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

Protein crystallography data

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

Other elements in 2wz7:

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

Sodium (Na) 1 atom

Gold Binding Sites:

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 2wz7

Go back to Gold Binding Sites List in 2wz7
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 2wz7

Go back to Gold Binding Sites List in 2wz7
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 2wz7

Go back to Gold Binding Sites List in 2wz7
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

Reference:

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
Page generated: Sat Dec 12 01:53:20 2020

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