Atomistry » Sodium » PDB 2zgx-3a03 » 2zj9
Atomistry »
  Sodium »
    PDB 2zgx-3a03 »
      2zj9 »

Sodium in PDB 2zj9: X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix

Enzymatic activity of X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix

All present enzymatic activity of X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix:
3.5.2.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix, PDB code: 2zj9 was solved by Y.Yamaguchi, G.Sato, Y.Yamagata, J.Wachino, Y.Arakawa, H.Kurosaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.16 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.065, 47.381, 81.461, 82.62, 80.91, 65.40
R / Rfree (%) 16.3 / 20.6

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix (pdb code 2zj9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix, PDB code: 2zj9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2zj9

Go back to Sodium Binding Sites List in 2zj9
Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1

b:21.8
occ:1.00
 O A:HOH468 2.2 23.4 1.0
NE2 A:GLN139 2.2 18.4 0.5
O A:TRP138 2.4 12.1 1.0
OE1 A:GLN100 2.5 19.1 1.0
O A:GLN136 2.7 10.5 1.0
O A:ASN137 3.0 13.5 1.0
C A:ASN137 3.2 11.5 1.0
C A:TRP138 3.3 12.5 1.0
CD A:GLN100 3.3 19.1 1.0
NE2 A:GLN100 3.5 17.2 1.0
CD A:GLN139 3.5 18.7 0.5
CA A:ASN137 3.7 11.0 1.0
N A:TRP138 3.7 11.2 1.0
C A:GLN136 3.7 10.5 1.0
O A:HOH426 3.9 14.5 1.0
O A:HOH486 4.0 26.5 1.0
CG A:GLN139 4.1 16.0 0.5
N A:GLN139 4.1 12.8 1.0
CA A:TRP138 4.1 11.6 1.0
N A:ASN137 4.2 9.6 1.0
CA A:GLN139 4.3 13.6 0.5
CA A:GLN139 4.3 13.8 0.5
CG A:GLN139 4.3 17.3 0.5
OE1 A:GLN139 4.5 20.4 0.5
O A:HOH457 4.6 16.3 1.0
CG A:GLN100 4.7 17.6 1.0
CB A:GLN139 4.8 14.5 0.5
CB A:GLN139 4.9 14.7 0.5

Sodium binding site 2 out of 2 in 2zj9

Go back to Sodium Binding Sites List in 2zj9
Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli with A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2

b:24.3
occ:1.00
 OE1 B:GLN139 2.2 26.5 1.0
OE1 B:GLN100 2.5 21.7 1.0
O B:TRP138 2.6 11.4 1.0
O B:GLN136 2.7 9.1 1.0
O B:ASN137 3.1 12.5 1.0
CD B:GLN100 3.3 20.0 1.0
CD B:GLN139 3.3 24.5 1.0
C B:ASN137 3.3 10.9 1.0
NE2 B:GLN100 3.4 20.1 1.0
C B:TRP138 3.5 11.4 1.0
C B:GLN136 3.8 9.8 1.0
CA B:ASN137 3.8 11.1 1.0
O B:HOH397 3.8 16.3 1.0
O B:HOH536 3.9 33.3 1.0
N B:TRP138 3.9 11.6 1.0
CG B:GLN139 4.1 18.9 1.0
N B:GLN139 4.2 12.7 1.0
N B:ASN137 4.3 9.2 1.0
CA B:TRP138 4.3 11.5 1.0
NE2 B:GLN139 4.3 27.4 1.0
O B:HOH601 4.3 38.0 1.0
CA B:GLN139 4.3 13.8 1.0
CG B:GLN100 4.7 17.6 1.0
CB B:GLN139 4.8 14.3 1.0

Reference:

Y.Yamaguchi, G.Sato, Y.Yamagata, Y.Doi, J.Wachino, Y.Arakawa, K.Matsuda, H.Kurosaki. Structure of Ampc Beta-Lactamase (Ampcd) From An Escherichia Coli Clinical Isolate with A Tripeptide Deletion (GLY286-SER287-ASP288) in the H10 Helix Acta Crystallogr.,Sect.F V. 65 540 2009.
ISSN: ESSN 1744-3091
PubMed: 19478427
DOI: 10.1107/S1744309109014249
Page generated: Mon Oct 7 05:37:44 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy