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Gold in PDB 3szc: Crystal Structure of Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide

Protein crystallography data

The structure of Crystal Structure of Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide, PDB code: 3szc was solved by M.M.Cherney, Y.Zhang, M.N.G.James, J.H.Weiner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.95 / 2.20
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 149.540, 149.540, 81.740, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 22.4

Gold Binding Sites:

The binding sites of Gold atom in the Crystal Structure of Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide (pdb code 3szc). 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 Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide, PDB code: 3szc:
Jump to Gold binding site number: 1; 2; 3;

Gold binding site 1 out of 3 in 3szc

Go back to Gold Binding Sites List in 3szc
Gold binding site 1 out of 3 in the Crystal Structure of Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide


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 Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au503

b:55.4
occ:0.65
SG A:CYS128 2.3 60.3 1.0
CB A:CYS128 3.1 39.1 1.0
CA A:CYS128 3.5 42.4 1.0
C8M A:FAD500 3.7 45.3 1.0
CD1 A:ILE261 3.8 46.5 1.0
CG2 A:ILE261 4.0 31.8 1.0
N A:CYS128 4.1 41.8 1.0
CZ A:PHE264 4.1 34.3 1.0
CD A:PRO262 4.3 26.2 1.0
CE1 A:PHE264 4.3 31.1 1.0
CD1 A:ILE127 4.5 35.2 1.0
C7M A:FAD500 4.5 41.8 1.0
C A:ILE127 4.7 41.5 1.0
C8 A:FAD500 4.7 43.6 1.0
CB A:ILE261 4.8 36.0 1.0
CA A:ILE261 4.8 33.8 1.0
CG1 A:ILE261 4.8 41.7 1.0
C A:CYS128 4.9 43.5 1.0
OG A:SER126 4.9 54.8 1.0
CG A:PRO262 5.0 29.6 1.0

Gold binding site 2 out of 3 in 3szc

Go back to Gold Binding Sites List in 3szc
Gold binding site 2 out of 3 in the Crystal Structure of Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide


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 Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au504

b:85.7
occ:0.24
SG A:CYS160 2.4 71.9 0.5
S A:H2S509 2.5 33.5 0.5
N A:LYS320 3.5 36.8 1.0
O A:LYS320 3.6 38.6 1.0
AU A:AU505 3.7 59.1 0.2
CB A:CYS160 3.9 52.3 1.0
CD1 A:ILE302 3.9 35.7 1.0
CE2 A:PHE264 3.9 32.4 1.0
CA A:PRO319 4.0 37.4 1.0
SG A:CYS160 4.0 46.2 0.6
C1' A:FAD500 4.1 38.2 1.0
CB A:PRO319 4.1 37.1 1.0
OG A:SER159 4.2 39.8 1.0
O A:SER159 4.2 51.8 1.0
C A:PRO319 4.3 38.5 1.0
C A:LYS320 4.3 39.3 1.0
CG1 A:ILE302 4.4 35.9 1.0
CA A:LYS320 4.4 36.4 1.0
CA A:CYS160 4.5 46.8 1.0
CD2 A:PHE264 4.5 34.0 1.0
C A:SER159 4.5 44.6 1.0
N A:CYS160 4.6 45.1 1.0
CB A:LYS320 4.8 38.2 1.0
C2' A:FAD500 4.8 34.2 1.0
O3' A:FAD500 4.8 38.9 1.0
CB A:SER159 4.9 42.2 1.0

Gold binding site 3 out of 3 in 3szc

Go back to Gold Binding Sites List in 3szc
Gold binding site 3 out of 3 in the Crystal Structure of Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide


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 Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans in Complex with Gold (I) Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au505

b:59.1
occ:0.18
SG A:CYS160 2.2 46.2 0.6
SG A:CYS160 2.4 71.9 0.5
S A:H2S508 2.7 94.9 1.0
S A:H2S506 3.1 74.3 1.0
CB A:CYS160 3.4 52.3 1.0
AU A:AU504 3.7 85.7 0.2
CA A:CYS160 3.7 46.8 1.0
C1' A:FAD500 3.8 38.2 1.0
N10 A:FAD500 3.9 34.9 1.0
CB A:PRO319 4.0 37.1 1.0
C9A A:FAD500 4.1 38.0 1.0
CG2 A:THR321 4.3 41.4 1.0
CD A:PRO163 4.4 39.5 1.0
C10 A:FAD500 4.4 33.5 1.0
C9 A:FAD500 4.4 38.2 1.0
C A:CYS160 4.5 47.7 1.0
C5X A:FAD500 4.6 40.6 1.0
O A:SER159 4.7 51.8 1.0
C4X A:FAD500 4.7 38.7 1.0
N5 A:FAD500 4.7 36.3 1.0
CG A:PRO163 4.7 38.0 1.0
SG A:CYS356 4.8 92.8 1.0
N A:PHE161 4.8 39.2 1.0
N1 A:FAD500 4.9 33.0 1.0
N A:CYS160 4.9 45.1 1.0
CG A:PRO319 5.0 41.8 1.0

Reference:

M.M.Cherney, Y.Zhang, M.N.James, J.H.Weiner. Structure-Activity Characterization of Sulfide:Quinone Oxidoreductase Variants. J.Struct.Biol. V. 178 319 2012.
ISSN: ISSN 1047-8477
PubMed: 22542586
DOI: 10.1016/J.JSB.2012.04.007
Page generated: Sat Dec 12 01:53:52 2020

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