Sodium in PDB 7a5z: Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product

Protein crystallography data

The structure of Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product, PDB code: 7a5z was solved by A.Lucic, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.88 / 1.29
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 64.647, 74.68, 78.766, 90, 90, 90
R / Rfree (%) 14 / 15.8

Other elements in 7a5z:

The structure of Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 3 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product (pdb code 7a5z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product, PDB code: 7a5z:

Sodium binding site 1 out of 1 in 7a5z

Go back to Sodium Binding Sites List in 7a5z
Sodium binding site 1 out of 1 in the Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Vim-2 Metallo-Beta-Lactamase with Hydrolysed Faropenem Imine Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:13.3
occ:1.00
H A:ASP117 2.4 11.3 1.0
HD21 A:ASN148 2.6 19.1 1.0
HA A:HIS116 3.0 11.8 1.0
O A:HOH463 3.1 46.4 1.0
O A:HOH546 3.2 41.5 1.0
N A:ASP117 3.2 9.4 1.0
HB3 A:HIS116 3.2 12.8 1.0
HD2 A:HIS116 3.3 16.0 1.0
H101 A:QZH301 3.3 14.8 1.0
O A:HOH432 3.3 36.0 1.0
ND2 A:ASN148 3.4 15.9 1.0
HB2 A:ASP117 3.4 18.5 1.0
CA A:HIS116 3.6 9.9 1.0
CD2 A:HIS116 3.7 13.3 1.0
CB A:HIS116 3.7 10.7 1.0
HD22 A:ASN148 3.8 19.1 1.0
CG A:ASP117 3.8 21.8 1.0
H121 A:QZH301 3.8 15.4 1.0
OD2 A:ASP117 3.9 39.9 1.0
CG A:HIS116 3.9 11.1 1.0
C A:HIS116 3.9 10.6 1.0
CB A:ASP117 3.9 15.4 1.0
H113 A:QZH301 4.0 14.7 1.0
HG2 A:GLU146 4.0 27.1 1.0
CA A:ASP117 4.2 10.8 1.0
C10 A:QZH301 4.2 12.3 1.0
OD1 A:ASP117 4.2 22.2 1.0
CG A:ASN148 4.3 14.2 1.0
OD1 A:ASN148 4.4 15.1 1.0
C11 A:QZH301 4.5 12.3 1.0
O12 A:QZH301 4.5 12.8 1.0
HA A:ASP117 4.6 13.0 1.0
HB2 A:HIS116 4.6 12.8 1.0
H112 A:QZH301 4.7 14.7 1.0
NE2 A:HIS116 4.8 13.9 1.0
O A:HOH401 4.8 15.5 0.5
CG A:GLU146 4.8 22.6 1.0
OE2 A:GLU146 4.9 61.0 1.0
HB3 A:ASP117 4.9 18.5 1.0
HG3 A:GLU146 4.9 27.1 1.0
N A:HIS116 4.9 9.7 1.0
H A:ASP118 5.0 12.8 1.0

Reference:

A.Lucic, P.Hinchliffe, T.R.Malla, C.L.Tooke, J.Brem, K.Calvopina, C.T.Lohans, P.Rabe, M.A.Mcdonough, T.Armistead, A.M.Orville, J.Spencer, C.J.Schofield. Faropenem Reacts with Serine and Metallo-Beta-Lactamases to Give Multiple Products Eur.J.Med.Chem. 2021.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2021.113257
Page generated: Wed Mar 3 15:32:46 2021

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