Atomistry » Sodium » PDB 2xzj-2yeq » 2ydg
Atomistry »
  Sodium »
    PDB 2xzj-2yeq »
      2ydg »

Sodium in PDB 2ydg: Ascorbate Co-Crystallized Hewl.

Enzymatic activity of Ascorbate Co-Crystallized Hewl.

All present enzymatic activity of Ascorbate Co-Crystallized Hewl.:
3.2.1.17;

Protein crystallography data

The structure of Ascorbate Co-Crystallized Hewl., PDB code: 2ydg was solved by E.De La Mora, I.Carmichael, E.F.Garman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.70 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.770, 78.770, 37.370, 90.00, 90.00, 90.00
R / Rfree (%) 19.231 / 22.77

Sodium Binding Sites:

The binding sites of Sodium atom in the Ascorbate Co-Crystallized Hewl. (pdb code 2ydg). 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 Ascorbate Co-Crystallized Hewl., PDB code: 2ydg:

Sodium binding site 1 out of 1 in 2ydg

Go back to Sodium Binding Sites List in 2ydg
Sodium binding site 1 out of 1 in the Ascorbate Co-Crystallized Hewl.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ascorbate Co-Crystallized Hewl. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1130

b:17.4
occ:1.00
O A:SER60 2.3 11.9 1.0
O A:CYS64 2.3 10.1 1.0
O A:ARG73 2.4 17.4 1.0
O5 A:A5C1131 2.7 24.1 1.0
OG A:SER72 2.8 17.5 1.0
O6 A:A5C1131 3.0 22.6 1.0
C A:CYS64 3.4 10.0 1.0
C6 A:A5C1131 3.4 23.9 1.0
C A:SER60 3.4 11.8 1.0
C A:ARG73 3.4 17.6 1.0
C5 A:A5C1131 3.5 24.3 1.0
CB A:SER72 3.6 18.0 1.0
N A:ARG73 3.9 18.0 1.0
CA A:ASN65 4.0 10.3 1.0
N A:ASN65 4.1 10.0 1.0
CA A:SER60 4.1 11.3 1.0
C A:SER72 4.1 18.1 1.0
N A:CYS64 4.2 9.8 1.0
CA A:ARG73 4.2 17.9 1.0
N A:ASN74 4.3 16.9 1.0
CB A:SER60 4.4 11.1 1.0
CA A:CYS64 4.4 9.8 1.0
C A:ARG61 4.5 13.2 1.0
N A:ARG61 4.5 12.5 1.0
CA A:ASN74 4.5 16.3 1.0
CA A:SER72 4.5 18.0 1.0
O A:SER72 4.5 18.1 1.0
O A:ARG61 4.6 13.5 1.0
N A:TRP62 4.7 12.8 1.0
CB A:ASN74 4.7 16.2 1.0
CA A:ARG61 4.7 13.2 1.0
CB A:THR69 4.7 13.8 1.0
C4 A:A5C1131 4.8 24.7 1.0
O3 A:A5C1131 4.8 23.8 1.0
CB A:ASN65 4.8 10.3 1.0
N A:TRP63 4.9 11.0 1.0
C A:TRP62 4.9 11.7 1.0
O4 A:A5C1131 5.0 25.1 1.0
N A:ASP66 5.0 9.9 1.0

Reference:

E.De La Mora, I.Carmichael, E.F.Garman. Effective Scavenging at Cryotemperatures: Further Increasing the Dose Tolerance of Protein Crystals. J.Synchrotron.Radiat. V. 18 346 2011.
ISSN: ISSN 0909-0495
PubMed: 21525642
DOI: 10.1107/S0909049511007163
Page generated: Tue Dec 15 06:00:30 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy