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Zinc in PDB 6zyr: Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B

Enzymatic activity of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B

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

Protein crystallography data

The structure of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B, PDB code: 6zyr 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) 66.96 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.555, 78.003, 261.107, 90, 90, 90
R / Rfree (%) 18.3 / 21.9

Other elements in 6zyr:

The structure of Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B (pdb code 6zyr). 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 L-Anti-1B, PDB code: 6zyr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6zyr

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Zinc binding site 1 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-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 L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:28.2
occ:1.00
 ND1 A:HIS79 2.1 27.9 1.0
NE2 A:HIS139 2.1 30.3 1.0
NE2 A:HIS77 2.1 22.9 1.0
S01 A:QT2303 2.4 32.0 1.0
CD2 A:HIS77 3.0 24.1 1.0
CD2 A:HIS139 3.0 27.9 1.0
CG A:HIS79 3.0 29.4 1.0
CE1 A:HIS79 3.1 27.6 1.0
CE1 A:HIS139 3.2 31.1 1.0
C02 A:QT2303 3.2 37.6 1.0
CE1 A:HIS77 3.3 24.1 1.0
CB A:HIS79 3.4 26.6 1.0
ZN A:ZN302 3.6 30.8 1.0
CB A:CYS158 3.9 27.9 1.0
SG A:CYS158 4.0 28.9 1.0
OD1 A:ASP81 4.0 28.5 1.0
NE2 A:HIS79 4.2 32.8 1.0
CG A:HIS77 4.2 23.1 1.0
CD2 A:HIS79 4.2 28.6 1.0
CG A:HIS139 4.2 33.0 1.0
ND1 A:HIS139 4.2 29.2 1.0
ND1 A:HIS77 4.3 21.5 1.0
O A:HOH446 4.4 61.3 1.0
CG2 A:THR140 4.5 29.3 1.0
C03 A:QT2303 4.6 49.5 1.0
OD2 A:ASP81 4.7 28.8 1.0
CG A:ASP81 4.8 27.6 1.0
CA A:HIS79 4.8 26.5 1.0
N17 A:QT2303 4.9 60.2 1.0

Zinc binding site 2 out of 8 in 6zyr

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Zinc binding site 2 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-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 L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:30.8
occ:1.00
 OD2 A:ASP81 1.9 28.8 1.0
NE2 A:HIS197 2.1 35.8 1.0
S01 A:QT2303 2.2 32.0 1.0
SG A:CYS158 2.3 28.9 1.0
CG A:ASP81 2.9 27.6 1.0
CE1 A:HIS197 3.0 34.9 1.0
CD2 A:HIS197 3.1 36.5 1.0
C02 A:QT2303 3.2 37.6 1.0
OD1 A:ASP81 3.3 28.5 1.0
CB A:CYS158 3.4 27.9 1.0
ZN A:ZN301 3.6 28.2 1.0
S09 A:QT2303 3.8 52.5 1.0
ND1 A:HIS197 4.1 35.4 1.0
C03 A:QT2303 4.2 49.5 1.0
CG A:HIS197 4.2 36.4 1.0
NE2 A:HIS77 4.2 22.9 1.0
CE1 A:HIS77 4.3 24.1 1.0
CB A:ASP81 4.3 25.9 1.0
CB A:SER196 4.3 32.9 1.0
CE A:LYS33 4.5 22.1 1.0
CA A:CYS158 4.5 30.8 1.0
CD A:LYS33 4.6 24.7 1.0
NE2 A:HIS139 4.6 30.3 1.0
C11 A:QT2303 4.6 62.0 1.0
OG A:SER196 4.7 29.3 1.0
C10 A:QT2303 4.8 61.3 1.0
O A:HOH493 4.8 40.3 1.0
C13 A:QT2303 5.0 67.9 1.0

Zinc binding site 3 out of 8 in 6zyr

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Zinc binding site 3 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-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 L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:28.6
occ:1.00
 H18 B:QT2303 1.7 43.3 1.0
ND1 B:HIS79 2.1 28.3 1.0
NE2 B:HIS139 2.1 27.8 1.0
NE2 B:HIS77 2.1 24.3 1.0
S01 B:QT2303 2.5 36.0 1.0
H2 B:QT2303 2.7 48.5 1.0
CD2 B:HIS77 2.9 23.8 1.0
CD2 B:HIS139 3.0 26.9 1.0
CG B:HIS79 3.0 25.8 1.0
C02 B:QT2303 3.0 40.3 1.0
CE1 B:HIS79 3.1 30.8 1.0
CE1 B:HIS139 3.1 31.5 1.0
CE1 B:HIS77 3.2 22.4 1.0
H1 B:QT2303 3.3 48.5 1.0
CB B:HIS79 3.3 24.1 1.0
ZN B:ZN302 3.6 29.5 1.0
CB B:CYS158 4.0 29.0 1.0
OD1 B:ASP81 4.0 26.7 1.0
SG B:CYS158 4.1 28.6 1.0
CG B:HIS77 4.1 29.1 1.0
NE2 B:HIS79 4.1 29.3 1.0
CD2 B:HIS79 4.1 27.2 1.0
CG B:HIS139 4.2 29.0 1.0
ND1 B:HIS139 4.2 29.7 1.0
ND1 B:HIS77 4.2 23.0 1.0
C03 B:QT2303 4.5 55.2 1.0
CG2 B:THR140 4.5 27.8 1.0
CA B:HIS79 4.7 23.0 1.0
N17 B:QT2303 4.8 68.0 1.0
OD2 B:ASP81 4.8 28.5 1.0
CG B:ASP81 4.8 28.1 1.0
O B:HOH526 4.9 62.7 1.0
O B:HOH402 4.9 57.5 1.0

Zinc binding site 4 out of 8 in 6zyr

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Zinc binding site 4 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-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 L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:29.5
occ:1.00
 NE2 B:HIS197 2.1 32.2 1.0
OD2 B:ASP81 2.1 28.5 1.0
S01 B:QT2303 2.1 36.0 1.0
SG B:CYS158 2.4 28.6 1.0
CE1 B:HIS197 2.9 30.8 1.0
CG B:ASP81 3.0 28.1 1.0
H18 B:QT2303 3.0 43.3 1.0
H1 B:QT2303 3.1 48.5 1.0
CD2 B:HIS197 3.1 31.4 1.0
OD1 B:ASP81 3.2 26.7 1.0
C02 B:QT2303 3.2 40.3 1.0
CB B:CYS158 3.4 29.0 1.0
ZN B:ZN301 3.6 28.6 1.0
S09 B:QT2303 3.9 53.1 1.0
H2 B:QT2303 3.9 48.5 1.0
ND1 B:HIS197 4.0 32.4 1.0
CE1 B:HIS77 4.1 22.4 1.0
C03 B:QT2303 4.1 55.2 1.0
NE2 B:HIS77 4.1 24.3 1.0
CG B:HIS197 4.2 33.3 1.0
CB B:SER196 4.3 28.6 1.0
CB B:ASP81 4.4 26.1 1.0
CD B:LYS33 4.4 22.7 1.0
CE B:LYS33 4.5 22.2 1.0
CA B:CYS158 4.5 28.1 1.0
NE2 B:HIS139 4.6 27.8 1.0
OG B:SER196 4.6 29.1 1.0
O08 B:QT2303 4.8 54.7 1.0
H8 B:QT2303 4.9 79.2 1.0
C04 B:QT2303 4.9 54.5 1.0

Zinc binding site 5 out of 8 in 6zyr

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Zinc binding site 5 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-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 L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:20.3
occ:1.00
 H18 C:QT2303 1.8 28.5 1.0
NE2 C:HIS139 2.1 18.1 1.0
NE2 C:HIS77 2.1 18.5 1.0
ND1 C:HIS79 2.1 18.6 1.0
S01 C:QT2303 2.4 23.7 1.0
CD2 C:HIS77 2.9 17.4 1.0
H2 C:QT2303 3.0 35.4 1.0
CD2 C:HIS139 3.1 18.9 1.0
CE1 C:HIS79 3.1 20.3 1.0
CE1 C:HIS139 3.1 19.8 1.0
CG C:HIS79 3.1 21.7 1.0
C02 C:QT2303 3.2 29.4 1.0
CE1 C:HIS77 3.2 17.5 1.0
H1 C:QT2303 3.4 35.4 1.0
CB C:HIS79 3.4 19.4 1.0
ZN C:ZN302 3.6 24.9 1.0
OD1 C:ASP81 4.0 24.0 1.0
CB C:CYS158 4.0 22.6 1.0
SG C:CYS158 4.0 23.2 1.0
CG C:HIS77 4.1 20.1 1.0
NE2 C:HIS79 4.2 19.5 1.0
ND1 C:HIS139 4.2 19.5 1.0
CG C:HIS139 4.2 18.0 1.0
CD2 C:HIS79 4.2 20.7 1.0
ND1 C:HIS77 4.2 20.9 1.0
O C:HOH538 4.3 50.5 1.0
CG2 C:THR140 4.5 22.2 1.0
OD2 C:ASP81 4.7 22.8 1.0
C03 C:QT2303 4.7 37.8 1.0
CG C:ASP81 4.8 26.8 1.0
CA C:HIS79 4.8 19.3 1.0
O C:HOH414 4.8 35.8 1.0

Zinc binding site 6 out of 8 in 6zyr

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Zinc binding site 6 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-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 L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:24.9
occ:1.00
 H18 C:QT2303 1.8 28.5 1.0
OD2 C:ASP81 2.0 22.8 1.0
NE2 C:HIS197 2.1 21.4 1.0
S01 C:QT2303 2.3 23.7 1.0
SG C:CYS158 2.4 23.2 1.0
CE1 C:HIS197 3.0 22.2 1.0
CG C:ASP81 3.0 26.8 1.0
CD2 C:HIS197 3.2 21.2 1.0
H1 C:QT2303 3.2 35.4 1.0
OD1 C:ASP81 3.3 24.0 1.0
C02 C:QT2303 3.4 29.4 1.0
CB C:CYS158 3.5 22.6 1.0
ZN C:ZN301 3.6 20.3 1.0
S09 C:QT2303 3.7 41.8 1.0
NE2 C:HIS77 4.1 18.5 1.0
ND1 C:HIS197 4.1 22.5 1.0
O C:HOH414 4.1 35.8 1.0
H2 C:QT2303 4.1 35.4 1.0
CE1 C:HIS77 4.1 17.5 1.0
C03 C:QT2303 4.2 37.8 1.0
CG C:HIS197 4.2 22.8 1.0
H14 C:QT2303 4.3 58.2 1.0
H9 C:QT2303 4.3 56.0 1.0
CB C:SER196 4.3 21.8 1.0
CB C:ASP81 4.3 23.4 1.0
CE C:LYS33 4.5 22.2 1.0
CD C:LYS33 4.5 20.1 1.0
OG C:SER196 4.6 19.6 1.0
NE2 C:HIS139 4.6 18.1 1.0
CA C:CYS158 4.6 25.2 1.0
C10 C:QT2303 4.8 44.0 1.0
C11 C:QT2303 4.8 46.5 1.0
C13 C:QT2303 4.9 48.4 1.0
H8 C:QT2303 4.9 56.0 1.0
N17 C:QT2303 4.9 43.5 1.0

Zinc binding site 7 out of 8 in 6zyr

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Zinc binding site 7 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-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 L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:41.5
occ:1.00
 OD2 D:ASP81 2.0 42.8 1.0
NE2 D:HIS197 2.1 42.2 1.0
S01 D:QT2303 2.3 40.3 1.0
SG D:CYS158 2.3 35.9 1.0
CG D:ASP81 3.0 41.8 1.0
CE1 D:HIS197 3.0 41.9 1.0
CD2 D:HIS197 3.1 41.0 1.0
H1 D:QT2303 3.3 56.1 1.0
CB D:CYS158 3.3 37.1 1.0
H18 D:QT2303 3.3 48.5 1.0
OD1 D:ASP81 3.4 40.4 1.0
C02 D:QT2303 3.4 46.7 1.0
ZN D:ZN302 3.6 38.6 1.0
S09 D:QT2303 3.9 61.4 1.0
CE1 D:HIS77 4.1 41.8 1.0
NE2 D:HIS77 4.1 37.3 1.0
H2 D:QT2303 4.1 56.1 1.0
ND1 D:HIS197 4.1 43.4 1.0
CG D:HIS197 4.2 47.5 1.0
H9 D:QT2303 4.3 79.6 1.0
CB D:ASP81 4.3 42.8 1.0
H14 D:QT2303 4.3 83.5 1.0
C03 D:QT2303 4.3 58.0 1.0
CB D:SER196 4.3 35.8 1.0
CD D:LYS33 4.5 34.7 1.0
CA D:CYS158 4.5 36.0 1.0
CE D:LYS33 4.5 33.5 1.0
NE2 D:HIS139 4.6 37.9 1.0
OG D:SER196 4.8 36.9 1.0
C11 D:QT2303 4.9 66.3 1.0
C13 D:QT2303 5.0 69.5 1.0
C10 D:QT2303 5.0 67.7 1.0
H8 D:QT2303 5.0 79.6 1.0

Zinc binding site 8 out of 8 in 6zyr

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Zinc binding site 8 out of 8 in the Structure of Imp-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-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 L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:38.6
occ:1.00
 ND1 D:HIS79 2.1 41.5 1.0
NE2 D:HIS139 2.1 37.9 1.0
NE2 D:HIS77 2.1 37.3 1.0
S01 D:QT2303 2.3 40.3 1.0
H18 D:QT2303 2.4 48.5 1.0
CD2 D:HIS77 2.9 36.5 1.0
CE1 D:HIS79 3.0 42.5 1.0
CG D:HIS79 3.0 42.1 1.0
CD2 D:HIS139 3.0 34.6 1.0
CE1 D:HIS139 3.1 37.9 1.0
H2 D:QT2303 3.1 56.1 1.0
CE1 D:HIS77 3.2 41.8 1.0
C02 D:QT2303 3.3 46.7 1.0
CB D:HIS79 3.4 39.5 1.0
ZN D:ZN301 3.6 41.5 1.0
H1 D:QT2303 3.7 56.1 1.0
CB D:CYS158 3.9 37.1 1.0
SG D:CYS158 4.0 35.9 1.0
OD1 D:ASP81 4.0 40.4 1.0
NE2 D:HIS79 4.1 42.0 1.0
CD2 D:HIS79 4.1 41.5 1.0
CG D:HIS77 4.1 37.7 1.0
ND1 D:HIS139 4.2 36.8 1.0
CG D:HIS139 4.2 35.7 1.0
ND1 D:HIS77 4.3 37.3 1.0
CG2 D:THR140 4.6 39.5 1.0
OD2 D:ASP81 4.6 42.8 1.0
C03 D:QT2303 4.6 58.0 1.0
O D:HOH470 4.7 60.7 1.0
H14 D:QT2303 4.7 83.5 1.0
CG D:ASP81 4.8 41.8 1.0
N17 D:QT2303 4.8 65.1 1.0
CA D:HIS79 4.8 38.1 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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