Gold in PDB 2wz7: Crystal Structure of the N-Terminal Domain of E.Coli Ybgf

The structure of Crystal Structure of the N-Terminal Domain of E.Coli Ybgf, PDB code: 2wz7 was solved by A.M.Krachler, A.Sharma, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.62 / 2.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.737, 41.382, 237.697, 90.00, 90.00, 90.00
R / Rfree (%)	21.257 / 30.223

The structure of Crystal Structure of the N-Terminal Domain of E.Coli Ybgf also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Gold atom in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf (pdb code 2wz7). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 3 binding sites of Gold where determined in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf, PDB code: 2wz7:
Jump to Gold binding site number: 1; 2; 3;

Gold binding site 1 out of 3 in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf


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 N-Terminal Domain of E.Coli Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ D:Au1069 b:18.0 occ:0.50 AU D:AUC1069 0.0 18.0 0.5 C1 D:AUC1069 1.7 13.6 0.5 C2 D:AUC1069 1.8 15.7 0.5 N1 D:AUC1069 2.9 11.3 0.5 N2 D:AUC1069 3.0 15.6 0.5 CB E:GLN57 3.1 22.1 1.0 CG E:GLN57 3.7 27.4 1.0 NE2 C:GLN57 4.0 22.9 1.0 CB D:GLN57 4.0 29.3 1.0 O D:VAL53 4.1 16.3 1.0 N D:GLN57 4.1 27.9 1.0 CA D:GLN57 4.1 29.6 1.0 CG1 D:VAL53 4.1 14.8 1.0 CD1 D:ILE60 4.2 37.2 1.0 CG1 E:VAL53 4.3 14.0 1.0 CA E:GLN57 4.4 22.4 1.0 O E:VAL53 4.4 14.0 1.0 C D:ARG56 4.6 26.5 1.0 CB D:ARG56 4.6 25.4 0.5 CD E:GLN57 4.7 33.0 1.0 CD C:GLN57 4.8 22.1 1.0 CB D:ARG56 4.8 25.3 0.5 OE1 E:GLN57 4.9 35.7 1.0 CG D:ARG56 4.9 24.6 0.5 C D:VAL53 4.9 16.6 1.0 N E:GLN57 4.9 21.2 1.0 CG C:GLN57 5.0 20.0 1.0 CA D:VAL53 5.0 16.1 1.0

Gold binding site 2 out of 3 in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf


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 N-Terminal Domain of E.Coli Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ F:Au1066 b:67.3 occ:0.30 NE2 B:GLN57 2.7 11.4 1.0 O F:HOH2015 3.0 5.5 1.0 O F:GLN52 3.1 6.6 1.0 NH1 F:ARG56 3.1 12.9 1.0 C F:GLN52 3.2 6.9 1.0 CD F:ARG56 3.3 17.2 1.0 CD B:GLN57 3.5 10.3 1.0 N F:VAL53 3.5 6.8 1.0 CB F:GLN52 3.5 6.8 1.0 OE1 B:GLN57 3.6 12.6 1.0 CA F:VAL53 3.8 5.9 1.0 CB F:ARG56 3.9 15.2 1.0 CZ F:ARG56 3.9 18.2 1.0 CA F:GLN52 4.0 6.2 1.0 NE F:ARG56 4.0 20.3 1.0 CG F:ARG56 4.3 15.5 1.0 CG2 F:VAL53 4.4 4.6 1.0 NE2 F:GLN49 4.4 6.1 1.0 CB F:VAL53 4.7 6.2 1.0 CG B:GLN57 4.8 6.8 1.0 C F:VAL53 4.9 6.6 1.0 CG F:GLN52 4.9 6.2 1.0 OE1 F:GLN52 4.9 10.0 1.0

Gold binding site 3 out of 3 in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf


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 N-Terminal Domain of E.Coli Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ F:Au1067 b:57.3 occ:0.30 ND2 F:ASN32 2.5 12.9 1.0 ND2 B:ASN32 2.6 22.4 1.0 ND2 A:ASN32 3.0 10.9 1.0 CB F:ASN32 3.2 10.7 1.0 CG F:ASN32 3.3 12.7 1.0 CD1 B:LEU29 3.4 21.7 1.0 CD2 F:LEU29 3.6 13.5 1.0 CG B:ASN32 3.7 19.4 1.0 CB A:ASN32 3.8 12.7 1.0 CG A:ASN32 3.9 11.2 1.0 CB B:ASN32 4.0 15.6 1.0 CA F:LEU29 4.5 11.2 1.0 OD1 F:ASN32 4.5 17.4 1.0 CG F:LEU29 4.7 13.1 1.0 CA F:ASN32 4.7 10.2 1.0 O F:LEU29 4.8 10.8 1.0 CG B:LEU29 4.8 18.7 1.0 OD1 B:ASN32 4.8 22.5 1.0 CG A:LEU29 4.9 19.1 1.0 O F:GLN28 4.9 13.9 1.0 O B:LEU29 4.9 17.4 1.0

A.M.Krachler, A.Sharma, A.Cauldwell, G.Papadakos, C.Kleanthous. Tola Modulates the Oligomeric Status of Ybgf in the Bacterial Periplasm. J.Mol.Biol. V. 403 270 2010.
ISSN: ISSN 0022-2836
PubMed: 20816983
DOI: 10.1016/J.JMB.2010.08.050