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Zinc in PDB 5a5z: Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria

Enzymatic activity of Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria

All present enzymatic activity of Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria:
3.5.2.6;

Protein crystallography data

The structure of Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria, PDB code: 5a5z was solved by F.M.Klingler, T.A.Wichelhaus, D.Frank, J.Cuesta-Bernal, J.El-Delik, H.F.Mueller, H.Sjuts, S.Goettig, A.Koenigs, D.Pogoryelov, E.Proschak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.66 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.047, 108.047, 92.571, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria (pdb code 5a5z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria, PDB code: 5a5z:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5a5z

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Zinc binding site 1 out of 4 in the Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:46.3
occ:1.00
 ND1 A:HIS122 2.1 42.9 1.0
NE2 A:HIS120 2.1 40.2 1.0
NE2 A:HIS189 2.5 49.5 1.0
CD2 A:HIS189 3.0 61.2 1.0
CE1 A:HIS120 3.0 40.9 1.0
CG A:HIS122 3.1 41.9 1.0
CD2 A:HIS120 3.1 38.4 1.0
CE1 A:HIS122 3.1 40.9 1.0
ZN A:ZN303 3.1 0.6 1.0
CB A:HIS122 3.3 40.6 1.0
CE1 A:HIS189 3.7 54.6 1.0
SG A:CYS208 3.9 51.4 1.0
OD1 A:ASP124 4.1 47.6 1.0
ND1 A:HIS120 4.1 38.6 1.0
NE2 A:HIS122 4.2 41.9 1.0
CG A:HIS120 4.2 36.6 1.0
CD2 A:HIS122 4.2 39.9 1.0
C04 A:WJZ304 4.2 63.7 0.5
S01 A:WJZ304 4.2 0.0 0.5
CG A:HIS189 4.3 51.8 1.0
CB A:CYS208 4.3 44.1 1.0
OD2 A:ASP124 4.3 52.1 1.0
C05 A:WJZ304 4.5 56.8 0.5
CG2 A:THR190 4.6 40.4 1.0
ND1 A:HIS189 4.6 50.5 1.0
CG A:ASP124 4.6 47.0 1.0
O02 A:WJZ304 4.8 52.6 0.5
CA A:HIS122 4.8 38.5 1.0
O01 A:WJZ304 4.9 54.1 0.5

Zinc binding site 2 out of 4 in 5a5z

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Zinc binding site 2 out of 4 in the Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:0.6
occ:1.00
 S01 A:WJZ304 2.4 0.0 0.5
OD2 A:ASP124 2.4 52.1 1.0
N01 A:WJZ304 2.8 65.9 0.5
C03 A:WJZ304 2.9 70.9 0.5
NE2 A:HIS250 2.9 58.2 1.0
C04 A:WJZ304 3.0 63.7 0.5
SG A:CYS208 3.1 51.4 1.0
C02 A:WJZ304 3.1 74.1 0.5
ZN A:ZN302 3.1 46.3 1.0
CG A:ASP124 3.3 47.0 1.0
CE1 A:HIS250 3.5 55.2 1.0
O03 A:WJZ304 3.5 69.1 0.5
OD1 A:ASP124 3.6 47.6 1.0
O02 A:WJZ304 3.7 52.6 0.5
C05 A:WJZ304 3.7 56.8 0.5
CD2 A:HIS250 4.1 56.5 1.0
NE2 A:HIS189 4.1 49.5 1.0
CB A:CYS208 4.3 44.1 1.0
CB A:ASP124 4.4 41.4 1.0
C01 A:WJZ304 4.5 71.9 0.5
NE2 A:HIS120 4.5 40.2 1.0
CE1 A:HIS189 4.6 54.6 1.0
ND1 A:HIS122 4.6 42.9 1.0
ND1 A:HIS250 4.7 54.9 1.0
CE1 A:HIS120 4.8 40.9 1.0
O01 A:WJZ304 4.8 54.1 0.5
CB A:HIS122 5.0 40.6 1.0

Zinc binding site 3 out of 4 in 5a5z

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Zinc binding site 3 out of 4 in the Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:36.4
occ:1.00
 ND1 C:HIS122 2.1 49.1 1.0
NE2 C:HIS189 2.1 44.0 1.0
NE2 C:HIS120 2.2 42.6 1.0
ZN C:ZN303 2.9 82.8 1.0
CD2 C:HIS189 3.0 43.2 1.0
CD2 C:HIS120 3.1 39.8 1.0
CE1 C:HIS122 3.1 41.9 1.0
CG C:HIS122 3.1 42.9 1.0
CE1 C:HIS120 3.2 44.3 1.0
CE1 C:HIS189 3.2 44.5 1.0
CB C:HIS122 3.4 42.2 1.0
SG C:CYS208 3.6 51.9 1.0
CB C:CYS208 4.0 45.6 1.0
OD1 C:ASP124 4.0 45.2 1.0
S01 C:WJZ304 4.1 0.1 0.5
CG C:HIS189 4.2 42.8 1.0
NE2 C:HIS122 4.2 37.9 1.0
CG C:HIS120 4.2 39.3 1.0
ND1 C:HIS189 4.2 42.8 1.0
OD2 C:ASP124 4.2 52.1 1.0
ND1 C:HIS120 4.3 41.9 1.0
CD2 C:HIS122 4.3 41.5 1.0
CG2 C:THR190 4.5 41.1 1.0
CG C:ASP124 4.6 47.7 1.0
O01 C:WJZ304 4.6 53.3 0.5
CA C:HIS122 4.9 40.6 1.0

Zinc binding site 4 out of 4 in 5a5z

Go back to Zinc Binding Sites List in 5a5z
Zinc binding site 4 out of 4 in the Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta- Lactamases: Strategy to Combat Multidrug-Resistant Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:82.8
occ:1.00
 OD2 C:ASP124 2.5 52.1 1.0
S01 C:WJZ304 2.6 0.1 0.5
SG C:CYS208 2.9 51.9 1.0
ZN C:ZN302 2.9 36.4 1.0
NE2 C:HIS250 3.0 56.6 1.0
N01 C:WJZ304 3.1 63.4 0.5
O01 C:WJZ304 3.1 53.3 0.5
CG C:ASP124 3.3 47.7 1.0
OD1 C:ASP124 3.6 45.2 1.0
CE1 C:HIS250 3.7 51.1 1.0
C02 C:WJZ304 3.8 69.0 0.5
C03 C:WJZ304 3.8 64.4 0.5
C05 C:WJZ304 3.9 55.3 0.5
NE2 C:HIS189 3.9 44.0 1.0
C04 C:WJZ304 4.0 57.9 0.5
CB C:CYS208 4.1 45.6 1.0
CE1 C:HIS189 4.1 44.5 1.0
CD2 C:HIS250 4.2 52.4 1.0
NE2 C:HIS120 4.4 42.6 1.0
ND1 C:HIS122 4.5 49.1 1.0
CB C:ASP124 4.6 40.5 1.0
O03 C:WJZ304 4.9 63.0 0.5
CE1 C:HIS120 4.9 44.3 1.0
ND1 C:HIS250 4.9 51.3 1.0
O02 C:WJZ304 5.0 54.0 0.5
CD2 C:HIS189 5.0 43.2 1.0
CB C:HIS122 5.0 42.2 1.0

Reference:

F.M.Klingler, T.A.Wichelhaus, D.Frank, J.Cuesta-Bernal, J.El-Delik, H.F.Muller, H.Sjuts, S.Gottig, A.Koenigs, K.M.Pos, D.Pogoryelov, E.Proschak. Approved Drugs Containing Thiols As Inhibitors of Metallo-Beta-Lactamases: Strategy to Combat Multidrug-Resistant Bacteria. J. Med. Chem. V. 58 3626 2015.
ISSN: ISSN 1520-4804
PubMed: 25815530
DOI: 10.1021/JM501844D
Page generated: Sun Oct 27 12:39:32 2024

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