Cadmium in PDB 7nl4: OSNIP2;1 Silicon Transporter From Rice

The structure of OSNIP2;1 Silicon Transporter From Rice, PDB code: 7nl4 was solved by B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.78 / 3.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	94.888, 96.692, 99.787, 63.91, 71.16, 65.07
R / Rfree (%)	23.8 / 28.2

The binding sites of Cadmium atom in the OSNIP2;1 Silicon Transporter From Rice (pdb code 7nl4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the OSNIP2;1 Silicon Transporter From Rice, PDB code: 7nl4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in the OSNIP2;1 Silicon Transporter From Rice


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of OSNIP2;1 Silicon Transporter From Rice within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:117.4 occ:1.00 NE2 A:HIS120 2.6 69.0 1.0 NE2 H:HIS46 3.1 132.4 1.0 CE1 A:HIS120 3.5 74.5 1.0 CD2 H:HIS46 3.5 121.0 1.0 CD2 A:HIS120 3.7 74.9 1.0 CE1 H:HIS46 4.3 136.8 1.0 ND1 A:HIS120 4.7 78.0 1.0 CG A:HIS120 4.8 76.4 1.0 CG H:HIS46 4.8 121.3 1.0 CB F:PHE259 5.0 130.4 1.0

Cadmium binding site 2 out of 9 in the OSNIP2;1 Silicon Transporter From Rice


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of OSNIP2;1 Silicon Transporter From Rice within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:115.6 occ:1.00 NE2 B:HIS120 2.4 78.9 1.0 CD2 B:HIS120 3.4 78.4 1.0 CE1 B:HIS120 3.4 81.5 1.0 CE1 G:HIS46 3.5 94.3 1.0 ND1 G:HIS46 3.6 85.5 1.0 NE2 G:HIS46 4.4 97.7 1.0 ND1 B:HIS120 4.5 78.5 1.0 CG B:HIS120 4.6 68.4 1.0 CG G:HIS46 4.6 87.1 1.0 CB E:PHE259 4.8 121.9 1.0 CD2 G:HIS46 5.0 95.8 1.0

Cadmium binding site 3 out of 9 in the OSNIP2;1 Silicon Transporter From Rice


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of OSNIP2;1 Silicon Transporter From Rice within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd301 b:110.3 occ:1.00 NE2 C:HIS120 2.5 78.2 1.0 CE1 C:HIS120 3.1 78.5 1.0 CD2 C:HIS120 3.6 84.2 1.0 CE1 F:HIS46 4.0 111.6 1.0 ND1 F:HIS46 4.1 111.2 1.0 ND1 C:HIS120 4.3 75.4 1.0 CG C:HIS120 4.6 76.4 1.0 NE2 F:HIS46 4.9 109.8 1.0

Cadmium binding site 4 out of 9 in the OSNIP2;1 Silicon Transporter From Rice


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of OSNIP2;1 Silicon Transporter From Rice within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd301 b:98.2 occ:1.00 NE2 E:HIS120 2.5 80.8 1.0 CE1 E:HIS120 2.9 77.4 1.0 CE1 D:HIS46 3.3 102.2 1.0 ND1 D:HIS46 3.5 99.2 1.0 CD2 B:PHE259 3.7 97.2 1.0 CD2 E:HIS120 3.8 82.0 1.0 CG B:PHE259 4.1 103.8 1.0 CE2 B:PHE259 4.2 91.6 1.0 ND1 E:HIS120 4.2 72.0 1.0 NE2 D:HIS46 4.2 108.9 1.0 CB B:PHE259 4.3 99.5 1.0 CG D:HIS46 4.6 101.5 1.0 CG E:HIS120 4.6 72.8 1.0 CD1 B:PHE259 4.8 98.3 1.0 CZ B:PHE259 4.9 91.8 1.0 O B:PHE259 4.9 98.6 1.0 CD2 D:HIS46 4.9 102.1 1.0

Cadmium binding site 5 out of 9 in the OSNIP2;1 Silicon Transporter From Rice


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of OSNIP2;1 Silicon Transporter From Rice within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd302 b:113.2 occ:1.00 NE2 D:HIS120 2.6 75.2 1.0 CE1 D:HIS120 3.2 81.5 1.0 CD2 D:HIS120 3.8 89.7 1.0 CE1 E:HIS46 4.1 105.0 1.0 ND1 E:HIS46 4.2 104.8 1.0 CD2 H:PHE259 4.2 98.2 1.0 ND1 D:HIS120 4.5 87.7 1.0 CG D:HIS120 4.8 85.2 1.0 CB H:PHE259 4.9 106.4 1.0 CG H:PHE259 5.0 103.8 1.0 CE2 H:PHE259 5.0 98.6 1.0

Cadmium binding site 6 out of 9 in the OSNIP2;1 Silicon Transporter From Rice


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of OSNIP2;1 Silicon Transporter From Rice within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd303 b:111.6 occ:1.00 O D:HIS149 2.7 139.4 1.0 OD1 D:ASP152 3.0 122.8 1.0 C D:HIS149 3.7 141.0 1.0 ND1 D:HIS149 3.8 150.1 1.0 O D:LYS145 3.9 93.0 1.0 CG D:ASP152 4.0 116.5 1.0 CA D:HIS149 4.0 141.3 1.0 CE1 D:HIS149 4.2 152.3 1.0 CG D:HIS149 4.3 147.6 1.0 CB D:ASP152 4.3 117.5 1.0 CG D:LYS145 4.7 91.8 1.0 CB D:HIS149 4.7 145.2 1.0 N D:PRO150 4.8 116.2 1.0 C D:LYS145 4.8 86.9 1.0 OD2 D:ASP152 4.9 115.5 1.0 NE2 D:HIS149 5.0 150.1 1.0

Cadmium binding site 7 out of 9 in the OSNIP2;1 Silicon Transporter From Rice


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of OSNIP2;1 Silicon Transporter From Rice within 5.0Å range: probe atom residue distance (Å) B Occ F:Cd301 b:104.0 occ:1.00 NE2 F:HIS120 2.5 82.7 1.0 CE1 C:HIS46 3.4 93.5 1.0 CD2 F:HIS120 3.4 83.9 1.0 CE1 F:HIS120 3.5 82.6 1.0 ND1 C:HIS46 3.5 87.2 1.0 NE2 C:HIS46 4.3 97.3 1.0 CG C:HIS46 4.5 87.6 1.0 ND1 F:HIS120 4.6 81.5 1.0 CG F:HIS120 4.6 79.5 1.0 CD2 C:HIS46 5.0 86.8 1.0

Cadmium binding site 8 out of 9 in the OSNIP2;1 Silicon Transporter From Rice


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of OSNIP2;1 Silicon Transporter From Rice within 5.0Å range: probe atom residue distance (Å) B Occ G:Cd301 b:109.2 occ:1.00 NE2 G:HIS120 2.6 91.4 1.0 CD2 G:HIS120 3.1 83.1 1.0 NE2 B:HIS46 3.4 102.1 1.0 CD2 B:HIS46 3.6 100.7 1.0 CE1 G:HIS120 3.6 95.9 1.0 CG G:HIS120 4.3 79.1 1.0 ND1 G:HIS120 4.5 94.8 1.0 CE1 B:HIS46 4.7 101.5 1.0 CG B:HIS46 4.9 102.5 1.0

Cadmium binding site 9 out of 9 in the OSNIP2;1 Silicon Transporter From Rice


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of OSNIP2;1 Silicon Transporter From Rice within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd301 b:112.1 occ:1.00 NE2 H:HIS120 2.5 70.9 1.0 CE1 H:HIS120 3.3 76.3 1.0 CD2 H:HIS120 3.4 73.6 1.0 CE1 A:HIS46 3.7 102.7 1.0 ND1 A:HIS46 3.8 100.4 1.0 ND1 H:HIS120 4.4 80.9 1.0 CG H:HIS120 4.5 75.1 1.0 NE2 A:HIS46 4.8 106.1 1.0 CB D:PHE259 4.9 133.8 1.0 CG A:HIS46 5.0 99.5 1.0 CG D:PHE259 5.0 138.2 1.0

B.Van Den Berg, C.Pedebos, J.R.Bolla, C.V.Robinson, A.Basle, S.Khalid. Structural Basis For Silicic Acid Uptake By Higher Plants. J.Mol.Biol. V. 433 67226 2021.
ISSN: ESSN 1089-8638
PubMed: 34487790
DOI: 10.1016/J.JMB.2021.167226