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Zinc in PDB 6zys: Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B

Enzymatic activity of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B

All present enzymatic activity of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B:
3.5.2.6;

Protein crystallography data

The structure of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B, PDB code: 6zys was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.15 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.782, 77.969, 261.906, 90, 90, 90
R / Rfree (%) 17.4 / 20.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B (pdb code 6zys). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B, PDB code: 6zys:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6zys

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Zinc binding site 1 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:29.9
occ:1.00
 ND1 A:HIS79 2.0 26.8 1.0
NE2 A:HIS139 2.1 26.8 1.0
NE2 A:HIS77 2.1 25.2 1.0
S01 A:QST303 2.4 30.1 0.9
CE1 A:HIS79 3.0 28.9 1.0
CD2 A:HIS77 3.0 26.5 1.0
CD2 A:HIS139 3.0 27.0 1.0
CG A:HIS79 3.0 27.0 1.0
CE1 A:HIS139 3.1 30.1 1.0
CE1 A:HIS77 3.2 26.6 1.0
C02 A:QST303 3.3 36.5 0.9
CB A:HIS79 3.4 25.0 1.0
ZN A:ZN302 3.6 33.1 1.0
CB A:CYS158 3.9 32.0 1.0
OD1 A:ASP81 4.0 26.7 1.0
SG A:CYS158 4.0 30.7 1.0
NE2 A:HIS79 4.1 29.4 1.0
CD2 A:HIS79 4.1 28.3 1.0
CG A:HIS77 4.2 23.2 1.0
CG A:HIS139 4.2 29.5 1.0
ND1 A:HIS139 4.2 29.4 1.0
ND1 A:HIS77 4.2 26.4 1.0
CG2 A:THR140 4.5 27.2 1.0
C03 A:QST303 4.6 46.5 0.9
N17 A:QST303 4.8 54.0 0.9
OD2 A:ASP81 4.8 25.5 1.0
CG A:ASP81 4.8 26.9 1.0
CA A:HIS79 4.8 25.4 1.0

Zinc binding site 2 out of 8 in 6zys

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Zinc binding site 2 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:33.1
occ:1.00
 OD2 A:ASP81 2.0 25.5 1.0
S01 A:QST303 2.1 30.1 0.9
NE2 A:HIS197 2.1 31.5 1.0
SG A:CYS158 2.3 30.7 1.0
CG A:ASP81 2.9 26.9 1.0
CE1 A:HIS197 3.1 31.4 1.0
CD2 A:HIS197 3.1 30.2 1.0
OD1 A:ASP81 3.2 26.7 1.0
C02 A:QST303 3.4 36.5 0.9
CB A:CYS158 3.4 32.0 1.0
ZN A:ZN301 3.6 29.9 1.0
S09 A:QST303 4.1 45.4 0.9
ND1 A:HIS197 4.2 32.9 1.0
CG A:HIS197 4.2 31.9 1.0
CE1 A:HIS77 4.3 26.6 1.0
C12 A:QST303 4.3 57.1 0.9
NE2 A:HIS77 4.3 25.2 1.0
CB A:ASP81 4.3 25.3 1.0
C03 A:QST303 4.3 46.5 0.9
CB A:SER196 4.4 28.4 1.0
CE A:LYS33 4.5 23.2 1.0
CD A:LYS33 4.5 24.6 1.0
NE2 A:HIS139 4.5 26.8 1.0
CA A:CYS158 4.6 32.7 1.0
OG A:SER196 4.6 24.2 1.0
C10 A:QST303 4.9 55.5 0.9

Zinc binding site 3 out of 8 in 6zys

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Zinc binding site 3 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:27.2
occ:1.00
 ND1 B:HIS79 2.0 25.8 1.0
NE2 B:HIS139 2.1 27.7 1.0
NE2 B:HIS77 2.1 22.5 1.0
S01 B:QST303 2.3 31.6 1.0
CE1 B:HIS79 2.9 30.4 1.0
CD2 B:HIS77 3.0 24.3 1.0
CG B:HIS79 3.0 25.3 1.0
CE1 B:HIS139 3.1 29.6 1.0
CD2 B:HIS139 3.1 25.6 1.0
CE1 B:HIS77 3.2 26.2 1.0
C02 B:QST303 3.4 38.4 1.0
CB B:HIS79 3.4 24.8 1.0
ZN B:ZN302 3.6 31.3 1.0
CB B:CYS158 4.0 28.6 1.0
NE2 B:HIS79 4.0 29.0 1.0
SG B:CYS158 4.1 28.8 1.0
OD1 B:ASP81 4.1 27.6 1.0
CD2 B:HIS79 4.1 29.2 1.0
CG B:HIS77 4.2 24.2 1.0
ND1 B:HIS139 4.2 27.4 1.0
CG B:HIS139 4.2 29.4 1.0
ND1 B:HIS77 4.2 24.0 1.0
CG2 B:THR140 4.5 29.1 1.0
C03 B:QST303 4.6 45.2 1.0
N17 B:QST303 4.6 49.2 1.0
OD2 B:ASP81 4.7 31.1 1.0
CG B:ASP81 4.8 27.7 1.0
CA B:HIS79 4.8 24.7 1.0
O B:HOH409 4.8 50.7 1.0

Zinc binding site 4 out of 8 in 6zys

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Zinc binding site 4 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:31.3
occ:1.00
 OD2 B:ASP81 2.0 31.1 1.0
NE2 B:HIS197 2.1 31.2 1.0
S01 B:QST303 2.2 31.6 1.0
SG B:CYS158 2.3 28.8 1.0
CG B:ASP81 3.0 27.7 1.0
CE1 B:HIS197 3.0 30.5 1.0
CD2 B:HIS197 3.1 29.6 1.0
OD1 B:ASP81 3.3 27.6 1.0
C02 B:QST303 3.3 38.4 1.0
CB B:CYS158 3.4 28.6 1.0
ZN B:ZN301 3.6 27.2 1.0
S09 B:QST303 4.0 41.9 1.0
ND1 B:HIS197 4.1 32.8 1.0
CE1 B:HIS77 4.2 26.2 1.0
CG B:HIS197 4.2 34.3 1.0
NE2 B:HIS77 4.2 22.5 1.0
C03 B:QST303 4.3 45.2 1.0
C12 B:QST303 4.3 47.3 1.0
CB B:ASP81 4.3 24.9 1.0
CB B:SER196 4.4 28.4 1.0
CD B:LYS33 4.5 24.3 1.0
CE B:LYS33 4.5 22.6 1.0
CA B:CYS158 4.5 29.1 1.0
NE2 B:HIS139 4.6 27.7 1.0
OG B:SER196 4.7 25.8 1.0
C10 B:QST303 4.9 46.7 1.0
N17 B:QST303 4.9 49.2 1.0

Zinc binding site 5 out of 8 in 6zys

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Zinc binding site 5 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:22.0
occ:1.00
 ND1 C:HIS79 2.1 20.1 1.0
NE2 C:HIS139 2.1 17.5 1.0
NE2 C:HIS77 2.1 20.3 1.0
S01 C:QST303 2.3 25.3 1.0
CE1 C:HIS79 3.0 20.5 1.0
CD2 C:HIS77 3.0 20.8 1.0
CE1 C:HIS139 3.1 19.4 1.0
CD2 C:HIS139 3.1 19.0 1.0
CG C:HIS79 3.1 19.5 1.0
C02 C:QST303 3.1 28.9 1.0
CE1 C:HIS77 3.2 20.7 1.0
CB C:HIS79 3.5 19.3 1.0
ZN C:ZN302 3.5 25.7 1.0
SG C:CYS158 3.9 25.2 1.0
OD1 C:ASP81 4.0 24.1 1.0
CB C:CYS158 4.0 23.2 1.0
NE2 C:HIS79 4.1 21.5 1.0
ND1 C:HIS139 4.2 19.9 1.0
CD2 C:HIS79 4.2 20.7 1.0
CG C:HIS77 4.2 20.5 1.0
CG C:HIS139 4.2 18.9 1.0
ND1 C:HIS77 4.2 20.7 1.0
O C:HOH521 4.6 50.8 1.0
OD2 C:ASP81 4.6 21.8 1.0
C03 C:QST303 4.6 25.8 1.0
CG2 C:THR140 4.7 18.3 1.0
CG C:ASP81 4.7 22.5 1.0
O C:HOH425 4.8 30.8 1.0
O C:HOH482 4.8 59.4 1.0
CA C:HIS79 4.9 21.1 1.0

Zinc binding site 6 out of 8 in 6zys

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Zinc binding site 6 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:25.7
occ:1.00
 OD2 C:ASP81 2.0 21.8 1.0
NE2 C:HIS197 2.1 20.9 1.0
S01 C:QST303 2.3 25.3 1.0
SG C:CYS158 2.3 25.2 1.0
CG C:ASP81 3.0 22.5 1.0
CE1 C:HIS197 3.0 22.3 1.0
CD2 C:HIS197 3.2 19.6 1.0
OD1 C:ASP81 3.3 24.1 1.0
C02 C:QST303 3.5 28.9 1.0
ZN C:ZN301 3.5 22.0 1.0
CB C:CYS158 3.5 23.2 1.0
S09 C:QST303 3.7 32.8 1.0
O C:HOH425 4.0 30.8 1.0
ND1 C:HIS197 4.2 22.6 1.0
C03 C:QST303 4.2 25.8 1.0
CE1 C:HIS77 4.2 20.7 1.0
NE2 C:HIS77 4.3 20.3 1.0
CG C:HIS197 4.3 21.0 1.0
CB C:ASP81 4.3 22.4 1.0
CB C:SER196 4.4 20.2 1.0
C12 C:QST303 4.4 28.6 1.0
CD C:LYS33 4.5 18.9 1.0
CE C:LYS33 4.5 18.5 1.0
NE2 C:HIS139 4.6 17.5 1.0
OG C:SER196 4.7 21.0 1.0
CA C:CYS158 4.7 23.0 1.0
C10 C:QST303 4.8 34.5 1.0
CE1 C:HIS139 4.9 19.4 1.0
N17 C:QST303 5.0 33.0 1.0

Zinc binding site 7 out of 8 in 6zys

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Zinc binding site 7 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:43.1
occ:1.00
 OD2 D:ASP81 1.9 40.0 1.0
S01 D:QST303 2.1 38.2 0.9
NE2 D:HIS197 2.2 36.5 1.0
SG D:CYS158 2.3 36.1 1.0
CG D:ASP81 2.9 40.1 1.0
CE1 D:HIS197 3.1 38.0 1.0
CD2 D:HIS197 3.2 35.3 1.0
OD1 D:ASP81 3.3 42.3 1.0
CB D:CYS158 3.4 40.2 1.0
C02 D:QST303 3.4 44.0 0.9
ZN D:ZN302 3.6 40.7 1.0
S09 D:QST303 4.1 62.3 0.9
ND1 D:HIS197 4.2 37.8 1.0
CE1 D:HIS77 4.2 34.7 1.0
CB D:ASP81 4.3 41.4 1.0
CB D:SER196 4.3 33.6 1.0
CG D:HIS197 4.3 36.0 1.0
NE2 D:HIS77 4.3 35.5 1.0
C03 D:QST303 4.4 57.6 0.9
CE D:LYS33 4.5 35.8 1.0
CD D:LYS33 4.5 37.3 1.0
CA D:CYS158 4.5 37.2 1.0
OG D:SER196 4.6 34.0 1.0
NE2 D:HIS139 4.7 33.8 1.0
C12 D:QST303 4.7 64.7 0.9

Zinc binding site 8 out of 8 in 6zys

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Zinc binding site 8 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:40.7
occ:1.00
 ND1 D:HIS79 2.0 39.5 1.0
NE2 D:HIS139 2.1 33.8 1.0
NE2 D:HIS77 2.2 35.5 1.0
S01 D:QST303 2.4 38.2 0.9
CE1 D:HIS79 2.9 41.8 1.0
CG D:HIS79 3.0 40.0 1.0
CE1 D:HIS139 3.0 34.5 1.0
CD2 D:HIS77 3.0 35.1 1.0
CD2 D:HIS139 3.1 36.1 1.0
CE1 D:HIS77 3.2 34.7 1.0
C02 D:QST303 3.3 44.0 0.9
CB D:HIS79 3.4 38.8 1.0
ZN D:ZN301 3.6 43.1 1.0
CB D:CYS158 3.9 40.2 1.0
OD1 D:ASP81 4.0 42.3 1.0
SG D:CYS158 4.0 36.1 1.0
NE2 D:HIS79 4.0 43.7 1.0
CD2 D:HIS79 4.0 40.8 1.0
ND1 D:HIS139 4.1 37.4 1.0
CG D:HIS139 4.2 34.9 1.0
CG D:HIS77 4.2 36.9 1.0
ND1 D:HIS77 4.3 33.8 1.0
C03 D:QST303 4.5 57.6 0.9
OD2 D:ASP81 4.6 40.0 1.0
CG2 D:THR140 4.6 37.7 1.0
CG D:ASP81 4.7 40.1 1.0
N17 D:QST303 4.8 68.0 0.9
CA D:HIS79 4.8 38.9 1.0
O D:HOH439 5.0 63.5 1.0

Reference:

M.Rossi, V.Martinez, P.Hinchliffe, M.F.Mojica, V.Castillo, D.M.Moreno, R.Smith, B.Spellberg, G.L.Drusano, C.Banchio, R.A.Bonomo, J.Spencer, A.J.Vila, G.Mahler. 2-Mercaptomethyl-Thiazolidines Use Conserved Aromatic-S Interactions to Achieve Broad-Range Inhibition of Metallo-Beta-Lactamases Chem Sci 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC05172A
Page generated: Tue Oct 29 16:12:16 2024

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