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Cadmium in PDB 1npe: Crystal Structure of Nidogen/Laminin Complex

Protein crystallography data

The structure of Crystal Structure of Nidogen/Laminin Complex, PDB code: 1npe was solved by J.Takagi, Y.T.Yang, J.-H.Liu, J.-H.Wang, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.180, 75.830, 104.580, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 25.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Nidogen/Laminin Complex (pdb code 1npe). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Nidogen/Laminin Complex, PDB code: 1npe:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1npe

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Cadmium binding site 1 out of 6 in the Crystal Structure of Nidogen/Laminin Complex


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 Nidogen/Laminin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5001

b:25.3
occ:1.00
OD1 A:ASP1013 2.1 24.2 1.0
O A:VAL1034 2.3 16.6 1.0
O A:SER1010 2.4 14.9 1.0
O A:HOH23 2.5 24.8 1.0
O A:HOH3 2.6 16.8 1.0
O A:HOH25 2.7 21.4 1.0
CG A:ASP1013 3.0 22.9 1.0
OD2 A:ASP1013 3.2 25.8 1.0
C A:SER1010 3.4 13.9 1.0
C A:VAL1034 3.4 14.0 1.0
CA A:VAL1034 4.0 13.5 1.0
O A:GLN1011 4.2 18.6 1.0
CA A:SER1010 4.3 13.8 1.0
N A:GLN1011 4.3 15.7 1.0
ND2 A:ASN1035 4.3 10.0 1.0
O A:HOH111 4.4 39.8 1.0
CA A:GLN1011 4.4 18.1 1.0
O A:HOH110 4.4 32.5 1.0
CB A:ASP1013 4.4 20.8 1.0
C A:GLN1011 4.5 18.4 1.0
CG1 A:VAL1034 4.6 10.0 1.0
N A:ASN1035 4.6 14.2 1.0
CB A:SER1010 4.7 12.9 1.0
CA A:ASP1013 4.8 19.3 1.0
N A:ASP1013 4.9 18.1 1.0
CB A:VAL1034 4.9 12.8 1.0
CA A:ASN1035 4.9 13.2 1.0
O A:LEU1033 4.9 16.3 1.0

Cadmium binding site 2 out of 6 in 1npe

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Cadmium binding site 2 out of 6 in the Crystal Structure of Nidogen/Laminin Complex


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 Nidogen/Laminin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5003

b:45.3
occ:1.00
O A:HOH94 1.9 35.4 1.0
NE2 A:HIS1101 2.1 27.4 1.0
O A:HOH108 2.4 35.4 1.0
CE1 A:HIS1101 2.8 25.1 1.0
CD2 A:HIS1101 3.2 23.7 1.0
ND1 A:HIS1101 4.0 25.2 1.0
CG A:HIS1101 4.3 24.8 1.0
O A:GLY1099 4.3 19.2 1.0
O A:ALA1098 4.5 20.1 1.0

Cadmium binding site 3 out of 6 in 1npe

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Cadmium binding site 3 out of 6 in the Crystal Structure of Nidogen/Laminin Complex


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 Nidogen/Laminin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5005

b:43.5
occ:1.00
ND1 A:HIS944 2.5 21.4 1.0
O A:HOH102 2.7 33.5 1.0
OE1 B:GLU754 2.7 44.7 1.0
OE2 B:GLU754 3.0 45.8 1.0
CD B:GLU754 3.2 45.5 1.0
CG A:HIS944 3.3 22.1 1.0
CB A:HIS944 3.4 24.3 1.0
CE1 A:HIS944 3.5 20.4 1.0
CD2 A:HIS944 4.5 22.0 1.0
N A:HIS944 4.5 26.3 1.0
NE2 A:HIS944 4.6 23.8 1.0
CA A:HIS944 4.6 25.3 1.0
CG B:GLU754 4.7 43.1 1.0
CD B:LYS767 4.8 31.6 1.0

Cadmium binding site 4 out of 6 in 1npe

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Cadmium binding site 4 out of 6 in the Crystal Structure of Nidogen/Laminin Complex


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 Nidogen/Laminin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd5002

b:26.1
occ:1.00
OE1 B:GLU831 2.4 22.1 1.0
OE2 B:GLU831 2.6 24.3 1.0
O B:HOH89 2.6 22.3 1.0
CD B:GLU831 2.9 22.7 1.0
OG B:SER862 3.6 29.5 1.0
O B:HOH54 4.0 20.3 1.0
CG B:GLU831 4.4 23.6 1.0
CB B:SER862 4.4 22.6 1.0

Cadmium binding site 5 out of 6 in 1npe

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Cadmium binding site 5 out of 6 in the Crystal Structure of Nidogen/Laminin Complex


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 Nidogen/Laminin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd5004

b:31.5
occ:1.00
NE2 B:HIS759 2.2 22.8 1.0
ND1 A:HIS1160 2.6 24.3 1.0
O A:HOH84 2.8 28.3 1.0
CD2 B:HIS759 3.1 20.4 1.0
CE1 B:HIS759 3.1 23.3 1.0
CE1 A:HIS1160 3.5 23.5 1.0
CG A:HIS1160 3.7 26.0 1.0
CB A:HIS1160 3.9 25.6 1.0
CA A:HIS1160 4.1 24.9 1.0
ND1 B:HIS759 4.3 21.9 1.0
CG B:HIS759 4.3 22.9 1.0
O A:HIS1160 4.3 23.2 1.0
NE2 A:HIS1160 4.7 24.9 1.0
C A:HIS1160 4.7 24.5 1.0
CD2 A:HIS1160 4.8 25.6 1.0

Cadmium binding site 6 out of 6 in 1npe

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Cadmium binding site 6 out of 6 in the Crystal Structure of Nidogen/Laminin Complex


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 Nidogen/Laminin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd5006

b:74.5
occ:1.00
O B:HOH106 2.4 43.0 1.0
NE2 B:HIS875 2.4 46.2 1.0
O B:HOH105 2.5 48.7 1.0
CD2 B:HIS875 3.2 43.6 1.0
CE1 B:HIS875 3.5 45.4 1.0
CG B:HIS875 4.4 42.1 1.0
ND1 B:HIS875 4.5 44.6 1.0

Reference:

J.Takagi, Y.T.Yang, J.-H.Liu, J.-H.Wang, T.A.Springer. Complex Between Nidogen and Laminin Fragments Reveals A Paradigmatic Beta-Propeller Interface Nature V. 424 969 2003.
ISSN: ISSN 0028-0836
PubMed: 12931195
DOI: 10.1038/NATURE01873
Page generated: Wed Oct 28 09:55:12 2020
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