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

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

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

Protein crystallography data

The structure of Structure of Ndm-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B, PDB code: 6zyp 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) 42.62 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.974, 74.178, 77.956, 90, 90, 90
R / Rfree (%) 16.4 / 18.7

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6zyp

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Zinc binding site 1 out of 4 in the Structure of Ndm-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 Ndm-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:13.3
occ:1.00
H18 A:QT2303 1.9 16.7 1.0
OD2 A:ASP124 1.9 12.9 1.0
NE2 A:HIS250 2.1 10.9 1.0
SG A:CYS208 2.3 14.2 1.0
S01 A:QT2303 2.3 13.9 1.0
CG A:ASP124 3.0 15.9 1.0
CE1 A:HIS250 3.0 11.4 1.0
HE1 A:HIS250 3.1 13.7 1.0
CD2 A:HIS250 3.1 10.4 1.0
H1 A:QT2303 3.2 20.3 1.0
OD1 A:ASP124 3.3 12.3 1.0
C02 A:QT2303 3.3 16.9 1.0
HD2 A:HIS250 3.4 12.5 1.0
HB3 A:CYS208 3.4 17.3 1.0
CB A:CYS208 3.6 14.4 1.0
S09 A:QT2303 3.6 20.1 1.0
ZN A:ZN302 3.7 13.1 1.0
HB3 A:SER249 3.7 16.1 1.0
HE1 A:HIS120 3.9 15.3 1.0
HE3 A:LYS125 3.9 17.8 1.0
HG A:SER249 4.0 15.1 1.0
HB2 A:SER249 4.0 16.1 1.0
H9 A:QT2303 4.0 27.4 1.0
HB2 A:CYS208 4.1 17.3 1.0
H2 A:QT2303 4.1 20.3 1.0
ND1 A:HIS250 4.1 10.8 1.0
C03 A:QT2303 4.1 20.4 1.0
CB A:SER249 4.2 13.4 1.0
CG A:HIS250 4.2 12.4 1.0
CB A:ASP124 4.3 10.3 1.0
HG2 A:LYS125 4.4 20.0 1.0
HB2 A:ASP124 4.4 12.3 1.0
H14 A:QT2303 4.5 28.1 1.0
HB3 A:ASP124 4.5 12.3 1.0
CE1 A:HIS120 4.5 12.8 1.0
OG A:SER249 4.5 12.5 1.0
NE2 A:HIS120 4.5 11.7 1.0
H8 A:QT2303 4.5 27.4 1.0
HD2 A:LYS125 4.6 23.0 1.0
HA A:CYS208 4.6 14.2 1.0
NE2 A:HIS189 4.6 13.3 1.0
C11 A:QT2303 4.6 22.8 1.0
HE1 A:HIS189 4.6 19.0 1.0
CA A:CYS208 4.7 11.8 1.0
C10 A:QT2303 4.7 22.4 1.0
CE A:LYS125 4.8 14.8 1.0
CE1 A:HIS189 4.8 15.8 1.0
HD1 A:HIS250 4.9 13.0 1.0
C13 A:QT2303 4.9 23.4 1.0

Zinc binding site 2 out of 4 in 6zyp

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

b:13.1
occ:1.00
H18 A:QT2303 1.9 16.7 1.0
NE2 A:HIS120 2.0 11.7 1.0
ND1 A:HIS122 2.1 11.9 1.0
NE2 A:HIS189 2.1 13.3 1.0
S01 A:QT2303 2.3 13.9 1.0
H2 A:QT2303 3.0 20.3 1.0
HB2 A:HIS122 3.0 15.0 1.0
CE1 A:HIS122 3.0 14.5 1.0
CD2 A:HIS120 3.0 9.3 1.0
CE1 A:HIS189 3.0 15.8 1.0
CE1 A:HIS120 3.0 12.8 1.0
CG A:HIS122 3.1 11.4 1.0
CD2 A:HIS189 3.1 10.8 1.0
C02 A:QT2303 3.2 16.9 1.0
HE1 A:HIS122 3.2 17.4 1.0
HE1 A:HIS189 3.2 19.0 1.0
HD2 A:HIS120 3.2 11.2 1.0
HE1 A:HIS120 3.2 15.3 1.0
HD2 A:HIS189 3.3 12.9 1.0
H1 A:QT2303 3.4 20.3 1.0
CB A:HIS122 3.4 12.5 1.0
HB3 A:HIS122 3.6 15.0 1.0
ZN A:ZN301 3.7 13.3 1.0
HB2 A:CYS208 3.8 17.3 1.0
HB3 A:CYS208 3.9 17.3 1.0
SG A:CYS208 4.0 14.2 1.0
HG23 A:THR190 4.1 14.8 1.0
CB A:CYS208 4.1 14.4 1.0
ND1 A:HIS120 4.1 13.3 1.0
OD1 A:ASP124 4.1 12.3 1.0
NE2 A:HIS122 4.1 16.0 1.0
CG A:HIS120 4.1 10.2 1.0
ND1 A:HIS189 4.2 14.1 1.0
CD2 A:HIS122 4.2 14.6 1.0
CG A:HIS189 4.2 10.8 1.0
HG21 A:THR190 4.4 14.8 1.0
C03 A:QT2303 4.6 20.4 1.0
CG2 A:THR190 4.7 12.4 1.0
OD2 A:ASP124 4.8 12.9 1.0
HG2 A:LYS125 4.9 20.0 1.0
HG3 A:LYS125 4.9 20.0 1.0
CG A:ASP124 4.9 15.9 1.0
HD1 A:HIS120 4.9 15.9 1.0
HE2 A:HIS122 4.9 19.2 1.0
H14 A:QT2303 4.9 28.1 1.0
CA A:HIS122 4.9 9.0 1.0
HD1 A:HIS189 4.9 16.9 1.0
N17 A:QT2303 5.0 22.2 1.0

Zinc binding site 3 out of 4 in 6zyp

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Zinc binding site 3 out of 4 in the Structure of Ndm-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 Ndm-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:25.9
occ:1.00
NE2 B:HIS189 2.1 18.1 1.0
NE2 B:HIS120 2.1 17.5 1.0
ND1 B:HIS122 2.1 26.9 1.0
O B:HOH424 2.6 27.1 1.0
HB2 B:HIS122 2.9 17.0 1.0
CD2 B:HIS120 3.0 15.9 1.0
CD2 B:HIS189 3.0 21.2 1.0
CG B:HIS122 3.1 17.3 1.0
CE1 B:HIS122 3.1 20.3 1.0
CE1 B:HIS120 3.1 25.5 1.0
CE1 B:HIS189 3.1 15.2 1.0
HD2 B:HIS189 3.2 25.4 1.0
HD2 B:HIS120 3.2 19.1 1.0
HE1 B:HIS122 3.3 24.4 1.0
HE1 B:HIS120 3.3 30.6 1.0
HE1 B:HIS189 3.3 18.3 1.0
CB B:HIS122 3.4 14.1 1.0
HB3 B:HIS122 3.6 17.0 1.0
HG23 B:THR190 3.8 18.7 1.0
HG21 B:THR190 3.9 18.7 1.0
O B:HOH572 3.9 15.2 1.0
HB2 B:CYS208 4.1 16.1 1.0
OD1 B:ASP124 4.2 17.6 1.0
CG B:HIS120 4.2 12.0 1.0
ND1 B:HIS120 4.2 16.6 1.0
CG B:HIS189 4.2 19.2 1.0
NE2 B:HIS122 4.2 19.8 1.0
ND1 B:HIS189 4.2 22.1 1.0
CD2 B:HIS122 4.2 18.7 1.0
ZN B:ZN302 4.3 16.6 1.0
CG2 B:THR190 4.3 15.6 1.0
HB3 B:CYS208 4.3 16.1 1.0
SG B:CYS208 4.4 14.2 1.0
CB B:CYS208 4.5 13.4 1.0
HG22 B:THR190 4.7 18.7 1.0
CA B:HIS122 4.8 13.3 1.0
OD2 B:ASP124 5.0 19.4 1.0
HD1 B:HIS120 5.0 20.0 1.0
HE2 B:HIS122 5.0 23.7 1.0
CG B:ASP124 5.0 20.1 1.0
HD1 B:HIS189 5.0 26.5 1.0

Zinc binding site 4 out of 4 in 6zyp

Go back to Zinc Binding Sites List in 6zyp
Zinc binding site 4 out of 4 in the Structure of Ndm-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 Ndm-1 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:16.6
occ:1.00
NE2 B:HIS250 2.0 16.1 1.0
OD2 B:ASP124 2.0 19.4 1.0
SG B:CYS208 2.2 14.2 1.0
O B:HOH424 2.2 27.1 1.0
O B:HOH572 2.3 15.2 1.0
CE1 B:HIS250 3.0 17.0 1.0
CD2 B:HIS250 3.0 15.5 1.0
CG B:ASP124 3.1 20.1 1.0
HE1 B:HIS250 3.1 20.4 1.0
HD2 B:HIS250 3.2 18.6 1.0
O B:HOH498 3.2 39.9 1.0
HB3 B:CYS208 3.2 16.1 1.0
CB B:CYS208 3.4 13.4 1.0
OD1 B:ASP124 3.6 17.6 1.0
HB3 B:SER249 3.6 16.7 1.0
HB2 B:SER249 3.9 16.7 1.0
HE1 B:HIS120 3.9 30.6 1.0
HG B:SER249 3.9 17.2 1.0
HB2 B:CYS208 4.0 16.1 1.0
ND1 B:HIS250 4.1 17.0 1.0
CB B:SER249 4.1 13.9 1.0
HE3 B:LYS125 4.1 24.5 1.0
CG B:HIS250 4.1 16.1 1.0
ZN B:ZN301 4.3 25.9 1.0
HA B:CYS208 4.3 15.6 1.0
CB B:ASP124 4.4 13.2 1.0
HB2 B:ASP124 4.4 15.8 1.0
OG B:SER249 4.5 14.3 1.0
CA B:CYS208 4.5 13.0 1.0
HB3 B:ASP124 4.6 15.8 1.0
CE1 B:HIS120 4.6 25.5 1.0
HG2 B:LYS125 4.6 23.3 1.0
NE2 B:HIS189 4.6 18.1 1.0
HD2 B:LYS125 4.6 20.1 1.0
HE1 B:HIS189 4.8 18.3 1.0
O B:HOH554 4.8 27.3 1.0
NE2 B:HIS120 4.8 17.5 1.0
HD1 B:HIS250 4.9 20.4 1.0
CE1 B:HIS189 4.9 15.2 1.0
CE B:LYS125 5.0 20.4 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 16:39:05 2021

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