Cadmium in PDB 6qf5: X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip

The structure of X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip, PDB code: 6qf5 was solved by J.Lieske, M.Cerv, S.Kreida, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.89 / 3.70
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	122.200, 122.200, 94.140, 90.00, 90.00, 90.00
R / Rfree (%)	28.2 / 33.6

The binding sites of Cadmium atom in the X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip (pdb code 6qf5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip, PDB code: 6qf5:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:0.1 occ:0.40 ND1 B:HIS80 3.0 0.1 1.0 CE1 B:HIS80 3.3 0.6 1.0 OE2 B:GLU151 3.8 92.3 1.0 CG B:HIS80 4.3 0.7 1.0 NE2 B:HIS80 4.6 0.6 1.0 CD B:GLU151 4.7 90.1 1.0 OE1 B:GLU151 4.8 89.0 1.0 C B:CYS79 5.0 60.5 0.7 CA B:CYS79 5.0 60.0 0.7

Cadmium binding site 2 out of 4 in the X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:0.4 occ:0.60 NE2 B:HIS80 2.9 0.6 1.0 CE1 B:HIS80 3.3 0.6 1.0 CD2 B:HIS80 4.0 0.9 1.0 O B:ALA227 4.1 76.9 1.0 CB B:SER229 4.3 99.3 1.0 N B:SER229 4.4 97.3 1.0 ND1 B:HIS80 4.5 0.1 1.0 CG B:HIS80 4.8 0.7 1.0 CA B:SER229 5.0 99.0 1.0

Cadmium binding site 3 out of 4 in the X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd301 b:62.6 occ:1.00 OE1 C:GLU155 2.7 58.5 1.0 OE2 C:GLU155 2.8 62.2 1.0 O A:HOH302 2.8 77.6 1.0 OE1 A:GLN57 2.8 61.2 1.0 O A:HOH301 2.8 77.6 1.0 O C:HOH401 3.0 77.6 1.0 CD C:GLU155 3.1 60.5 1.0 CG2 C:THR159 3.7 38.9 1.0 CD A:GLN57 3.8 61.8 1.0 CD A:PRO160 4.0 69.0 1.0 NE2 A:GLN57 4.2 60.8 1.0 CB A:ALA161 4.6 35.6 1.0 CB C:THR159 4.6 37.5 1.0 CG C:GLU155 4.6 60.8 1.0 N A:ALA161 4.7 36.8 1.0 N A:PRO160 4.8 71.8 1.0 CA A:THR159 4.9 0.6 1.0 CG A:PRO160 5.0 69.3 1.0

Cadmium binding site 4 out of 4 in the X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of Human Aquaporin 2 Crystallized on A Silicon Chip within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd301 b:0.2 occ:1.00 NE2 D:HIS105 3.4 0.3 1.0 CD2 D:HIS105 4.1 0.9 1.0 CE1 D:HIS105 4.1 0.4 1.0 O D:VAL194 4.4 1.0 1.0

J.Lieske, M.Cerv, S.Kreida, D.Komadina, J.Fischer, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents. On-Chip Crystallization For Serial Crystallography Experiments and on-Chip Ligand-Binding Studies. Iucrj V. 6 714 2019.
ISSN: ESSN 2052-2525
PubMed: 31316815
DOI: 10.1107/S2052252519007395