Atomistry » Gold » PDB 1a52-3k3g » 3k3g
Atomistry »
  Gold »
    PDB 1a52-3k3g »
      3k3g »

Gold in PDB 3k3g: Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea

Protein crystallography data

The structure of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea, PDB code: 3k3g 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) 27.47 / 2.40
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 110.106, 110.106, 84.872, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 21.4

Gold Binding Sites:

The binding sites of Gold atom in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea (pdb code 3k3g). 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 Bound to 1,3-Dimethylurea, PDB code: 3k3g:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Gold binding site 1 out of 9 in 3k3g

Go back to Gold Binding Sites List in 3k3g
Gold binding site 1 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea


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 Bound to 1,3-Dimethylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au338

b:91.1
occ:0.25
OE1 A:GLN24 3.4 37.5 1.0
NE2 A:GLN24 3.8 37.4 1.0
O A:PHE27 4.0 41.1 1.0
CD A:GLN24 4.0 37.7 1.0
O A:ALA322 4.1 68.6 1.0
CAA A:MMU348 4.5 62.2 1.0
C A:PHE27 4.6 41.5 1.0
CA A:PHE27 4.7 41.3 1.0
CB A:PHE27 4.7 41.3 1.0
CD1 A:PHE27 4.9 41.9 1.0
O A:HOH365 4.9 59.3 1.0
CG2 A:ILE255 5.0 37.3 1.0

Gold binding site 2 out of 9 in 3k3g

Go back to Gold Binding Sites List in 3k3g
Gold binding site 2 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea


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 Bound to 1,3-Dimethylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au339

b:87.8
occ:0.75
SG A:CYS19 2.7 41.6 1.0
AU A:AU340 3.0 75.1 0.5
CG2 A:THR31 3.1 45.0 1.0
CB A:CYS19 3.2 39.2 1.0
CD1 A:LEU35 3.5 40.9 1.0
AU A:AU341 3.6 0.1 0.5
CB A:LEU35 3.9 40.7 1.0
O A:THR31 3.9 44.0 1.0
CG A:LEU35 4.1 41.1 1.0
CD2 A:LEU35 4.4 41.5 1.0
O A:CYS15 4.5 47.5 1.0
CB A:THR31 4.6 45.0 1.0
C A:THR31 4.6 44.0 1.0
AU A:AU342 4.6 77.2 0.2
CA A:LEU35 4.6 41.2 1.0
CA A:CYS19 4.7 40.9 1.0
N A:LEU35 4.9 41.3 1.0
CA A:THR31 5.0 44.5 1.0

Gold binding site 3 out of 9 in 3k3g

Go back to Gold Binding Sites List in 3k3g
Gold binding site 3 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea


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 Bound to 1,3-Dimethylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au340

b:75.1
occ:0.50
O A:CYS15 2.2 47.5 1.0
SG A:CYS19 2.4 41.6 1.0
SG A:CYS15 2.9 56.1 1.0
AU A:AU339 3.0 87.8 0.8
C A:CYS15 3.1 49.7 1.0
AU A:AU341 3.2 0.1 0.5
AU A:AU342 3.4 77.2 0.2
CB A:CYS19 3.4 39.2 1.0
CA A:CYS15 3.8 51.8 1.0
CB A:CYS15 3.8 52.4 1.0
N A:CYS19 4.0 41.1 1.0
N A:ASP16 4.1 47.5 1.0
CA A:CYS19 4.3 40.9 1.0
CA A:ASP16 4.5 46.4 1.0
CB A:VAL18 4.9 42.4 1.0
C A:VAL18 4.9 41.8 1.0

Gold binding site 4 out of 9 in 3k3g

Go back to Gold Binding Sites List in 3k3g
Gold binding site 4 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea


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 Bound to 1,3-Dimethylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au341

b:0.1
occ:0.50
AU A:AU342 3.1 77.2 0.2
AU A:AU340 3.2 75.1 0.5
SG A:CYS15 3.3 56.1 1.0
CB A:CYS15 3.5 52.4 1.0
C A:CYS15 3.5 49.7 1.0
O A:CYS15 3.6 47.5 1.0
AU A:AU339 3.6 87.8 0.8
N A:ASP16 3.6 47.5 1.0
CA A:ASP16 3.9 46.4 1.0
CD1 A:ILE12 4.1 63.8 1.0
O A:ILE12 4.2 61.1 1.0
CA A:CYS15 4.2 51.8 1.0
CB A:ASP16 4.3 46.4 1.0
CG2 A:THR31 4.5 45.0 1.0
CG1 A:ILE12 4.8 63.6 1.0
OD1 A:ASP16 4.9 47.8 1.0

Gold binding site 5 out of 9 in 3k3g

Go back to Gold Binding Sites List in 3k3g
Gold binding site 5 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea


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 Bound to 1,3-Dimethylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au342

b:77.2
occ:0.25
SG A:CYS15 1.9 56.1 1.0
AU A:AU341 3.1 0.1 0.5
CB A:CYS15 3.4 52.4 1.0
AU A:AU340 3.4 75.1 0.5
CD1 A:ILE12 4.3 63.8 1.0
CA A:CYS15 4.5 51.8 1.0
O A:CYS15 4.6 47.5 1.0
AU A:AU339 4.6 87.8 0.8
C A:CYS15 4.7 49.7 1.0

Gold binding site 6 out of 9 in 3k3g

Go back to Gold Binding Sites List in 3k3g
Gold binding site 6 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea


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 Bound to 1,3-Dimethylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au343

b:74.9
occ:0.50
SG A:CYS51 2.8 49.9 1.0
AU A:AU344 3.0 96.5 0.8
O A:THR47 3.3 45.5 1.0
CG1 A:VAL50 3.3 44.1 1.0
N A:CYS51 3.5 44.6 1.0
CB A:VAL50 3.7 44.7 1.0
CB A:CYS51 3.7 44.3 1.0
CD1 A:LEU100 3.7 45.6 1.0
CA A:CYS51 3.9 44.6 1.0
C A:VAL50 4.0 45.0 1.0
CG2 A:THR47 4.3 45.2 1.0
C A:THR47 4.3 44.5 1.0
CA A:VAL50 4.4 44.8 1.0
CG A:LEU100 4.5 43.4 1.0
CA A:THR47 4.6 44.7 1.0
O A:VAL50 4.7 45.6 1.0
CG2 A:VAL50 4.9 44.3 1.0

Gold binding site 7 out of 9 in 3k3g

Go back to Gold Binding Sites List in 3k3g
Gold binding site 7 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea


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 Bound to 1,3-Dimethylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au344

b:96.5
occ:0.75
SG A:CYS51 2.4 49.9 1.0
AU A:AU343 3.0 74.9 0.5
CB A:CYS51 3.7 44.3 1.0
CG2 A:THR47 3.7 45.2 1.0
CG A:PRO90 3.7 37.6 1.0
CG A:MET99 3.8 46.4 1.0
CD1 A:LEU100 3.8 45.6 1.0
CB A:PRO90 3.9 37.9 1.0
O A:THR47 4.1 45.5 1.0
CD A:PRO90 4.7 38.9 1.0
C A:THR47 4.8 44.5 1.0
CA A:CYS51 4.9 44.6 1.0
CB A:MET99 4.9 45.3 1.0
SD A:MET99 4.9 50.5 1.0

Gold binding site 8 out of 9 in 3k3g

Go back to Gold Binding Sites List in 3k3g
Gold binding site 8 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea


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 Bound to 1,3-Dimethylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au345

b:97.6
occ:0.50
SG A:CYS224 2.6 41.9 1.0
CB A:CYS224 3.1 41.7 1.0
AU A:AU346 3.1 92.5 0.5
CA A:CYS224 4.6 41.9 1.0

Gold binding site 9 out of 9 in 3k3g

Go back to Gold Binding Sites List in 3k3g
Gold binding site 9 out of 9 in the Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea


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 Bound to 1,3-Dimethylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au346

b:92.5
occ:0.50
SG A:CYS224 1.7 41.9 1.0
CB A:CYS224 2.8 41.7 1.0
AU A:AU345 3.1 97.6 0.5
CA A:CYS224 3.7 41.9 1.0
O A:CYS224 4.0 42.0 1.0
C A:CYS224 4.3 41.9 1.0
CB A:LEU227 4.4 44.9 1.0
CD1 A:LEU227 4.5 45.2 1.0
CG1 A:ILE228 4.6 47.3 1.0
CE1 A:PHE177 4.7 46.1 1.0
CZ A:PHE177 4.8 46.3 1.0
CD1 A:ILE228 4.9 47.0 1.0
N A:CYS224 4.9 41.9 1.0

Reference:

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
Page generated: Sat Dec 12 01:53:40 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy