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Cadmium in PDB 4k1z: Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-Ome

Protein crystallography data

The structure of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-Ome, PDB code: 4k1z 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) 41.15 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.810, 107.810, 157.910, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 22.2

Other elements in 4k1z:

The structure of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-Ome also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Chlorine (Cl) 2 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- 4MAN-Ome (pdb code 4k1z). 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- 4MAN-Ome, PDB code: 4k1z:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 4k1z

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Cadmium binding site 1 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:28.3
occ:0.63
 O A:HOH494 3.0 38.1 1.0
O A:LYS30 3.1 17.8 1.0
O A:HOH459 3.2 29.4 1.0
O A:HOH463 3.6 22.0 1.0
O A:HOH483 4.0 36.1 1.0
C A:LYS30 4.2 19.8 1.0
CB A:LYS30 4.7 15.1 1.0
CA A:LYS30 4.9 17.1 1.0
O A:ASP2 4.9 30.4 1.0

Cadmium binding site 2 out of 9 in 4k1z

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Cadmium binding site 2 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-Ome


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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- 4MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:37.4
occ:0.68
 O A:HOH490 2.8 39.0 1.0
O A:ASN131 3.0 30.5 1.0
OD1 A:ASN153 3.1 23.6 1.0
O A:LEU107 3.2 17.1 1.0
O A:GLY152 3.2 27.9 1.0
OE1 B:GLU122 3.4 59.0 1.0
C A:ASN131 4.0 26.2 1.0
C A:GLY152 4.1 26.9 1.0
C A:LEU107 4.1 18.3 1.0
CD B:GLU122 4.1 63.5 1.0
CA A:LEU107 4.2 23.0 1.0
CG A:ASN153 4.3 22.4 1.0
CA A:GLN132 4.3 22.2 1.0
OE2 B:GLU122 4.4 60.7 1.0
O A:ASP151 4.4 38.0 1.0
CB A:LEU107 4.4 19.1 1.0
N A:GLN132 4.6 23.5 1.0
N A:ASN153 4.7 19.1 1.0
CA A:ASN153 4.8 25.7 1.0
CA A:GLY152 4.9 25.4 1.0

Cadmium binding site 3 out of 9 in 4k1z

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Cadmium binding site 3 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:38.0
occ:0.44
 O A:HOH455 2.4 26.2 1.0
OD2 A:ASP80 2.6 42.0 1.0
O A:HOH482 2.6 36.1 1.0
OD1 A:ASP82 2.6 31.3 1.0
OD2 A:ASP82 2.7 35.5 1.0
O A:HOH492 2.8 33.5 1.0
OD1 A:ASP80 2.8 32.5 1.0
O A:HOH458 2.8 41.0 1.0
CG A:ASP82 3.0 31.1 1.0
CG A:ASP80 3.1 30.6 1.0
O A:HOH523 4.3 30.7 1.0
O A:HOH500 4.3 35.8 1.0
O A:HOH542 4.4 40.8 1.0
NZ A:LYS59 4.4 38.6 1.0
CB A:ASP82 4.5 28.1 1.0
CB A:ASP80 4.5 28.6 1.0
OD1 A:ASN83 4.6 29.8 1.0
O A:HOH543 4.6 42.1 1.0
O A:HOH484 4.7 27.3 1.0
O A:HOH521 4.9 29.7 1.0
ND2 A:ASN83 4.9 28.0 1.0
CG A:ASN83 5.0 26.6 1.0

Cadmium binding site 4 out of 9 in 4k1z

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Cadmium binding site 4 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:36.0
occ:0.54
 O A:HOH484 2.5 27.3 1.0
O A:HOH542 3.0 40.8 1.0
O A:ASP82 3.0 20.4 1.0
O A:HOH505 3.2 44.8 1.0
OD1 A:ASP82 3.3 31.3 1.0
O A:HOH500 3.4 35.8 1.0
CH2 A:TRP182 3.5 25.2 1.0
CZ3 A:TRP182 3.5 24.5 1.0
CB A:ASP82 3.7 28.1 1.0
CG A:ASP82 3.7 31.1 1.0
CZ2 A:TRP182 3.7 20.2 1.0
O A:HOH506 3.8 45.0 1.0
CE3 A:TRP182 3.8 25.7 1.0
C A:ASP82 3.9 22.3 1.0
CE2 A:TRP182 4.0 20.6 1.0
CD2 A:TRP182 4.1 21.0 1.0
CA A:ASP82 4.4 22.8 1.0
OD2 A:ASP82 4.6 35.5 1.0
O A:HOH455 4.6 26.2 1.0
O A:HOH510 4.7 40.4 1.0
OD1 A:ASN83 4.8 29.8 1.0
O A:HOH412 4.8 20.3 1.0
NE1 A:TRP182 4.8 21.1 1.0
N A:ASN83 4.9 17.1 1.0
O A:HOH482 4.9 36.1 1.0
CG A:TRP182 5.0 19.7 1.0

Cadmium binding site 5 out of 9 in 4k1z

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Cadmium binding site 5 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd303

b:36.8
occ:0.69
 O A:HOH498 2.8 35.9 1.0
OD1 B:ASN153 3.0 15.7 1.0
O B:ASN131 3.1 25.1 1.0
O B:LEU107 3.1 17.7 1.0
O B:HOH527 3.2 41.8 1.0
O B:GLY152 3.3 18.0 1.0
O B:HOH509 3.6 26.1 1.0
O B:HOH468 3.9 37.1 1.0
C B:GLY152 4.0 19.2 1.0
C B:LEU107 4.0 15.7 1.0
C B:ASN131 4.1 19.1 1.0
CA B:GLN132 4.1 23.7 1.0
CA B:LEU107 4.2 13.7 1.0
CG B:ASN153 4.2 20.1 1.0
O B:ASP151 4.3 33.5 1.0
CB B:LEU107 4.4 12.3 1.0
CB B:GLN132 4.5 25.0 1.0
N B:ASN153 4.6 16.1 1.0
N B:GLN132 4.6 18.4 1.0
CA B:ASN153 4.7 16.5 1.0
CA B:GLY152 4.7 23.2 1.0
CG B:LEU107 4.8 21.2 1.0
OE1 A:GLU122 4.8 45.5 1.0
OE2 A:GLU122 4.9 45.6 1.0

Cadmium binding site 6 out of 9 in 4k1z

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Cadmium binding site 6 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd304

b:49.1
occ:0.49
 OD2 B:ASP80 2.5 30.1 1.0
OD2 B:ASP82 2.7 35.9 1.0
O B:HOH456 2.8 40.9 1.0
O B:HOH506 2.8 39.2 1.0
OD1 B:ASP82 2.9 33.5 1.0
CG B:ASP82 3.2 32.5 1.0
CG B:ASP80 3.4 25.8 1.0
OD1 B:ASP80 3.7 24.0 1.0
O B:HOH507 4.1 37.6 1.0
NZ B:LYS59 4.2 38.5 1.0
O B:HOH412 4.3 33.4 1.0
O B:HOH488 4.6 30.0 1.0
OD1 B:ASN83 4.6 13.6 1.0
CB B:ASP82 4.7 20.8 1.0
O B:HOH458 4.7 26.5 1.0
CB B:ASP80 4.8 15.1 1.0
ND2 B:ASN83 4.9 11.9 1.0

Cadmium binding site 7 out of 9 in 4k1z

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Cadmium binding site 7 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd303

b:47.0
occ:0.72
 O D:HOH536 2.8 48.8 1.0
O C:ASN131 3.0 26.1 1.0
OD1 C:ASN153 3.1 23.8 1.0
O C:LEU107 3.1 15.0 1.0
O C:HOH487 3.2 44.8 1.0
O C:HOH496 3.3 32.8 1.0
O C:GLY152 3.4 20.9 1.0
C C:LEU107 4.0 21.2 1.0
C C:GLY152 4.0 21.6 1.0
C C:ASN131 4.1 26.7 1.0
CA C:LEU107 4.2 22.0 1.0
CA C:GLN132 4.2 33.6 1.0
CG C:ASN153 4.2 29.0 1.0
CB C:LEU107 4.3 17.7 1.0
O C:ASP151 4.4 31.9 1.0
CB C:GLN132 4.6 37.5 1.0
N C:ASN153 4.6 20.6 1.0
N C:GLN132 4.6 23.5 1.0
O C:HOH497 4.7 40.3 1.0
CA C:ASN153 4.7 24.4 1.0
CA C:GLY152 4.7 26.7 1.0
CG C:LEU107 4.8 20.8 1.0
OE1 D:GLU122 4.8 77.8 1.0

Cadmium binding site 8 out of 9 in 4k1z

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Cadmium binding site 8 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd303

b:42.9
occ:0.62
 O D:ASN131 2.9 30.8 1.0
OD1 D:ASN153 3.0 25.4 1.0
O D:LEU107 3.1 20.6 1.0
O C:HOH513 3.2 52.2 1.0
O D:HOH508 3.2 29.4 1.0
O D:GLY152 3.4 28.3 1.0
OE1 C:GLU122 3.6 62.2 1.0
O D:HOH519 3.9 40.0 1.0
C D:ASN131 4.0 26.0 1.0
O D:HOH520 4.0 42.5 1.0
C D:LEU107 4.0 21.3 1.0
CA D:GLN132 4.1 33.3 1.0
C D:GLY152 4.1 31.0 1.0
CD C:GLU122 4.2 60.7 1.0
CA D:LEU107 4.2 22.3 1.0
CG D:ASN153 4.3 28.4 1.0
OE2 C:GLU122 4.3 60.8 1.0
CB D:GLN132 4.4 35.0 1.0
CB D:LEU107 4.5 19.4 1.0
N D:GLN132 4.5 24.9 1.0
O D:ASP151 4.6 33.1 1.0
N D:ASN153 4.7 26.9 1.0
CA D:ASN153 4.7 28.0 1.0
CA D:GLY152 4.9 35.0 1.0

Cadmium binding site 9 out of 9 in 4k1z

Go back to Cadmium Binding Sites List in 4k1z
Cadmium binding site 9 out of 9 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd304

b:50.6
occ:0.52
 OD2 D:ASP80 2.4 30.3 1.0
O D:HOH514 2.4 29.9 1.0
O D:HOH525 2.6 30.2 1.0
OD1 D:ASP82 2.6 25.4 1.0
O D:HOH509 2.6 28.4 1.0
OD2 D:ASP82 3.1 28.5 1.0
CG D:ASP80 3.2 26.4 1.0
CG D:ASP82 3.2 27.0 1.0
OD1 D:ASP80 3.3 24.4 1.0
O D:HOH534 4.0 40.4 1.0
NZ D:LYS59 4.2 28.6 1.0
OD1 D:ASN83 4.4 28.1 1.0
ND2 D:ASN83 4.6 20.4 1.0
CB D:ASP80 4.6 22.4 1.0
CB D:ASP82 4.7 16.4 1.0
CG D:ASN83 4.7 26.8 1.0
O D:HOH526 4.8 35.5 1.0
O D:HOH457 4.8 24.5 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 17:34:05 2024

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