Gold in PDB 3k3f: Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris

The structure of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris, PDB code: 3k3f was solved by E.J.Levin, M.Zhou, New York Consortium On Membrane Protein Structure(Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.78 / 2.30
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	110.131, 110.131, 84.861, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 20.4

The binding sites of Gold atom in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris (pdb code 3k3f). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 9 binding sites of Gold where determined in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris, PDB code: 3k3f:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Gold binding site 1 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Au338 b:64.9 occ:0.25 OE1 A:GLN24 3.6 44.8 1.0 NE2 A:GLN24 3.9 48.0 1.0 O A:ALA322 3.9 65.0 1.0 CD A:GLN24 4.2 46.7 1.0 O A:PHE27 4.3 47.2 1.0 O A:HOH373 4.7 72.0 1.0 C A:PHE27 4.9 47.6 1.0 CD2 A:LEU77 4.9 53.2 1.0 CB A:PHE27 5.0 49.6 1.0 CG2 A:ILE255 5.0 44.3 1.0

Gold binding site 2 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Au339 b:74.1 occ:0.50 SG A:CYS19 2.6 44.8 1.0 AU A:AU340 2.8 59.3 0.2 CB A:CYS19 3.1 41.8 1.0 CG2 A:THR31 3.2 50.3 1.0 AU A:AU345 3.7 0.6 0.5 CB A:LEU35 3.9 46.8 1.0 CD1 A:LEU35 3.9 48.9 1.0 O A:THR31 4.0 48.1 1.0 CG A:LEU35 4.3 48.0 1.0 O A:CYS15 4.4 36.5 1.0 CD2 A:LEU35 4.5 47.9 1.0 SG A:CYS15 4.5 40.6 1.0 C A:THR31 4.6 48.0 1.0 CA A:CYS19 4.6 44.9 1.0 AU A:AU346 4.6 81.2 0.2 CB A:THR31 4.6 49.3 1.0 CA A:LEU35 4.7 47.4 1.0 N A:LEU35 4.9 46.8 1.0 CA A:THR31 5.0 48.5 1.0

Gold binding site 3 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Au340 b:59.3 occ:0.25 SG A:CYS15 2.1 40.6 1.0 O A:CYS15 2.3 36.5 1.0 SG A:CYS19 2.3 44.8 1.0 AU A:AU339 2.8 74.1 0.5 C A:CYS15 3.2 39.3 1.0 CB A:CYS19 3.3 41.8 1.0 AU A:AU345 3.3 0.6 0.5 AU A:AU346 3.4 81.2 0.2 CB A:CYS15 3.6 39.3 1.0 CA A:CYS15 3.8 39.2 1.0 N A:CYS19 3.8 44.4 1.0 N A:ASP16 4.1 40.8 1.0 CA A:CYS19 4.1 44.9 1.0 CA A:ASP16 4.5 42.7 1.0 CB A:VAL18 4.9 46.7 1.0 C A:VAL18 4.9 45.6 1.0

Gold binding site 4 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Au341 b:64.3 occ:0.40 SG A:CYS51 2.6 53.4 1.0 AU A:AU343 3.0 67.1 0.4 O A:THR47 3.4 48.5 1.0 CG1 A:VAL50 3.4 49.1 1.0 CB A:CYS51 3.5 47.2 1.0 N A:CYS51 3.5 47.5 1.0 CD1 A:LEU100 3.7 53.3 1.0 CB A:VAL50 3.7 47.8 1.0 CA A:CYS51 3.8 47.2 1.0 C A:VAL50 4.1 47.7 1.0 C A:THR47 4.4 47.5 1.0 CG2 A:THR47 4.4 47.2 1.0 CA A:VAL50 4.5 47.8 1.0 CG A:LEU100 4.5 49.9 1.0 CA A:THR47 4.7 46.8 1.0 O A:VAL50 4.8 48.2 1.0

Gold binding site 5 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Au342 b:86.2 occ:0.35 SG A:CYS224 2.6 48.2 1.0 CB A:CYS224 3.0 47.0 1.0 AU A:AU344 3.1 85.2 0.3 CA A:CYS224 4.6 47.6 1.0

Gold binding site 6 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Au343 b:67.1 occ:0.40 SG A:CYS51 2.0 53.4 1.0 AU A:AU341 3.0 64.3 0.4 CB A:CYS51 3.4 47.2 1.0 CG A:PRO90 3.5 43.8 1.0 CG A:MET99 3.8 49.4 1.0 CD1 A:LEU100 3.8 53.3 1.0 CG2 A:THR47 3.9 47.2 1.0 CB A:PRO90 4.0 43.4 1.0 O A:THR47 4.2 48.5 1.0 CA A:CYS51 4.7 47.2 1.0 CB A:MET99 4.8 49.8 1.0 CD A:PRO90 4.8 43.6 1.0 C A:THR47 4.9 47.5 1.0 SD A:MET99 5.0 54.5 1.0

Gold binding site 7 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Au344 b:85.2 occ:0.35 SG A:CYS224 1.7 48.2 1.0 CB A:CYS224 2.7 47.0 1.0 AU A:AU342 3.1 86.2 0.3 CA A:CYS224 3.6 47.6 1.0 O A:CYS224 3.9 47.0 1.0 C A:CYS224 4.2 47.0 1.0 CB A:LEU227 4.3 49.5 1.0 CG1 A:ILE228 4.5 53.0 1.0 CD1 A:LEU227 4.5 48.4 1.0 CD1 A:ILE228 4.7 53.2 1.0 CE1 A:PHE177 4.9 46.8 1.0 N A:CYS224 4.9 47.0 1.0 CZ A:PHE177 5.0 46.3 1.0

Gold binding site 8 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 8 of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Au345 b:0.6 occ:0.50 AU A:AU346 3.2 81.2 0.2 SG A:CYS15 3.3 40.6 1.0 AU A:AU340 3.3 59.3 0.2 N A:ASP16 3.5 40.8 1.0 C A:CYS15 3.5 39.3 1.0 CB A:CYS15 3.6 39.3 1.0 O A:CYS15 3.6 36.5 1.0 AU A:AU339 3.7 74.1 0.5 CA A:ASP16 3.7 42.7 1.0 O A:ILE12 4.2 33.6 1.0 CB A:ASP16 4.2 43.4 1.0 CA A:CYS15 4.2 39.2 1.0 CD1 A:ILE12 4.2 35.4 1.0 CG2 A:THR31 4.6 50.3 1.0 OD1 A:ASP16 4.7 50.7 1.0 CG1 A:ILE12 4.8 34.3 1.0 CG A:ASP16 5.0 45.6 1.0

Gold binding site 9 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 9 of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Au346 b:81.2 occ:0.25 SG A:CYS15 2.3 40.6 1.0 AU A:AU345 3.2 0.6 0.5 CB A:CYS15 3.3 39.3 1.0 AU A:AU340 3.4 59.3 0.2 CA A:CYS15 4.6 39.2 1.0 CD1 A:ILE12 4.6 35.4 1.0 AU A:AU339 4.6 74.1 0.5 O A:CYS15 4.7 36.5 1.0 C A:CYS15 4.8 39.3 1.0

E.J.Levin, M.Quick, M.Zhou. Crystal Structure of A Bacterial Homologue of the Kidney Urea Transporter. Nature V. 462 757 2009.
ISSN: ISSN 0028-0836
PubMed: 19865084
DOI: 10.1038/NATURE08558