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Gold in PDB 1e3u: Mad Structure of OXA10 Class D Beta-Lactamase

Enzymatic activity of Mad Structure of OXA10 Class D Beta-Lactamase

All present enzymatic activity of Mad Structure of OXA10 Class D Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of Mad Structure of OXA10 Class D Beta-Lactamase, PDB code: 1e3u was solved by L.Maveyraud, D.Golemi, L.P.Kotra, S.Tranier, S.Vakulenko, S.Mobashery, J.P.Samama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.530, 82.940, 101.420, 90.00, 95.03, 90.00
R / Rfree (%) 18.1 / 21

Gold Binding Sites:

The binding sites of Gold atom in the Mad Structure of OXA10 Class D Beta-Lactamase (pdb code 1e3u). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 8 binding sites of Gold where determined in the Mad Structure of OXA10 Class D Beta-Lactamase, PDB code: 1e3u:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Gold binding site 1 out of 8 in 1e3u

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Gold binding site 1 out of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au301

b:18.6
occ:1.00
 AU A:AUC301 0.0 18.6 1.0
C1 A:AUC301 1.7 19.0 1.0
C2 A:AUC301 1.7 19.1 1.0
O A:HOH401 2.3 47.8 1.0
N2 A:AUC301 2.9 18.4 1.0
N1 A:AUC301 2.9 18.5 1.0
NE1 A:TRP154 3.1 16.8 1.0
CD1 A:TRP154 3.3 16.5 1.0
CE2 A:TRP154 3.6 15.8 1.0
NZ A:LYS70 3.7 11.9 1.0
O A:ALA66 3.8 12.2 1.0
CG A:TRP154 3.8 15.6 1.0
CA A:SER67 3.9 12.2 1.0
CD2 A:TRP154 4.0 15.1 1.0
CG A:LYS70 4.0 11.2 1.0
C A:ALA66 4.1 12.3 1.0
N A:SER67 4.2 12.3 1.0
CZ2 A:TRP154 4.3 16.4 1.0
CE A:LYS70 4.3 11.4 1.0
CB A:SER67 4.6 14.3 1.0
N A:LYS70 4.6 11.4 1.0
C A:SER67 4.7 11.9 1.0
CB A:TRP154 4.8 16.1 1.0
OG A:SER67 4.8 15.8 1.0
CB A:PHE69 4.8 12.5 1.0
O A:SER67 4.8 12.0 1.0
CD A:LYS70 4.8 11.6 1.0
CB A:PHE120 5.0 13.0 1.0
CG2 A:VAL117 5.0 14.5 1.0
CE3 A:TRP154 5.0 15.2 1.0

Gold binding site 2 out of 8 in 1e3u

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Gold binding site 2 out of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au301

b:18.8
occ:1.00
 AU B:AUC301 0.0 18.8 1.0
C1 B:AUC301 1.7 18.8 1.0
C2 B:AUC301 1.7 19.2 1.0
N2 B:AUC301 2.9 18.9 1.0
N1 B:AUC301 2.9 18.3 1.0
NE1 B:TRP154 3.1 18.5 1.0
CD1 B:TRP154 3.2 18.7 1.0
O B:ALA66 3.6 10.7 1.0
CE2 B:TRP154 3.6 16.8 1.0
NZ B:LYS70 3.7 13.9 1.0
CG B:TRP154 3.8 16.6 1.0
CA B:SER67 3.9 11.2 1.0
CG B:LYS70 4.0 10.9 1.0
CD2 B:TRP154 4.0 15.1 1.0
C B:ALA66 4.0 11.3 1.0
CE B:LYS70 4.2 12.7 1.0
N B:SER67 4.2 11.1 1.0
CZ2 B:TRP154 4.3 17.4 1.0
CB B:PHE69 4.6 12.5 1.0
N B:LYS70 4.7 11.7 1.0
C B:SER67 4.7 11.2 1.0
CB B:SER67 4.7 11.7 1.0
CB B:TRP154 4.7 17.1 1.0
CD B:LYS70 4.8 11.9 1.0
O B:SER67 4.8 11.5 1.0
OG B:SER67 4.8 13.9 1.0
CB B:PHE120 4.9 13.6 1.0

Gold binding site 3 out of 8 in 1e3u

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Gold binding site 3 out of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Au301

b:17.1
occ:1.00
 AU C:AUC301 0.0 17.1 1.0
C1 C:AUC301 1.7 17.4 1.0
C2 C:AUC301 1.7 16.7 1.0
N2 C:AUC301 2.9 16.3 1.0
N1 C:AUC301 2.9 17.2 1.0
AU C:AUC302 3.2 15.0 1.0
C1 C:AUC302 3.2 15.4 1.0
CA C:VAL117 3.6 15.0 1.0
CG2 C:VAL117 3.7 15.9 1.0
N1 C:AUC302 4.0 15.3 1.0
CB C:PHE120 4.0 15.1 1.0
C2 C:AUC302 4.0 14.6 1.0
CB C:VAL117 4.1 15.2 1.0
O C:VAL117 4.3 15.0 1.0
N C:VAL117 4.3 15.0 1.0
CG1 C:VAL117 4.4 15.0 1.0
C C:VAL117 4.5 15.2 1.0
O C:ALA116 4.6 15.1 1.0
C C:ALA116 4.6 15.3 1.0
NE1 C:TRP154 4.6 13.4 1.0
N2 C:AUC302 4.7 15.0 1.0
CG C:PHE120 4.7 15.9 1.0
CD1 C:PHE120 4.7 16.1 1.0

Gold binding site 4 out of 8 in 1e3u

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Gold binding site 4 out of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Au302

b:15.0
occ:1.00
 AU C:AUC302 0.0 15.0 1.0
C2 C:AUC302 1.7 14.6 1.0
C1 C:AUC302 1.7 15.4 1.0
N1 C:AUC302 2.9 15.3 1.0
N2 C:AUC302 2.9 15.0 1.0
NE1 C:TRP154 3.0 13.4 1.0
AU C:AUC301 3.2 17.1 1.0
CD1 C:TRP154 3.4 12.9 1.0
C2 C:AUC301 3.6 16.7 1.0
O C:ALA66 3.7 11.2 1.0
CA C:SER67 3.8 11.2 1.0
C1 C:AUC301 3.9 17.4 1.0
CG C:LYS70 3.9 14.4 1.0
CE2 C:TRP154 3.9 12.5 1.0
N2 C:AUC301 3.9 16.3 1.0
C C:ALA66 4.1 11.2 1.0
N C:SER67 4.2 11.6 1.0
CG C:TRP154 4.4 12.3 1.0
CB C:SER67 4.4 13.1 1.0
CD C:LYS70 4.5 17.5 1.0
CZ2 C:TRP154 4.6 12.7 1.0
N C:LYS70 4.6 9.9 1.0
C C:SER67 4.6 11.2 1.0
CD2 C:TRP154 4.7 11.9 1.0
CB C:PHE69 4.7 10.5 1.0
O C:SER67 4.7 11.3 1.0
N1 C:AUC301 4.8 17.2 1.0
CB C:PHE120 4.9 15.1 1.0

Gold binding site 5 out of 8 in 1e3u

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Gold binding site 5 out of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Au303

b:28.9
occ:1.00
 AU C:AUC303 0.0 28.9 1.0
C1 C:AUC303 1.7 28.5 1.0
C2 C:AUC303 1.7 28.8 1.0
N2 C:AUC303 2.9 28.9 1.0
N1 C:AUC303 2.9 28.4 1.0
O C:GLU129 3.7 16.1 1.0
CB C:GLN133 3.7 14.3 1.0
OE1 C:GLN133 4.0 17.7 1.0
CG C:GLN133 4.0 14.4 1.0
C C:GLU129 4.2 16.2 1.0
CB C:GLU129 4.3 17.7 1.0
CD1 C:ILE146 4.3 14.6 1.0
CD C:GLN133 4.5 16.6 1.0
N C:VAL130 4.6 16.0 1.0
CA C:VAL130 4.6 15.6 1.0
CG1 C:ILE146 4.9 13.0 1.0
CA C:GLU129 4.9 16.5 1.0

Gold binding site 6 out of 8 in 1e3u

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Gold binding site 6 out of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Au301

b:14.6
occ:1.00
 AU D:AUC301 0.0 14.6 1.0
C1 D:AUC301 1.7 14.1 1.0
C2 D:AUC301 1.7 14.5 1.0
N2 D:AUC301 2.9 15.1 1.0
N1 D:AUC301 2.9 14.4 1.0
NE1 D:TRP154 3.1 12.1 1.0
AU D:AUC302 3.2 16.2 1.0
CD1 D:TRP154 3.5 11.2 1.0
C1 D:AUC302 3.6 15.4 1.0
O D:ALA66 3.7 10.5 1.0
CA D:SER67 3.7 10.8 1.0
CG D:LYS70 3.8 16.0 1.0
C2 D:AUC302 3.9 16.1 1.0
N1 D:AUC302 3.9 15.3 1.0
CE2 D:TRP154 4.0 11.2 1.0
C D:ALA66 4.1 10.0 1.0
N D:SER67 4.2 10.4 1.0
CD D:LYS70 4.4 17.9 1.0
CB D:SER67 4.4 13.2 1.0
CG D:TRP154 4.4 10.5 1.0
N D:LYS70 4.6 10.7 1.0
C D:SER67 4.6 10.9 1.0
CZ2 D:TRP154 4.6 12.2 1.0
CD2 D:TRP154 4.7 11.0 1.0
O D:SER67 4.7 11.6 1.0
CB D:PHE69 4.7 11.7 1.0
CB D:PHE120 4.8 15.1 1.0
N2 D:AUC302 4.8 16.1 1.0

Gold binding site 7 out of 8 in 1e3u

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Gold binding site 7 out of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Au302

b:16.2
occ:1.00
 AU D:AUC302 0.0 16.2 1.0
C2 D:AUC302 1.7 16.1 1.0
C1 D:AUC302 1.7 15.4 1.0
N1 D:AUC302 2.9 15.3 1.0
N2 D:AUC302 2.9 16.1 1.0
C2 D:AUC301 3.2 14.5 1.0
AU D:AUC301 3.2 14.6 1.0
CA D:VAL117 3.6 17.1 1.0
CG2 D:VAL117 3.7 16.1 1.0
O D:HOH542 3.9 26.6 1.0
N2 D:AUC301 3.9 15.1 1.0
C1 D:AUC301 4.0 14.1 1.0
CB D:PHE120 4.0 15.1 1.0
CB D:VAL117 4.1 16.2 1.0
N D:VAL117 4.3 16.3 1.0
O D:VAL117 4.3 17.5 1.0
CG1 D:VAL117 4.5 16.1 1.0
O D:HOH613 4.5 32.0 1.0
C D:VAL117 4.5 17.9 1.0
O D:ALA116 4.6 15.3 1.0
C D:ALA116 4.6 15.9 1.0
CG D:PHE120 4.7 15.2 1.0
CD1 D:PHE120 4.7 15.3 1.0
NE1 D:TRP154 4.7 12.1 1.0
N1 D:AUC301 4.7 14.4 1.0

Gold binding site 8 out of 8 in 1e3u

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Gold binding site 8 out of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 8 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Au303

b:34.6
occ:1.00
 AU D:AUC303 0.0 34.6 1.0
C1 D:AUC303 1.7 34.0 1.0
C2 D:AUC303 1.7 34.8 1.0
N1 D:AUC303 2.9 34.2 1.0
N2 D:AUC303 2.9 34.8 1.0
O D:HOH531 3.5 45.3 1.0
O D:GLU129 3.8 17.1 1.0
CB D:GLN133 3.8 15.9 1.0
NE2 D:GLN133 4.0 16.6 1.0
C D:GLU129 4.1 17.5 1.0
CG D:GLN133 4.1 17.2 1.0
CB D:GLU129 4.1 24.2 1.0
CD1 D:ILE146 4.4 13.9 1.0
N D:VAL130 4.5 16.8 1.0
CA D:VAL130 4.6 16.7 1.0
CD D:GLN133 4.6 18.7 1.0
CA D:GLU129 4.7 18.9 1.0
CG1 D:ILE146 4.9 13.5 1.0
CG D:GLU129 5.0 31.8 1.0

Reference:

L.Maveyraud, D.Golemi, L.P.Kotra, S.Tranier, S.Vakulenko, S.Mobashery, J.P.Samama. Insights Into Class D Beta-Lactamases Are Revealed By the Crystal Structure of the OXA10 Enzyme From Pseudomonas Aeruginosa Structure V. 8 1289 2000.
ISSN: ISSN 0969-2126
PubMed: 11188693
DOI: 10.1016/S0969-2126(00)00534-7
Page generated: Sat Dec 12 01:52:59 2020

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