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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: Sun Aug 17 12:33:27 2025

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