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

Protein crystallography data

The structure of Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B, PDB code: 6zyo 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) 51.76 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.53, 79.74, 68.04, 90, 130.5, 90
R / Rfree (%) 12.4 / 16.3

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 6zyo

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Zinc binding site 1 out of 6 in the Structure of Vim-2 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 Vim-2 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:14.8
occ:1.00
ND1 A:HIS116 2.0 14.2 1.0
NE2 A:HIS179 2.1 13.7 1.0
NE2 A:HIS114 2.1 13.2 1.0
S01 A:QST306 2.3 18.6 1.0
H18 A:QST306 2.6 22.4 1.0
H1 A:QST306 2.9 23.1 1.0
CE1 A:HIS116 2.9 15.0 1.0
HB2 A:HIS116 3.0 16.2 1.0
CE1 A:HIS114 3.0 13.3 1.0
CE1 A:HIS179 3.0 13.5 1.0
CG A:HIS116 3.1 15.3 1.0
CD2 A:HIS114 3.1 14.4 1.0
CD2 A:HIS179 3.1 13.0 1.0
HE1 A:HIS116 3.1 18.1 1.0
C02 A:QST306 3.1 19.2 1.0
HE1 A:HIS114 3.2 16.0 1.0
HE1 A:HIS179 3.2 16.2 1.0
HD2 A:HIS114 3.3 17.3 1.0
HD2 A:HIS179 3.3 15.6 1.0
CB A:HIS116 3.5 13.5 1.0
H2 A:QST306 3.6 23.1 1.0
HB2 A:CYS198 3.6 16.4 1.0
HB3 A:HIS116 3.7 16.2 1.0
ZN A:ZN302 3.8 18.0 1.0
HB3 A:CYS198 3.9 16.4 1.0
NE2 A:HIS116 4.0 17.1 1.0
ND1 A:HIS114 4.1 12.0 1.0
CB A:CYS198 4.1 13.7 1.0
OD1 A:ASP118 4.1 17.4 1.0
ND1 A:HIS179 4.1 13.7 1.0
CD2 A:HIS116 4.1 16.6 1.0
CG A:HIS114 4.2 12.6 1.0
CG A:HIS179 4.2 11.8 1.0
H171 A:QST306 4.2 36.1 1.0
SG A:CYS198 4.4 15.5 1.0
C03 A:QST306 4.5 26.9 1.0
H A:HIS116 4.5 15.3 1.0
OD2 A:ASP118 4.7 16.0 1.0
HE2 A:HIS116 4.8 20.5 1.0
N17 A:QST306 4.8 30.1 1.0
CG A:ASP118 4.9 15.1 1.0
CA A:HIS116 4.9 13.4 1.0
HG2 A:ARG119 4.9 17.2 1.0
HD1 A:HIS114 4.9 14.4 1.0
HB3 A:SER180 4.9 15.4 1.0
HD1 A:HIS179 4.9 16.5 1.0
HD2 A:HIS116 5.0 20.0 1.0

Zinc binding site 2 out of 6 in 6zyo

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Zinc binding site 2 out of 6 in the Structure of Vim-2 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 Vim-2 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:18.0
occ:1.00
OD2 A:ASP118 2.0 16.0 1.0
NE2 A:HIS240 2.1 13.6 1.0
S01 A:QST306 2.2 18.6 1.0
SG A:CYS198 2.4 15.5 1.0
CE1 A:HIS240 3.0 14.2 1.0
CG A:ASP118 3.1 15.1 1.0
CD2 A:HIS240 3.1 15.0 1.0
HE1 A:HIS240 3.2 17.0 1.0
HH21 A:ARG119 3.2 26.2 1.0
H18 A:QST306 3.3 22.4 1.0
H2 A:QST306 3.3 23.1 1.0
HD2 A:HIS240 3.3 18.0 1.0
HE A:ARG119 3.4 19.8 1.0
HB3 A:CYS198 3.4 16.4 1.0
C02 A:QST306 3.4 19.2 1.0
OD1 A:ASP118 3.5 17.4 1.0
CB A:CYS198 3.5 13.7 1.0
HE1 A:HIS114 3.7 16.0 1.0
ZN A:ZN301 3.8 14.8 1.0
S09 A:QST306 3.8 25.3 1.0
NH2 A:ARG119 3.9 21.9 1.0
HB2 A:CYS198 3.9 16.4 1.0
NE A:ARG119 4.0 16.5 1.0
H11 A:QST306 4.1 36.7 1.0
H171 A:QST306 4.1 36.1 1.0
C03 A:QST306 4.1 26.9 1.0
ND1 A:HIS240 4.2 14.4 1.0
H12 A:QST306 4.2 36.7 1.0
CG A:HIS240 4.2 14.0 1.0
H1 A:QST306 4.3 23.1 1.0
CB A:ASP118 4.3 15.9 1.0
CE1 A:HIS114 4.4 13.3 1.0
CZ A:ARG119 4.4 19.7 1.0
HB2 A:ASP118 4.4 19.0 1.0
HH22 A:ARG119 4.4 26.2 1.0
NE2 A:HIS114 4.5 13.2 1.0
HB3 A:ASP118 4.6 19.0 1.0
C12 A:QST306 4.6 30.6 1.0
HA3 A:GLY239 4.6 17.1 1.0
N17 A:QST306 4.7 30.1 1.0
HA A:CYS198 4.7 15.6 1.0
O A:HOH510 4.7 17.4 1.0
HG2 A:ARG119 4.7 17.2 1.0
CA A:CYS198 4.8 13.0 1.0
NE2 A:HIS179 4.8 13.7 1.0
HE1 A:HIS179 4.8 16.2 1.0
C10 A:QST306 4.9 28.5 1.0
HD1 A:HIS240 4.9 17.2 1.0
CE1 A:HIS179 5.0 13.5 1.0
HB2 A:HIS116 5.0 16.2 1.0

Zinc binding site 3 out of 6 in 6zyo

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Zinc binding site 3 out of 6 in the Structure of Vim-2 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 Vim-2 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:18.4
occ:1.00
HO2 A:FMT304 1.4 21.0 1.0
O1 A:FMT305 2.0 19.3 1.0
O2 A:FMT304 2.0 17.5 1.0
NE2 A:HIS153 2.1 17.4 1.0
HO2 A:FMT305 2.6 24.4 1.0
C A:FMT304 2.7 19.9 1.0
O1 A:FMT304 2.8 21.0 1.0
CE1 A:HIS153 2.8 18.7 1.0
HE1 A:HIS153 2.9 22.5 1.0
C A:FMT305 2.9 21.2 1.0
O2 A:FMT305 3.1 20.3 1.0
CD2 A:HIS153 3.3 16.2 1.0
HD2 A:HIS153 3.6 19.5 1.0
H A:FMT304 3.8 23.8 1.0
HB1 A:ALA132 3.8 20.0 1.0
HB2 A:ALA132 3.9 20.0 1.0
H A:FMT305 3.9 25.4 1.0
ND1 A:HIS153 4.1 17.9 1.0
CB A:ALA132 4.3 16.6 1.0
CG A:HIS153 4.3 16.3 1.0
HA A:ALA132 4.3 19.3 1.0
HG22 A:THR152 4.5 19.8 1.0
HG21 A:THR152 4.6 19.8 1.0
HD1 A:HIS153 4.8 21.5 1.0
CA A:ALA132 4.9 16.1 1.0
O A:HOH446 4.9 27.2 1.0

Zinc binding site 4 out of 6 in 6zyo

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Zinc binding site 4 out of 6 in the Structure of Vim-2 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 Vim-2 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:18.1
occ:1.00
H18 B:QST306 1.9 22.8 1.0
OD2 B:ASP118 2.0 16.2 1.0
NE2 B:HIS240 2.1 13.3 1.0
S01 B:QST306 2.3 19.0 1.0
SG B:CYS198 2.4 15.5 1.0
CE1 B:HIS240 3.0 14.2 1.0
CG B:ASP118 3.0 15.9 1.0
CD2 B:HIS240 3.1 13.2 1.0
HH21 B:ARG119 3.1 25.5 1.0
HE1 B:HIS240 3.2 17.0 1.0
H2 B:QST306 3.3 26.9 1.0
HD2 B:HIS240 3.3 15.8 1.0
HE B:ARG119 3.3 21.3 1.0
HB3 B:CYS198 3.4 15.4 1.0
C02 B:QST306 3.4 22.5 1.0
OD1 B:ASP118 3.4 16.9 1.0
CB B:CYS198 3.5 12.8 1.0
HE1 B:HIS114 3.7 15.6 1.0
ZN B:ZN302 3.8 15.1 1.0
NH2 B:ARG119 3.8 21.2 1.0
S09 B:QST306 3.8 25.8 1.0
HB2 B:CYS198 3.9 15.4 1.0
NE B:ARG119 4.0 17.8 1.0
H12 B:QST306 4.1 37.0 1.0
H171 B:QST306 4.1 36.4 1.0
ND1 B:HIS240 4.2 14.7 1.0
H13 B:QST306 4.2 37.0 1.0
C03 B:QST306 4.2 27.3 1.0
CG B:HIS240 4.2 13.7 1.0
H1 B:QST306 4.3 26.9 1.0
CB B:ASP118 4.3 15.5 1.0
CZ B:ARG119 4.3 17.7 1.0
CE1 B:HIS114 4.4 13.0 1.0
HH22 B:ARG119 4.4 25.5 1.0
HB2 B:ASP118 4.4 18.6 1.0
NE2 B:HIS114 4.5 14.4 1.0
C12 B:QST306 4.5 30.8 1.0
HB3 B:ASP118 4.6 18.6 1.0
HA3 B:GLY239 4.6 17.3 1.0
HA B:CYS198 4.7 14.8 1.0
O B:HOH524 4.7 21.3 1.0
N17 B:QST306 4.7 30.3 1.0
HG2 B:ARG119 4.7 17.3 1.0
NE2 B:HIS179 4.7 13.8 1.0
CA B:CYS198 4.8 12.3 1.0
HE1 B:HIS179 4.8 17.2 1.0
C10 B:QST306 4.9 29.9 1.0
O B:HOH461 4.9 28.1 1.0
HD1 B:HIS240 4.9 17.7 1.0
CE1 B:HIS179 5.0 14.3 1.0

Zinc binding site 5 out of 6 in 6zyo

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Zinc binding site 5 out of 6 in the Structure of Vim-2 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 Vim-2 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:15.1
occ:1.00
ND1 B:HIS116 2.0 14.4 1.0
NE2 B:HIS179 2.1 13.8 1.0
NE2 B:HIS114 2.1 14.4 1.0
S01 B:QST306 2.3 19.0 1.0
CE1 B:HIS116 2.9 16.9 1.0
HB2 B:HIS116 3.0 18.8 1.0
H1 B:QST306 3.0 26.9 1.0
CG B:HIS116 3.0 15.9 1.0
HE1 B:HIS116 3.0 20.3 1.0
CD2 B:HIS179 3.0 13.6 1.0
CE1 B:HIS179 3.0 14.3 1.0
CE1 B:HIS114 3.1 13.0 1.0
CD2 B:HIS114 3.1 13.9 1.0
HD2 B:HIS179 3.2 16.3 1.0
HE1 B:HIS179 3.2 17.2 1.0
HE1 B:HIS114 3.2 15.6 1.0
HD2 B:HIS114 3.2 16.7 1.0
C02 B:QST306 3.3 22.5 1.0
CB B:HIS116 3.4 15.6 1.0
H18 B:QST306 3.6 22.8 1.0
HB2 B:CYS198 3.6 15.4 1.0
HB3 B:HIS116 3.7 18.8 1.0
H2 B:QST306 3.7 26.9 1.0
ZN B:ZN301 3.8 18.1 1.0
HB3 B:CYS198 3.9 15.4 1.0
NE2 B:HIS116 4.0 18.4 1.0
CB B:CYS198 4.1 12.8 1.0
OD1 B:ASP118 4.1 16.9 1.0
CD2 B:HIS116 4.1 17.3 1.0
ND1 B:HIS114 4.1 14.0 1.0
ND1 B:HIS179 4.2 14.2 1.0
CG B:HIS179 4.2 13.7 1.0
CG B:HIS114 4.2 13.2 1.0
H171 B:QST306 4.2 36.4 1.0
SG B:CYS198 4.4 15.5 1.0
H B:HIS116 4.6 17.2 1.0
C03 B:QST306 4.6 27.3 1.0
HE2 B:HIS116 4.8 22.1 1.0
OD2 B:ASP118 4.8 16.2 1.0
CA B:HIS116 4.9 14.2 1.0
CG B:ASP118 4.9 15.9 1.0
N17 B:QST306 4.9 30.3 1.0
HG2 B:ARG119 4.9 17.3 1.0
HD1 B:HIS114 4.9 16.8 1.0
HB3 B:SER180 4.9 17.5 1.0
HD1 B:HIS179 4.9 17.1 1.0
HD22 B:ASN210 5.0 65.4 1.0
HD2 B:HIS116 5.0 20.8 1.0

Zinc binding site 6 out of 6 in 6zyo

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Zinc binding site 6 out of 6 in the Structure of Vim-2 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 Vim-2 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:19.7
occ:1.00
O1 B:FMT305 1.9 23.3 1.0
NE2 B:HIS153 2.0 16.2 1.0
O1 B:FMT304 2.1 22.6 1.0
HO2 B:FMT305 2.4 31.5 1.0
C B:FMT305 2.7 26.3 1.0
CE1 B:HIS153 2.8 19.2 1.0
HO2 B:FMT304 2.8 27.7 1.0
HE1 B:HIS153 2.8 23.1 1.0
O2 B:FMT305 2.9 26.2 1.0
C B:FMT304 2.9 24.0 1.0
CD2 B:HIS153 3.2 17.3 1.0
O2 B:FMT304 3.2 23.1 1.0
HD2 B:HIS153 3.5 20.8 1.0
H B:FMT305 3.8 31.5 1.0
HB1 B:ALA132 3.8 17.9 1.0
H B:FMT304 3.9 28.8 1.0
HB2 B:ALA132 4.0 17.9 1.0
ND1 B:HIS153 4.0 18.1 1.0
HG22 B:THR152 4.2 20.5 1.0
HG21 B:THR152 4.2 20.5 1.0
CG B:HIS153 4.2 16.9 1.0
CB B:ALA132 4.3 14.9 1.0
HA B:ALA132 4.4 17.1 1.0
CG2 B:THR152 4.7 17.1 1.0
HD1 B:HIS153 4.7 21.7 1.0
CA B:ALA132 5.0 14.3 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: Mon Jan 25 16:39:04 2021

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