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Sodium in PDB 3u0f: The Structure of Beta-Ketoacyl Synthase From Brucella Melitensis Bound to the Fragment 7-Hydroxycoumarin

Enzymatic activity of The Structure of Beta-Ketoacyl Synthase From Brucella Melitensis Bound to the Fragment 7-Hydroxycoumarin

All present enzymatic activity of The Structure of Beta-Ketoacyl Synthase From Brucella Melitensis Bound to the Fragment 7-Hydroxycoumarin:
2.3.1.41;

Protein crystallography data

The structure of The Structure of Beta-Ketoacyl Synthase From Brucella Melitensis Bound to the Fragment 7-Hydroxycoumarin, PDB code: 3u0f was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural 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) 39.28 / 1.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.560, 83.250, 73.810, 90.00, 121.20, 90.00
R / Rfree (%) 12.2 / 13.4

Other elements in 3u0f:

The structure of The Structure of Beta-Ketoacyl Synthase From Brucella Melitensis Bound to the Fragment 7-Hydroxycoumarin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Beta-Ketoacyl Synthase From Brucella Melitensis Bound to the Fragment 7-Hydroxycoumarin (pdb code 3u0f). 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 The Structure of Beta-Ketoacyl Synthase From Brucella Melitensis Bound to the Fragment 7-Hydroxycoumarin, PDB code: 3u0f:

Sodium binding site 1 out of 1 in 3u0f

Go back to Sodium Binding Sites List in 3u0f
Sodium binding site 1 out of 1 in the The Structure of Beta-Ketoacyl Synthase From Brucella Melitensis Bound to the Fragment 7-Hydroxycoumarin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Beta-Ketoacyl Synthase From Brucella Melitensis Bound to the Fragment 7-Hydroxycoumarin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:14.4
occ:1.00
 OE1 A:GLU342 2.3 7.0 1.0
OD1 A:ASN294 2.4 6.8 1.0
O A:ASN389 2.5 6.0 1.0
OG A:SER388 2.6 7.0 1.0
O A:ASN294 2.7 5.6 1.0
O A:HOH491 2.8 18.4 1.0
O A:PRO295 2.9 6.6 1.0
CD A:GLU342 3.3 6.6 1.0
C A:ASN294 3.4 5.4 1.0
CG A:ASN294 3.4 6.0 1.0
N A:ASN389 3.5 4.8 1.0
C A:PRO295 3.5 5.8 1.0
C A:ASN389 3.5 5.4 1.0
CB A:SER388 3.8 6.0 1.0
CB A:GLU342 3.9 5.1 1.0
CB A:ASN294 3.9 5.8 1.0
C A:SER388 4.0 4.9 1.0
CA A:SER388 4.0 5.4 1.0
N A:PRO295 4.0 5.5 1.0
CA A:ASN389 4.1 4.8 1.0
CG A:GLU342 4.1 5.3 1.0
OE2 A:GLU342 4.1 9.9 1.0
N A:HIS296 4.1 5.7 1.0
O A:HOH462 4.1 9.4 1.0
CA A:PRO295 4.2 5.5 1.0
CA A:ASN294 4.3 5.7 1.0
CA A:HIS296 4.5 6.6 1.0
O A:HOH477 4.6 8.6 1.0
OG A:SER390 4.6 12.0 0.6
ND2 A:ASN294 4.6 6.2 1.0
N A:SER390 4.7 6.7 1.0
NZ A:LYS328 4.8 9.0 1.0
CB A:ASN389 4.8 5.2 1.0
O A:SER388 4.9 5.4 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: Mon Oct 7 13:24:52 2024

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