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Zinc in PDB 4u4l: Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor

Enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor, PDB code: 4u4l was solved by M.Kosmopoulou, P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.88 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.570, 69.023, 69.646, 87.39, 88.21, 76.75
R / Rfree (%) 15.4 / 18.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor (pdb code 4u4l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor, PDB code: 4u4l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4u4l

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Zinc binding site 1 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:19.5
occ:1.00
HS01 A:3C7303 1.3 32.5 1.0
ND1 A:HIS122 2.0 19.5 1.0
NE2 A:HIS120 2.1 15.3 1.0
NE2 A:HIS189 2.1 18.0 1.0
S01 A:3C7303 2.4 27.1 1.0
CE1 A:HIS122 2.9 20.8 1.0
CE1 A:HIS120 3.0 17.3 1.0
CD2 A:HIS189 3.0 17.4 1.0
CG A:HIS122 3.1 17.7 1.0
CD2 A:HIS120 3.1 15.5 1.0
CE1 A:HIS189 3.2 20.7 1.0
H021 A:3C7303 3.2 46.2 1.0
C02 A:3C7303 3.3 38.5 1.0
CB A:HIS122 3.5 17.2 1.0
H022 A:3C7303 3.6 46.2 1.0
ZN A:ZN302 3.7 21.4 1.0
SG A:CYS208 3.9 19.6 1.0
CB A:CYS208 4.0 17.0 1.0
NE2 A:HIS122 4.0 20.6 1.0
ND1 A:HIS120 4.1 14.9 1.0
CD2 A:HIS122 4.1 18.6 1.0
CG A:HIS120 4.2 14.8 1.0
CG A:HIS189 4.2 17.6 1.0
ND1 A:HIS189 4.3 19.8 1.0
OD1 A:ASP124 4.3 16.9 1.0
CG2 A:THR190 4.5 10.9 1.0
O A:HOH562 4.6 29.1 1.0
C03 A:3C7303 4.7 40.6 1.0
OD2 A:ASP124 4.8 18.4 1.0
H03 A:3C7303 4.9 48.7 1.0
CA A:HIS122 4.9 18.0 1.0

Zinc binding site 2 out of 8 in 4u4l

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Zinc binding site 2 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:21.4
occ:1.00
OD2 A:ASP124 2.0 18.4 1.0
NE2 A:HIS250 2.1 19.9 1.0
SG A:CYS208 2.3 19.6 1.0
S01 A:3C7303 2.3 27.1 1.0
CE1 A:HIS250 2.8 21.5 1.0
CG A:ASP124 3.0 18.1 1.0
H03 A:3C7303 3.2 48.7 1.0
CD2 A:HIS250 3.2 18.9 1.0
H08 A:3C7303 3.2 51.8 1.0
HS01 A:3C7303 3.3 32.5 1.0
OD1 A:ASP124 3.4 16.9 1.0
CB A:CYS208 3.5 17.0 1.0
C02 A:3C7303 3.5 38.5 1.0
ZN A:ZN301 3.7 19.5 1.0
C03 A:3C7303 3.8 40.6 1.0
H021 A:3C7303 3.8 46.2 1.0
ND1 A:HIS250 4.0 21.8 1.0
CB A:SER249 4.0 18.7 1.0
C08 A:3C7303 4.2 43.1 1.0
CG A:HIS250 4.2 22.3 1.0
CB A:ASP124 4.3 13.0 1.0
OG A:SER249 4.4 20.0 1.0
N07 A:3C7303 4.4 42.1 1.0
H022 A:3C7303 4.5 46.2 1.0
CE1 A:HIS120 4.6 17.3 1.0
NE2 A:HIS189 4.6 18.0 1.0
NE2 A:HIS120 4.6 15.3 1.0
CA A:CYS208 4.7 16.3 1.0
CE A:LYS125 4.8 14.5 1.0
CD A:LYS125 4.9 10.9 1.0
OG A:SER75 4.9 15.0 1.0
CG A:LYS125 4.9 11.1 1.0
C09 A:3C7303 5.0 43.3 1.0

Zinc binding site 3 out of 8 in 4u4l

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Zinc binding site 3 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:18.8
occ:1.00
OD2 B:ASP124 1.9 15.3 1.0
NE2 B:HIS250 2.1 14.4 1.0
SG B:CYS208 2.3 18.0 1.0
S01 B:3C7303 2.3 21.5 1.0
CG B:ASP124 3.0 17.3 1.0
CE1 B:HIS250 3.0 16.7 1.0
H08 B:3C7303 3.0 43.9 1.0
CD2 B:HIS250 3.1 17.1 1.0
H03 B:3C7303 3.2 42.5 1.0
HS01 B:3C7303 3.3 25.8 1.0
OD1 B:ASP124 3.4 16.8 1.0
C02 B:3C7303 3.5 34.8 1.0
CB B:CYS208 3.5 14.7 1.0
H021 B:3C7303 3.6 41.7 1.0
ZN B:ZN302 3.7 18.0 1.0
C03 B:3C7303 3.8 35.4 1.0
C08 B:3C7303 4.0 36.6 1.0
CB B:SER249 4.1 14.9 1.0
ND1 B:HIS250 4.1 17.3 1.0
CG B:HIS250 4.2 17.9 1.0
CB B:ASP124 4.3 10.4 1.0
N07 B:3C7303 4.3 35.3 1.0
OG B:SER249 4.4 14.2 1.0
H022 B:3C7303 4.4 41.7 1.0
CE1 B:HIS120 4.5 16.0 1.0
NE2 B:HIS120 4.5 13.6 1.0
CA B:CYS208 4.7 12.8 1.0
NE2 B:HIS189 4.7 14.4 1.0
CE B:LYS125 4.7 13.6 1.0
CD B:LYS125 4.8 13.9 1.0
H121 B:3C7303 4.8 43.8 1.0
C09 B:3C7303 4.9 39.2 1.0
CG B:LYS125 4.9 13.1 1.0
OG B:SER75 5.0 17.1 1.0

Zinc binding site 4 out of 8 in 4u4l

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Zinc binding site 4 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:18.0
occ:1.00
HS01 B:3C7303 1.2 25.8 1.0
NE2 B:HIS120 2.0 13.6 1.0
ND1 B:HIS122 2.1 17.5 1.0
NE2 B:HIS189 2.1 14.4 1.0
S01 B:3C7303 2.4 21.5 1.0
CE1 B:HIS120 3.0 16.0 1.0
CE1 B:HIS122 3.0 18.2 1.0
CD2 B:HIS120 3.0 15.6 1.0
CD2 B:HIS189 3.1 15.2 1.0
CG B:HIS122 3.1 17.9 1.0
CE1 B:HIS189 3.1 15.2 1.0
H021 B:3C7303 3.1 41.7 1.0
C02 B:3C7303 3.2 34.8 1.0
H022 B:3C7303 3.4 41.7 1.0
CB B:HIS122 3.5 13.6 1.0
ZN B:ZN301 3.7 18.8 1.0
CB B:CYS208 4.0 14.7 1.0
SG B:CYS208 4.0 18.0 1.0
ND1 B:HIS120 4.1 15.3 1.0
NE2 B:HIS122 4.1 19.0 1.0
CG B:HIS120 4.2 15.4 1.0
CD2 B:HIS122 4.2 19.5 1.0
ND1 B:HIS189 4.2 13.2 1.0
CG B:HIS189 4.2 14.1 1.0
OD1 B:ASP124 4.3 16.8 1.0
CG2 B:THR190 4.5 10.2 1.0
C03 B:3C7303 4.7 35.4 1.0
O B:HOH561 4.7 39.1 1.0
OD2 B:ASP124 4.8 15.3 1.0
CA B:HIS122 4.9 15.3 1.0
H03 B:3C7303 4.9 42.5 1.0

Zinc binding site 5 out of 8 in 4u4l

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Zinc binding site 5 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:20.4
occ:1.00
OD2 C:ASP124 2.0 16.5 1.0
NE2 C:HIS250 2.1 26.4 1.0
SG C:CYS208 2.3 17.0 1.0
S01 C:3C7304 2.4 25.9 1.0
CE1 C:HIS250 3.0 21.7 1.0
CG C:ASP124 3.0 17.6 1.0
H03 C:3C7304 3.0 34.8 1.0
H08 C:3C7304 3.1 41.4 1.0
CD2 C:HIS250 3.2 25.3 1.0
HS01 C:3C7304 3.2 31.1 1.0
OD1 C:ASP124 3.4 15.6 1.0
C02 C:3C7304 3.4 26.4 1.0
H021 C:3C7304 3.4 31.7 1.0
CB C:CYS208 3.5 14.3 1.0
C03 C:3C7304 3.7 29.0 1.0
ZN C:ZN302 3.8 18.9 1.0
C08 C:3C7304 4.1 34.5 1.0
ND1 C:HIS250 4.1 21.1 1.0
CB C:SER249 4.1 17.3 1.0
CG C:HIS250 4.3 25.9 1.0
CB C:ASP124 4.3 16.9 1.0
N07 C:3C7304 4.4 33.0 1.0
H022 C:3C7304 4.4 31.7 1.0
OG C:SER249 4.5 16.7 1.0
CE1 C:HIS120 4.6 14.4 1.0
NE2 C:HIS120 4.6 15.4 1.0
CA C:CYS208 4.6 14.8 1.0
H121 C:3C7304 4.7 40.5 1.0
NE2 C:HIS189 4.7 10.8 1.0
CE C:LYS125 4.8 13.0 1.0
CD C:LYS125 4.8 12.3 1.0
CG C:LYS125 4.9 14.2 1.0
OG C:SER75 5.0 15.5 1.0

Zinc binding site 6 out of 8 in 4u4l

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Zinc binding site 6 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:18.9
occ:1.00
HS01 C:3C7304 1.3 31.1 1.0
ND1 C:HIS122 2.0 16.4 1.0
NE2 C:HIS120 2.1 15.4 1.0
NE2 C:HIS189 2.2 10.8 1.0
S01 C:3C7304 2.5 25.9 1.0
CE1 C:HIS122 2.9 19.0 1.0
CD2 C:HIS189 3.0 14.8 1.0
CE1 C:HIS120 3.0 14.4 1.0
CG C:HIS122 3.1 15.8 1.0
H021 C:3C7304 3.1 31.7 1.0
CD2 C:HIS120 3.2 14.7 1.0
C02 C:3C7304 3.2 26.4 1.0
CE1 C:HIS189 3.2 11.3 1.0
H022 C:3C7304 3.4 31.7 1.0
CB C:HIS122 3.5 15.4 1.0
ZN C:ZN301 3.8 20.4 1.0
SG C:CYS208 4.1 17.0 1.0
NE2 C:HIS122 4.1 18.1 1.0
CB C:CYS208 4.1 14.3 1.0
CD2 C:HIS122 4.2 16.9 1.0
ND1 C:HIS120 4.2 15.8 1.0
CG C:HIS189 4.2 12.4 1.0
CG C:HIS120 4.3 13.4 1.0
ND1 C:HIS189 4.3 14.8 1.0
OD1 C:ASP124 4.4 15.6 1.0
O C:HOH499 4.4 31.4 1.0
CG2 C:THR190 4.4 10.7 1.0
C03 C:3C7304 4.7 29.0 1.0
H03 C:3C7304 4.9 34.8 1.0
CA C:HIS122 4.9 14.9 1.0
OD2 C:ASP124 5.0 16.5 1.0

Zinc binding site 7 out of 8 in 4u4l

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Zinc binding site 7 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:25.7
occ:1.00
OD2 D:ASP124 2.0 21.3 1.0
NE2 D:HIS250 2.1 23.8 1.0
SG D:CYS208 2.3 21.3 1.0
S01 D:3C7304 2.4 27.3 1.0
CE1 D:HIS250 2.9 25.4 1.0
CG D:ASP124 3.1 21.1 1.0
CD2 D:HIS250 3.1 24.9 1.0
H08 D:3C7304 3.2 53.0 1.0
H03 D:3C7304 3.2 52.8 1.0
HS01 D:3C7304 3.4 32.8 1.0
OD1 D:ASP124 3.4 18.2 1.0
C02 D:3C7304 3.5 42.8 1.0
CB D:CYS208 3.5 24.0 1.0
H021 D:3C7304 3.7 51.3 1.0
ZN D:ZN302 3.7 23.3 1.0
C03 D:3C7304 3.8 44.0 1.0
CB D:SER249 4.0 21.5 1.0
ND1 D:HIS250 4.1 26.4 1.0
C08 D:3C7304 4.2 44.2 1.0
CG D:HIS250 4.2 26.1 1.0
CB D:ASP124 4.4 18.4 1.0
N07 D:3C7304 4.4 45.2 1.0
OG D:SER249 4.4 22.3 1.0
H022 D:3C7304 4.5 51.3 1.0
CE1 D:HIS120 4.5 18.4 1.0
NE2 D:HIS120 4.5 19.7 1.0
CA D:CYS208 4.7 18.9 1.0
NE2 D:HIS189 4.7 18.2 1.0
CE D:LYS125 4.8 18.9 1.0
CD D:LYS125 4.8 19.2 1.0
C09 D:3C7304 4.9 44.8 1.0
CG D:LYS125 4.9 17.9 1.0

Zinc binding site 8 out of 8 in 4u4l

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Zinc binding site 8 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:23.3
occ:1.00
HS01 D:3C7304 1.2 32.8 1.0
ND1 D:HIS122 2.0 27.5 1.0
NE2 D:HIS189 2.2 18.2 1.0
NE2 D:HIS120 2.2 19.7 1.0
S01 D:3C7304 2.4 27.3 1.0
CE1 D:HIS122 2.9 27.8 1.0
CD2 D:HIS189 3.0 17.4 1.0
CG D:HIS122 3.1 25.6 1.0
CD2 D:HIS120 3.1 18.0 1.0
CE1 D:HIS120 3.1 18.4 1.0
CE1 D:HIS189 3.2 18.7 1.0
H021 D:3C7304 3.3 51.3 1.0
C02 D:3C7304 3.4 42.8 1.0
CB D:HIS122 3.5 20.1 1.0
H022 D:3C7304 3.6 51.3 1.0
ZN D:ZN301 3.7 25.7 1.0
SG D:CYS208 3.9 21.3 1.0
CB D:CYS208 4.0 24.0 1.0
NE2 D:HIS122 4.0 27.2 1.0
CD2 D:HIS122 4.1 25.8 1.0
CG D:HIS189 4.2 17.4 1.0
ND1 D:HIS120 4.2 15.5 1.0
CG D:HIS120 4.3 13.6 1.0
ND1 D:HIS189 4.3 18.1 1.0
OD1 D:ASP124 4.3 18.2 1.0
CG2 D:THR190 4.5 14.4 1.0
C03 D:3C7304 4.8 44.0 1.0
OD2 D:ASP124 4.9 21.3 1.0
CA D:HIS122 4.9 19.6 1.0

Reference:

M.Kosmopoulou, P.Hinchliffe, J.Spencer. Crystal Structure of the Metallo-Beta-Lactamase Ndm-1 in Complex with A Bisthiazolidine Inhibitor To Be Published.
Page generated: Wed Dec 16 05:47:46 2020

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