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Sodium in PDB 4ddo: Crystal Structure of 3-Oxoacyl-[Acyl-Carrier-Protein] Synthase II From Burkholderia Vietnamiensis

Enzymatic activity of Crystal Structure of 3-Oxoacyl-[Acyl-Carrier-Protein] Synthase II From Burkholderia Vietnamiensis

All present enzymatic activity of Crystal Structure of 3-Oxoacyl-[Acyl-Carrier-Protein] Synthase II From Burkholderia Vietnamiensis:
2.3.1.179;

Protein crystallography data

The structure of Crystal Structure of 3-Oxoacyl-[Acyl-Carrier-Protein] Synthase II From Burkholderia Vietnamiensis, PDB code: 4ddo 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) 50.00 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 56.820, 101.320, 131.180, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 3-Oxoacyl-[Acyl-Carrier-Protein] Synthase II From Burkholderia Vietnamiensis (pdb code 4ddo). 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 Crystal Structure of 3-Oxoacyl-[Acyl-Carrier-Protein] Synthase II From Burkholderia Vietnamiensis, PDB code: 4ddo:

Sodium binding site 1 out of 1 in 4ddo

Go back to Sodium Binding Sites List in 4ddo
Sodium binding site 1 out of 1 in the Crystal Structure of 3-Oxoacyl-[Acyl-Carrier-Protein] Synthase II From Burkholderia Vietnamiensis


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 3-Oxoacyl-[Acyl-Carrier-Protein] Synthase II From Burkholderia Vietnamiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:18.2
occ:1.00
 OE1 A:GLU358 2.7 12.0 1.0
O A:ASN405 2.8 12.4 1.0
OD1 A:ASN311 2.8 16.3 1.0
O A:ASN311 2.9 14.2 1.0
OG A:SER404 3.0 12.4 1.0
O A:ALA312 3.1 14.8 1.0
O A:HOH631 3.2 14.6 1.0
CB A:GLU358 3.5 11.5 1.0
C A:ALA312 3.5 14.8 1.0
N A:ASN405 3.6 12.4 1.0
CD A:GLU358 3.6 11.6 1.0
C A:ASN311 3.6 14.5 1.0
O A:HOH634 3.8 15.4 1.0
C A:ASN405 3.8 12.9 1.0
CG A:GLU358 3.8 11.6 1.0
CG A:ASN311 3.8 14.9 1.0
N A:HIS313 3.9 14.4 1.0
O A:HOH618 3.9 12.4 1.0
CA A:HIS313 4.1 14.5 1.0
CB A:ASN311 4.2 15.0 1.0
CA A:ASN405 4.3 12.7 1.0
CB A:SER404 4.3 12.1 1.0
N A:ALA312 4.3 14.6 1.0
C A:SER404 4.3 12.4 1.0
CA A:SER404 4.4 12.3 1.0
CA A:ALA312 4.4 14.8 1.0
NZ A:LYS344 4.5 11.6 1.0
CA A:ASN311 4.5 14.5 1.0
OE2 A:GLU358 4.7 11.9 1.0
CB A:ASN405 4.8 13.5 1.0
CA A:GLU358 4.8 10.9 1.0
N A:GLY406 5.0 13.0 1.0

Reference:

L.Baugh, L.A.Gallagher, R.Patrapuvich, M.C.Clifton, A.S.Gardberg, T.E.Edwards, B.Armour, D.W.Begley, S.H.Dieterich, D.M.Dranow, J.Abendroth, J.W.Fairman, D.Fox, B.L.Staker, I.Phan, A.Gillespie, R.Choi, S.Nakazawa-Hewitt, M.T.Nguyen, A.Napuli, L.Barrett, G.W.Buchko, R.Stacy, P.J.Myler, L.J.Stewart, C.Manoil, W.C.Van Voorhis. Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome. Plos One V. 8 53851 2013.
ISSN: ESSN 1932-6203
PubMed: 23382856
DOI: 10.1371/JOURNAL.PONE.0053851
Page generated: Sun Aug 17 18:56:46 2025

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