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Cadmium in PDB 4k1y: Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome

Protein crystallography data

The structure of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome, PDB code: 4k1y was solved by G.A.Bezerra, R.Viertlmayr, T.R.Moura, P.Delatorre, B.A.M.Rocha, B.S.Cavada, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.94 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 139.880, 95.660, 94.610, 90.00, 132.29, 90.00
R / Rfree (%) 20.4 / 22.8

Other elements in 4k1y:

The structure of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Calcium (Ca) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome (pdb code 4k1y). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome, PDB code: 4k1y:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 4k1y

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Cadmium binding site 1 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:45.8
occ:1.00
 O A:HOH430 2.5 27.5 1.0
OD2 A:ASP80 2.6 28.4 1.0
O A:HOH431 2.8 29.6 1.0
OD2 A:ASP82 3.0 41.3 1.0
CB A:ASP82 3.2 33.6 1.0
CG A:ASP82 3.3 35.2 1.0
CG A:ASP80 3.4 34.1 1.0
OD1 A:ASP80 3.7 36.5 1.0
OD1 A:ASN83 3.8 32.1 1.0
NZ A:LYS59 4.1 23.6 1.0
O A:HOH404 4.2 38.0 1.0
OD1 A:ASP82 4.3 44.0 1.0
CG A:ASN83 4.6 35.5 1.0
ND2 A:ASN83 4.6 41.8 1.0
CA A:ASP82 4.6 30.3 1.0
CB A:ASP80 4.7 28.1 1.0
CE A:LYS59 4.8 35.5 1.0

Cadmium binding site 2 out of 9 in 4k1y

Go back to Cadmium Binding Sites List in 4k1y
Cadmium binding site 2 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:61.4
occ:0.57
 OD1 A:ASP235 2.6 38.7 1.0
OD2 A:ASP235 2.8 42.0 1.0
CG A:ASP235 3.0 42.1 1.0
CB A:ASN237 4.1 39.0 1.0
O A:ASN237 4.4 41.7 1.0
CB A:ASP235 4.5 36.1 1.0
OD1 A:ASN237 4.6 35.0 1.0
C A:ASN237 4.8 41.3 1.0
CG A:ASN237 4.9 35.7 1.0
CA A:ASN237 4.9 37.0 1.0
O A:ASP235 4.9 30.8 1.0
N A:ASN237 5.0 42.7 1.0

Cadmium binding site 3 out of 9 in 4k1y

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Cadmium binding site 3 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd303

b:54.1
occ:1.00
 OD2 B:ASP80 2.6 37.2 1.0
O B:HOH441 2.8 31.5 1.0
O B:HOH427 2.9 31.9 1.0
OD2 B:ASP82 2.9 49.2 1.0
OD1 B:ASP80 3.0 38.2 1.0
CB B:ASP82 3.0 31.6 1.0
CG B:ASP80 3.1 36.1 1.0
CG B:ASP82 3.2 46.8 1.0
O B:HOH426 4.1 36.8 1.0
OD1 B:ASP82 4.2 50.5 1.0
NZ B:LYS59 4.3 36.3 1.0
CA B:ASP82 4.4 32.6 1.0
CB B:ASP80 4.5 38.8 1.0
ND2 B:ASN83 4.5 31.5 1.0
OD1 B:ASN83 4.6 29.1 1.0
N B:ASP82 4.8 34.3 1.0
CG B:ASN83 4.9 31.2 1.0

Cadmium binding site 4 out of 9 in 4k1y

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Cadmium binding site 4 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd304

b:57.6
occ:0.71
 OD1 B:ASP235 2.6 43.2 1.0
OD2 B:ASP235 2.8 51.2 1.0
CG B:ASP235 3.0 47.0 1.0
O B:ASN237 4.2 39.6 1.0
CB B:ASN237 4.3 46.9 1.0
CB B:ASP235 4.5 44.1 1.0
C B:ASN237 4.7 43.3 1.0
O B:LYS30 4.9 46.8 1.0
O B:ASP235 4.9 37.9 1.0
OD1 B:ASN237 4.9 52.0 1.0
CA B:ASN237 4.9 45.3 1.0

Cadmium binding site 5 out of 9 in 4k1y

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Cadmium binding site 5 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd303

b:40.6
occ:1.00
 OD2 C:ASP80 2.4 37.7 1.0
OD2 C:ASP82 2.5 54.1 1.0
CG C:ASP82 2.9 35.6 1.0
OD1 C:ASP80 3.0 38.5 1.0
CG C:ASP80 3.0 37.5 1.0
CB C:ASP82 3.0 28.1 1.0
NZ C:LYS59 3.6 35.1 1.0
OD1 C:ASP82 3.9 38.6 1.0
O C:HOH441 4.1 38.8 1.0
CE C:LYS59 4.4 37.0 1.0
CA C:ASP82 4.4 27.8 1.0
OD1 C:ASN83 4.4 29.2 1.0
CB C:ASP80 4.5 29.8 1.0
ND2 C:ASN83 4.5 27.8 1.0
O C:HOH416 4.6 29.8 1.0
N C:ASP82 4.7 30.9 1.0
CG C:ASN83 4.8 31.1 1.0

Cadmium binding site 6 out of 9 in 4k1y

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Cadmium binding site 6 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd304

b:73.8
occ:0.61
 OD1 C:ASP235 2.6 51.2 1.0
O C:HOH434 2.8 33.9 1.0
O C:HOH435 3.1 39.9 1.0
OD2 C:ASP235 3.1 44.3 1.0
CG C:ASP235 3.2 44.2 1.0
O C:HOH447 3.3 36.8 1.0
CB C:ASN237 3.8 39.7 1.0
O C:ASN237 4.1 31.4 1.0
OD1 C:ASN237 4.3 50.9 1.0
CG C:ASN237 4.5 35.0 1.0
O C:HOH436 4.6 32.1 1.0
CA C:ASN237 4.7 37.5 1.0
CB C:ASP235 4.7 38.3 1.0
C C:ASN237 4.7 39.1 1.0
N C:ASN237 4.9 38.0 1.0

Cadmium binding site 7 out of 9 in 4k1y

Go back to Cadmium Binding Sites List in 4k1y
Cadmium binding site 7 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd305

b:84.0
occ:0.75
 OE2 C:GLU87 2.5 42.3 1.0
O C:HOH449 2.8 32.6 1.0
OE2 C:GLU183 2.9 46.3 1.0
O C:HOH450 3.0 32.8 1.0
OE1 C:GLU87 3.1 37.7 1.0
CD C:GLU87 3.1 37.5 1.0
O C:HOH423 3.7 34.8 1.0
CD C:GLU183 3.7 42.1 1.0
CG C:GLU183 3.7 44.1 1.0
OG C:SER184 4.3 35.9 1.0
CG C:GLU87 4.6 32.4 1.0
CB C:GLU183 4.7 39.2 1.0
N C:SER184 4.7 34.8 1.0
NE2 C:HIS180 4.8 32.1 1.0
OE1 C:GLU183 4.8 57.4 1.0
CA C:GLU183 4.8 29.9 1.0

Cadmium binding site 8 out of 9 in 4k1y

Go back to Cadmium Binding Sites List in 4k1y
Cadmium binding site 8 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd303

b:56.1
occ:1.00
 OD2 D:ASP80 2.4 32.6 1.0
O D:HOH423 2.6 24.6 1.0
O D:HOH424 2.8 27.5 1.0
OD2 D:ASP82 2.8 39.4 1.0
OD1 D:ASP80 2.9 35.6 1.0
CG D:ASP80 3.0 31.9 1.0
CB D:ASP82 3.1 29.4 1.0
CG D:ASP82 3.2 35.5 1.0
NZ D:LYS59 3.6 38.6 1.0
OD1 D:ASP82 4.1 44.3 1.0
ND2 D:ASN83 4.3 33.5 1.0
OD1 D:ASN83 4.4 29.6 1.0
CB D:ASP80 4.5 26.9 1.0
CA D:ASP82 4.5 29.4 1.0
CG D:ASN83 4.7 33.5 1.0
CE D:LYS59 4.8 31.4 1.0
N D:ASP82 4.8 33.1 1.0

Cadmium binding site 9 out of 9 in 4k1y

Go back to Cadmium Binding Sites List in 4k1y
Cadmium binding site 9 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd304

b:86.0
occ:0.71
 OD1 D:ASP235 2.6 48.1 1.0
OD2 D:ASP235 3.1 34.2 1.0
CG D:ASP235 3.2 40.8 1.0
O D:ASN237 3.6 45.1 1.0
O D:HOH401 4.0 35.1 1.0
O D:LYS30 4.2 47.7 1.0
O D:ASP235 4.5 36.0 1.0
C D:ASN237 4.6 49.8 1.0
CB D:ASP235 4.7 36.6 1.0
CB D:ASN237 4.7 47.6 1.0
CG D:PRO234 4.8 35.6 1.0
CD D:PRO234 5.0 31.9 1.0

Reference:

G.A.Bezerra, R.Viertlmayr, T.R.Moura, P.Delatorre, B.A.Rocha, K.S.Do Nascimento, J.G.Figueiredo, I.G.Bezerra, C.S.Teixeira, R.C.Simoes, C.S.Nagano, N.M.De Alencar, K.Gruber, B.S.Cavada. Structural Studies of An Anti-Inflammatory Lectin From Canavalia Boliviana Seeds in Complex with Dimannosides. Plos One V. 9 97015 2014.
ISSN: ESSN 1932-6203
PubMed: 24865454
DOI: 10.1371/JOURNAL.PONE.0097015
Page generated: Fri Jul 19 17:34:00 2024

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