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Sodium in PDB 3u0e: Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320

Enzymatic activity of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320

All present enzymatic activity of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320:
2.3.1.41;

Protein crystallography data

The structure of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320, PDB code: 3u0e was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.070, 83.750, 73.610, 90.00, 121.50, 90.00
R / Rfree (%) 13.7 / 15.6

Other elements in 3u0e:

The structure of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320 (pdb code 3u0e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320, PDB code: 3u0e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3u0e

Go back to Sodium Binding Sites List in 3u0e
Sodium binding site 1 out of 2 in the Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:8.3
occ:1.00
OE1 A:GLU342 2.3 8.5 1.0
OD1 A:ASN294 2.4 8.2 1.0
O A:ASN389 2.5 8.2 1.0
OG A:SER388 2.6 7.8 1.0
O A:ASN294 2.6 7.7 1.0
O A:PRO295 2.8 8.7 1.0
CD A:GLU342 3.3 8.5 1.0
C A:ASN294 3.4 8.1 1.0
CG A:ASN294 3.4 8.0 1.0
C A:PRO295 3.4 8.7 1.0
C A:ASN389 3.5 8.2 1.0
N A:ASN389 3.5 7.6 1.0
CB A:SER388 3.8 7.7 1.0
O A:HOH470 3.9 27.1 1.0
CB A:GLU342 3.9 7.0 1.0
CB A:ASN294 3.9 8.1 1.0
C A:SER388 4.0 7.4 1.0
CA A:SER388 4.0 7.7 1.0
N A:PRO295 4.0 8.4 1.0
CG A:GLU342 4.0 7.7 1.0
N A:HIS296 4.1 9.2 1.0
CA A:ASN389 4.1 7.8 1.0
OE2 A:GLU342 4.1 10.5 1.0
O A:HOH492 4.1 12.3 1.0
CA A:PRO295 4.2 8.5 1.0
CA A:ASN294 4.2 8.2 1.0
CA A:HIS296 4.4 10.2 1.0
OG A:SER390 4.5 9.6 0.5
N A:SER390 4.6 8.3 0.5
ND2 A:ASN294 4.6 8.6 1.0
N A:SER390 4.6 8.4 0.5
O A:HOH501 4.7 12.7 1.0
CB A:ASN389 4.8 8.0 1.0
NZ A:LYS328 4.9 10.5 1.0
O A:SER388 4.9 7.1 1.0
CB A:SER390 4.9 9.2 0.5
CA A:SER390 5.0 8.9 0.5

Sodium binding site 2 out of 2 in 3u0e

Go back to Sodium Binding Sites List in 3u0e
Sodium binding site 2 out of 2 in the Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Beta-Ketoacyl Synthase From Brucella Melitensis in Complex with Fragment 9320 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:16.4
occ:1.00
OE2 A:GLU121 1.9 24.5 1.0
CD A:GLU121 2.6 20.2 1.0
OE1 A:GLU121 2.8 24.3 1.0
CG A:GLU121 4.0 17.2 1.0
CB A:ASP117 4.8 9.8 1.0
O A:HOH738 4.9 31.7 1.0

Reference:

E.I.Patterson, J.D.Nanson, J.Abendroth, C.Bryan, B.Sankaran, P.J.Myler, J.K.Forwood. Structural Characterization of Beta-Ketoacyl Acp Synthase I Bound to Platencin and Fragment Screening Molecules at Two Substrate Binding Sites. Proteins 2019.
ISSN: ESSN 1097-0134
PubMed: 31237717
DOI: 10.1002/PROT.25765
Page generated: Tue Dec 15 06:26:55 2020

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