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Cadmium in PDB 6ahg: Trimeric Structure of Concanavalin A From Canavalia Ensiformis

Protein crystallography data

The structure of Trimeric Structure of Concanavalin A From Canavalia Ensiformis, PDB code: 6ahg was solved by J.H.Park, D.S.Kim, Y.R.Park, S.J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.29 / 2.83
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 136.461, 136.461, 193.146, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 27.9

Other elements in 6ahg:

The structure of Trimeric Structure of Concanavalin A From Canavalia Ensiformis also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis (pdb code 6ahg). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis, PDB code: 6ahg:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 6ahg

Go back to Cadmium Binding Sites List in 6ahg
Cadmium binding site 1 out of 6 in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Trimeric Structure of Concanavalin A From Canavalia Ensiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:39.6
occ:1.00
 OD2 A:ASP10 2.2 41.9 1.0
O A:HOH401 2.3 41.8 1.0
NE2 A:HIS24 2.3 39.9 1.0
O A:HOH404 2.3 31.0 1.0
OE2 A:GLU8 2.4 44.4 1.0
OD1 A:ASP19 3.0 49.5 1.0
OD2 A:ASP19 3.0 46.8 1.0
CD A:GLU8 3.1 44.2 1.0
CG A:ASP19 3.1 48.0 1.0
CG A:ASP10 3.2 41.9 1.0
CE1 A:HIS24 3.2 39.8 1.0
OE1 A:GLU8 3.2 44.0 1.0
CD2 A:HIS24 3.3 40.2 1.0
CB A:ASP10 3.8 42.0 1.0
O A:HOH406 3.9 39.2 1.0
OG A:SER34 4.1 41.2 1.0
OD1 A:ASP10 4.2 41.2 1.0
CB A:ASP19 4.3 47.7 1.0
CG A:GLU8 4.3 43.9 1.0
ND1 A:HIS24 4.4 40.1 1.0
CA A:CA301 4.4 17.1 1.0
CG A:HIS24 4.4 40.3 1.0
O A:VAL32 4.6 44.5 1.0
CA A:ASP19 4.7 47.4 1.0

Cadmium binding site 2 out of 6 in 6ahg

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Cadmium binding site 2 out of 6 in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Trimeric Structure of Concanavalin A From Canavalia Ensiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:53.6
occ:1.00
 OD1 A:ASP82 2.2 47.0 1.0
OD2 B:ASP16 2.3 50.4 1.0
O B:HOH401 2.3 41.8 1.0
OD1 A:ASP80 2.4 48.4 1.0
OD1 A:ASN83 2.8 48.8 1.0
CG B:ASP16 3.0 51.8 1.0
OD1 B:ASP16 3.0 52.7 1.0
OD2 A:ASP80 3.1 49.5 1.0
CG A:ASP80 3.1 48.9 1.0
CG A:ASP82 3.1 46.9 1.0
OD2 A:ASP82 3.3 46.8 1.0
NZ A:LYS59 3.5 49.7 1.0
CG A:ASN83 3.9 47.8 1.0
NH1 B:ARG228 4.4 43.9 1.0
CB B:ASP16 4.4 51.4 1.0
O A:HOH405 4.5 49.4 1.0
ND2 A:ASN83 4.5 47.5 1.0
CB A:ASP82 4.5 46.8 1.0
CB A:ASP80 4.6 47.9 1.0
N A:ASN83 4.6 46.3 1.0
NH2 B:ARG228 4.6 44.8 1.0
CZ2 A:TRP182 4.8 20.0 1.0
O B:ASP16 4.8 51.5 1.0
CE A:LYS59 4.9 49.0 1.0

Cadmium binding site 3 out of 6 in 6ahg

Go back to Cadmium Binding Sites List in 6ahg
Cadmium binding site 3 out of 6 in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Trimeric Structure of Concanavalin A From Canavalia Ensiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:54.1
occ:1.00
 OD1 C:ASP82 2.2 46.6 1.0
OD2 A:ASP16 2.3 50.8 1.0
O C:HOH403 2.4 51.7 1.0
OD1 C:ASP80 2.4 48.0 1.0
OD1 C:ASN83 2.7 50.0 1.0
CG A:ASP16 3.0 51.9 1.0
OD1 A:ASP16 3.0 54.0 1.0
OD2 C:ASP80 3.1 49.8 1.0
CG C:ASP80 3.1 48.8 1.0
CG C:ASP82 3.1 46.7 1.0
OD2 C:ASP82 3.3 47.2 1.0
NZ C:LYS59 3.5 50.4 1.0
CG C:ASN83 3.8 48.9 1.0
NH1 A:ARG228 4.4 42.6 1.0
ND2 C:ASN83 4.4 48.9 1.0
CB A:ASP16 4.4 51.1 1.0
CB C:ASP82 4.5 46.8 1.0
CB C:ASP80 4.5 48.0 1.0
N C:ASN83 4.5 47.1 1.0
NH2 A:ARG228 4.6 43.7 1.0
O A:ASP16 4.7 51.0 1.0
CZ2 C:TRP182 4.9 50.6 1.0
CB C:ASN83 5.0 47.9 1.0
C C:ASP82 5.0 47.6 1.0
CE C:LYS59 5.0 49.4 1.0
CZ A:ARG228 5.0 43.6 1.0

Cadmium binding site 4 out of 6 in 6ahg

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Cadmium binding site 4 out of 6 in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Trimeric Structure of Concanavalin A From Canavalia Ensiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:41.6
occ:1.00
 O B:HOH404 2.3 37.8 1.0
NE2 B:HIS24 2.3 39.0 1.0
OD2 B:ASP10 2.3 42.0 1.0
OE2 B:GLU8 2.5 43.9 1.0
O B:HOH406 2.9 35.5 1.0
OD1 B:ASP19 3.0 50.6 1.0
OD2 B:ASP19 3.1 47.2 1.0
CD B:GLU8 3.1 43.8 1.0
CG B:ASP19 3.2 48.8 1.0
CG B:ASP10 3.2 41.9 1.0
CE1 B:HIS24 3.2 39.0 1.0
OE1 B:GLU8 3.2 43.9 1.0
CD2 B:HIS24 3.3 39.5 1.0
CB B:ASP10 3.8 41.8 1.0
O B:HOH407 3.9 44.7 1.0
OG B:SER34 4.0 41.0 1.0
OD1 B:ASP10 4.1 41.0 1.0
CB B:ASP19 4.3 48.6 1.0
ND1 B:HIS24 4.4 39.4 1.0
CG B:GLU8 4.4 42.9 1.0
CG B:HIS24 4.4 39.7 1.0
CA B:CA301 4.5 16.8 1.0
O B:VAL32 4.6 45.3 1.0
CA B:ASP19 4.7 48.4 1.0

Cadmium binding site 5 out of 6 in 6ahg

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Cadmium binding site 5 out of 6 in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Trimeric Structure of Concanavalin A From Canavalia Ensiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd303

b:52.9
occ:1.00
 O C:HOH401 2.2 50.4 1.0
OD2 C:ASP16 2.3 51.5 1.0
OD1 B:ASP82 2.3 50.2 1.0
OD1 B:ASP80 2.4 48.8 1.0
OD1 B:ASN83 2.7 50.1 1.0
CG C:ASP16 3.0 52.7 1.0
OD1 C:ASP16 3.0 55.0 1.0
CG B:ASP80 3.1 49.6 1.0
OD2 B:ASP80 3.1 50.6 1.0
CG B:ASP82 3.1 49.9 1.0
OD2 B:ASP82 3.2 50.4 1.0
NZ B:LYS59 3.7 50.5 1.0
CG B:ASN83 3.9 49.4 1.0
NH1 C:ARG228 4.3 43.2 1.0
CB C:ASP16 4.4 51.6 1.0
CB B:ASP82 4.5 49.4 1.0
CB B:ASP80 4.5 48.7 1.0
ND2 B:ASN83 4.5 49.2 1.0
N B:ASN83 4.5 48.0 1.0
NH2 C:ARG228 4.6 44.0 1.0
O C:ASP16 4.6 52.1 1.0
CZ2 B:TRP182 4.9 48.4 1.0
CZ C:ARG228 4.9 43.6 1.0
CB B:ASN83 5.0 48.5 1.0
C B:ASP82 5.0 48.7 1.0

Cadmium binding site 6 out of 6 in 6ahg

Go back to Cadmium Binding Sites List in 6ahg
Cadmium binding site 6 out of 6 in the Trimeric Structure of Concanavalin A From Canavalia Ensiformis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Trimeric Structure of Concanavalin A From Canavalia Ensiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd302

b:42.2
occ:1.00
 O C:HOH404 2.2 39.1 1.0
NE2 C:HIS24 2.3 39.8 1.0
OD2 C:ASP10 2.3 41.4 1.0
OE2 C:GLU8 2.5 40.1 1.0
OD1 C:ASP19 3.0 52.8 1.0
OD2 C:ASP19 3.1 50.3 1.0
CG C:ASP10 3.2 41.4 1.0
CG C:ASP19 3.2 51.0 1.0
OE1 C:GLU8 3.2 39.6 1.0
CE1 C:HIS24 3.2 39.7 1.0
CD C:GLU8 3.3 39.9 1.0
CD2 C:HIS24 3.3 39.9 1.0
CB C:ASP10 3.8 41.0 1.0
OG C:SER34 3.9 41.2 1.0
O C:HOH405 3.9 35.1 1.0
OD1 C:ASP10 4.1 40.8 1.0
CB C:ASP19 4.4 50.3 1.0
ND1 C:HIS24 4.4 39.9 1.0
CA C:CA301 4.4 18.5 1.0
CG C:HIS24 4.4 40.2 1.0
O C:VAL32 4.5 42.5 1.0
CG C:GLU8 4.7 39.1 1.0
CA C:ASP19 4.8 49.8 1.0

Reference:

Y.R.Park, D.S.Kim, D.H.Lee, H.G.Kang, J.H.Park, S.J.Lee. Cadmium-Substituted Concanavalin A and Its Trimeric Complexation J. Microbiol. Biotechnol. V.(12) 2106 2018.
ISSN: ISSN 1017-7825
PubMed: 30380822
DOI: 10.4014/JMB.1809.09027
Page generated: Fri Jul 19 19:03:09 2024

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