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Zinc in PDB 5nbk: Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data

Enzymatic activity of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data

All present enzymatic activity of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data:
3.5.2.6;

Protein crystallography data

The structure of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data, PDB code: 5nbk was solved by J.E.Raczynska, I.G.Shabalin, M.Jaskolski, W.Minor, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.66 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.047, 108.047, 92.571, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.9

Other elements in 5nbk:

The structure of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data (pdb code 5nbk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data, PDB code: 5nbk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5nbk

Go back to Zinc Binding Sites List in 5nbk
Zinc binding site 1 out of 4 in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:39.7
occ:0.90
 NE2 A:HIS120 2.1 32.7 1.0
ND1 A:HIS122 2.3 35.2 1.0
NE2 A:HIS189 2.3 37.2 1.0
ZN A:ZN302 2.9 50.7 0.5
O A:HOH446 2.9 46.0 0.9
CE1 A:HIS120 3.1 33.5 1.0
CD2 A:HIS120 3.1 32.3 1.0
CD2 A:HIS189 3.1 36.7 1.0
CE1 A:HIS122 3.2 35.7 1.0
CG A:HIS122 3.2 35.4 1.0
CE1 A:HIS189 3.4 38.3 1.0
CB A:HIS122 3.5 34.8 1.0
SG A:CYS208 3.8 47.6 1.0
OD1 A:ASP124 3.9 51.0 1.0
CB A:CYS208 4.1 42.5 1.0
OD2 A:ASP124 4.1 49.8 1.0
ND1 A:HIS120 4.2 33.3 1.0
CG A:HIS120 4.2 31.8 1.0
O A:HOH441 4.3 48.4 0.9
NE2 A:HIS122 4.3 36.0 1.0
CG A:HIS189 4.4 37.0 1.0
CD2 A:HIS122 4.4 35.6 1.0
CG A:ASP124 4.5 46.7 1.0
ND1 A:HIS189 4.5 38.2 1.0
CG2 A:THR190 4.7 33.1 1.0
CA A:HIS122 4.9 34.9 1.0

Zinc binding site 2 out of 4 in 5nbk

Go back to Zinc Binding Sites List in 5nbk
Zinc binding site 2 out of 4 in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data


Mono view


Stereo pair view

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

b:50.7
occ:0.50
 OD2 A:ASP124 2.1 49.8 1.0
O A:HOH446 2.3 46.0 0.9
NE2 A:HIS250 2.7 56.3 1.0
SG A:CYS208 2.7 47.6 1.0
O A:HOH441 2.7 48.4 0.9
ZN A:ZN301 2.9 39.7 0.9
CG A:ASP124 3.0 46.7 1.0
OD1 A:ASP124 3.3 51.0 1.0
CE1 A:HIS250 3.5 57.0 1.0
CD2 A:HIS250 3.8 55.9 1.0
NE2 A:HIS189 3.9 37.2 1.0
CB A:CYS208 4.0 42.5 1.0
CB A:ASP124 4.3 43.4 1.0
NE2 A:HIS120 4.3 32.7 1.0
CE1 A:HIS189 4.4 38.3 1.0
CE1 A:HIS120 4.6 33.5 1.0
ND1 A:HIS122 4.7 35.2 1.0
ND1 A:HIS250 4.7 56.5 1.0
CG A:HIS250 4.9 55.8 1.0
CD2 A:HIS189 4.9 36.7 1.0

Zinc binding site 3 out of 4 in 5nbk

Go back to Zinc Binding Sites List in 5nbk
Zinc binding site 3 out of 4 in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:42.9
occ:1.00
 NE2 C:HIS120 2.1 38.3 1.0
NE2 C:HIS189 2.2 35.7 1.0
ND1 C:HIS122 2.3 43.3 1.0
O C:HOH440 2.4 37.4 1.0
ZN C:ZN302 2.9 42.8 0.5
CD2 C:HIS189 3.0 35.5 1.0
CE1 C:HIS120 3.1 38.8 1.0
CD2 C:HIS120 3.1 37.8 1.0
CE1 C:HIS122 3.3 42.9 1.0
CG C:HIS122 3.3 42.7 1.0
CE1 C:HIS189 3.3 37.1 1.0
CB C:HIS122 3.5 41.3 1.0
SG C:CYS208 3.7 45.0 1.0
OD1 C:ASP124 3.8 47.7 1.0
CB C:CYS208 4.0 43.2 1.0
OD2 C:ASP124 4.1 49.7 1.0
ND1 C:HIS120 4.2 38.3 1.0
CG C:HIS120 4.2 37.1 1.0
CG C:HIS189 4.3 36.4 1.0
ND1 C:HIS189 4.4 37.3 1.0
NE2 C:HIS122 4.4 43.0 1.0
CD2 C:HIS122 4.4 43.5 1.0
CG C:ASP124 4.4 46.6 1.0
O C:HOH441 4.5 50.9 1.0
O C:HOH444 4.7 42.8 1.0
CG2 C:THR190 4.7 35.1 1.0
CA C:HIS122 5.0 40.8 1.0

Zinc binding site 4 out of 4 in 5nbk

Go back to Zinc Binding Sites List in 5nbk
Zinc binding site 4 out of 4 in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:42.8
occ:0.50
 OD2 C:ASP124 2.2 49.7 1.0
O C:HOH440 2.4 37.4 1.0
SG C:CYS208 2.5 45.0 1.0
NE2 C:HIS250 2.6 55.2 1.0
O C:HOH444 2.7 42.8 1.0
O C:HOH441 2.8 50.9 1.0
ZN C:ZN301 2.9 42.9 1.0
CG C:ASP124 3.2 46.6 1.0
CE1 C:HIS250 3.5 56.6 1.0
OD1 C:ASP124 3.5 47.7 1.0
CD2 C:HIS250 3.6 54.0 1.0
CB C:CYS208 3.7 43.2 1.0
NE2 C:HIS189 3.7 35.7 1.0
CE1 C:HIS189 4.1 37.1 1.0
NE2 C:HIS120 4.4 38.3 1.0
CB C:ASP124 4.5 44.6 1.0
CE1 C:HIS120 4.6 38.8 1.0
ND1 C:HIS250 4.6 55.8 1.0
CD2 C:HIS189 4.7 35.5 1.0
CG C:HIS250 4.8 53.9 1.0
ND1 C:HIS122 4.9 43.3 1.0
CB C:SER249 5.0 46.1 1.0

Reference:

J.E.Raczynska, I.G.Shabalin, W.Minor, A.Wlodawer, M.Jaskolski. A Close Look Onto Structural Models and Primary Ligands of Metallo-Beta-Lactamases. Drug Resist. Updat. V. 40 1 2018.
ISSN: ESSN 1532-2084
PubMed: 30466711
DOI: 10.1016/J.DRUP.2018.08.001
Page generated: Sun Oct 27 22:42:31 2024

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