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Zinc in PDB 2qdt: Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex

Enzymatic activity of Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex

All present enzymatic activity of Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex:
3.5.2.6;

Protein crystallography data

The structure of Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex, PDB code: 2qdt was solved by G.Garau, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.54 / 2.00
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.319, 105.319, 97.960, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 19.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex (pdb code 2qdt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex, PDB code: 2qdt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2qdt

Go back to Zinc Binding Sites List in 2qdt
Zinc binding site 1 out of 4 in the Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:35.2
occ:1.00
 NE2 A:HIS160 2.0 30.3 1.0
NE2 A:HIS84 2.1 31.7 1.0
ND1 A:HIS86 2.1 33.2 1.0
S A:I38501 2.3 34.8 1.0
CD2 A:HIS160 2.9 30.5 1.0
CD2 A:HIS84 3.0 32.1 1.0
CE1 A:HIS86 3.0 33.5 1.0
CE1 A:HIS84 3.1 30.1 1.0
CE1 A:HIS160 3.1 30.0 1.0
C1 A:I38501 3.2 39.2 1.0
CG A:HIS86 3.2 33.5 1.0
CB A:HIS86 3.6 31.9 1.0
ZN A:ZN402 3.7 35.6 1.0
CG A:HIS160 4.1 31.5 1.0
CG A:HIS84 4.1 31.1 1.0
ND1 A:HIS84 4.1 30.2 1.0
ND1 A:HIS160 4.1 31.2 1.0
CD2 A:HIS89 4.2 34.2 1.0
NE2 A:HIS86 4.2 32.0 1.0
NE2 A:HIS89 4.3 34.6 1.0
CD2 A:HIS86 4.3 33.1 1.0
OD1 A:ASP88 4.3 32.0 1.0
C2 A:I38501 4.6 42.0 1.0
O A:HOH606 4.8 45.6 1.0
OG A:SER185 4.9 32.4 1.0
CE2 A:PHE124 4.9 35.9 1.0

Zinc binding site 2 out of 4 in 2qdt

Go back to Zinc Binding Sites List in 2qdt
Zinc binding site 2 out of 4 in the Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:35.6
occ:1.00
 OD2 A:ASP88 2.0 32.7 1.0
NE2 A:HIS89 2.1 34.6 1.0
NE2 A:HIS225 2.1 32.6 1.0
S A:I38501 2.3 34.8 1.0
CG A:ASP88 2.7 33.0 1.0
OD1 A:ASP88 2.9 32.0 1.0
CE1 A:HIS89 2.9 34.4 1.0
CE1 A:HIS225 3.0 34.2 1.0
CD2 A:HIS89 3.0 34.2 1.0
CD2 A:HIS225 3.1 34.4 1.0
C1 A:I38501 3.2 39.2 1.0
C2 A:I38501 3.5 42.0 1.0
ZN A:ZN401 3.7 35.2 1.0
N4 A:I38501 3.9 51.0 1.0
ND1 A:HIS89 4.0 33.9 1.0
CG A:HIS89 4.1 33.4 1.0
ND1 A:HIS225 4.1 33.0 1.0
CB A:ASP88 4.2 32.5 1.0
C3 A:I38501 4.2 46.1 1.0
CG A:HIS225 4.2 34.6 1.0
O A:HOH606 4.2 45.6 1.0
NE2 A:HIS84 4.3 31.7 1.0
CE1 A:HIS84 4.5 30.1 1.0
O62 A:I38501 4.9 55.5 1.0
CZ3 A:TRP17 5.0 36.9 1.0
OG A:SER185 5.0 32.4 1.0

Zinc binding site 3 out of 4 in 2qdt

Go back to Zinc Binding Sites List in 2qdt
Zinc binding site 3 out of 4 in the Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:98.9
occ:0.25
 ZN A:ZN403 0.0 98.9 0.2
NE2 A:HIS29 1.3 48.3 0.5
CE1 A:HIS29 1.3 47.1 0.5
NE2 A:HIS29 1.8 47.8 0.5
CE1 A:HIS29 2.1 47.1 0.5
CD2 A:HIS29 2.5 46.7 0.5
ND1 A:HIS29 2.6 46.2 0.5
CD2 A:HIS29 3.1 45.4 0.5
ND1 A:HIS29 3.3 45.9 0.5
CG A:HIS29 3.5 44.5 0.5
CG A:HIS29 3.5 44.7 0.5
ZN A:ZN403 3.6 0.0 0.3
CB A:HIS29 4.9 42.9 1.0

Zinc binding site 4 out of 4 in 2qdt

Go back to Zinc Binding Sites List in 2qdt
Zinc binding site 4 out of 4 in the Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For the Broad-Spectrum Inhibition of Metallo-{Beta}- Lactamases: L1- IS38 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:0.0
occ:0.25
 ZN A:ZN403 0.0 0.0 0.3
ZN A:ZN403 3.6 98.9 0.2
CE1 A:HIS29 3.7 47.1 0.5
OD2 A:ASP28 4.0 45.3 1.0
NE2 A:HIS29 4.1 47.8 0.5
NE2 A:HIS29 4.2 48.3 0.5
OG1 A:THR172 4.3 49.6 1.0
CE1 A:HIS29 4.4 47.1 0.5
CB A:ASP28 4.6 42.1 1.0
CG A:ASP28 4.6 44.1 1.0
ND1 A:HIS29 4.8 45.9 0.5

Reference:

B.M.Lienard, G.Garau, L.Horsfall, A.I.Karsisiotis, C.Damblon, P.Lassaux, C.Papamicael, G.C.Roberts, M.Galleni, O.Dideberg, J.M.Frere, C.J.Schofield. Structural Basis For the Broad-Spectrum Inhibition of Metallo-Beta-Lactamases By Thiols. Org.Biomol.Chem. V. 6 2282 2008.
ISSN: ISSN 1477-0520
PubMed: 18563261
DOI: 10.1039/B802311E
Page generated: Wed Dec 16 03:50:08 2020

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