.0
NE2 A:HIS84 4.1 48.5 1.0
O A:HOH2038 4.2 59.1 1.0
CD2 A:HIS84 4.4 46.7 1.0
N A:HIS84 4.6 44.6 1.0
C A:HIS84 5.0 45.4 1.0

Cadmium binding site 3 out of 3 in 2bmy

Go back to Cadmium Binding Sites List in 2bmy
Cadmium binding site 3 out of 3 in the Banana Lectin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Banana Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1143

b:73.5
occ:1.00
ND1 B:HIS54 2.2 48.8 1.0
OD2 B:ASP41 2.5 36.6 1.0
OD1 B:ASP41 2.8 33.7 1.0
O B:HOH2027 2.9 56.1 1.0
CG B:ASP41 3.0 32.5 1.0
CE1 B:HIS54 3.0 48.4 1.0
CG B:HIS54 3.2 47.7 1.0
CB B:HIS54 3.6 44.4 1.0
NE2 B:HIS54 4.1 49.5 1.0
CD2 B:HIS54 4.2 48.4 1.0
CE1 B:PHE32 4.4 36.7 1.0
CZ B:PHE32 4.5 36.1 1.0
CB B:ASP41 4.5 30.2 1.0
CA B:HIS54 4.5 41.4 1.0

Reference:

J.L.Meagher, H.C.Winter, P.Ezell, I.J.Goldstein, J.A.Stuckey. Crystal Structure of Banana Lectin Reveals A Novel Second Sugar Binding Site. Glycobiology V. 15 1033 2005.
ISSN: ISSN 0959-6658
PubMed: 15944373
DOI: 10.1093/GLYCOB/CWI088
Page generated: Sat Dec 12 08:16:40 2020

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