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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

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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

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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

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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

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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

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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

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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

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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

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