Sodium in PDB 6xl8: Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation

Enzymatic activity of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation

All present enzymatic activity of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation:
2.8.2.30;

Protein crystallography data

The structure of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation, PDB code: 6xl8 was solved by L.C.Pedersen, J.Liu, R.Wander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.70 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.217, 147.469, 51.037, 90, 94.35, 90
R / Rfree (%) 21.6 / 27.1

Other elements in 6xl8:

The structure of Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation also contains other interesting chemical elements:

Iodine (I) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation (pdb code 6xl8). 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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation, PDB code: 6xl8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6xl8

Go back to Sodium Binding Sites List in 6xl8
Sodium binding site 1 out of 2 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:43.1
occ:1.00
 OG1 A:THR256 2.4 48.7 1.0
OD1 A:ASP252 2.4 37.5 1.0
O6B C:IDS2 2.6 48.7 1.0
O3 C:GNS1 2.7 49.5 1.0
O A:ASP252 3.1 39.8 1.0
C6 C:IDS2 3.6 48.8 1.0
CG A:ASP252 3.7 39.9 1.0
CB A:THR256 3.8 46.5 1.0
NZ A:LYS161 3.8 43.6 1.0
O5 C:IDS2 3.9 46.7 1.0
O3S C:GNS1 4.0 53.4 1.0
N A:THR256 4.0 40.7 1.0
C A:ASP252 4.0 36.7 1.0
C3 C:GNS1 4.0 48.1 1.0
CE A:LYS161 4.2 37.6 1.0
C5 C:IDS2 4.3 47.8 1.0
CA A:THR256 4.3 43.4 1.0
OD2 A:ASP252 4.4 33.8 1.0
O6A C:IDS2 4.4 41.4 1.0
CB A:GLN255 4.5 38.7 1.0
CA A:ASP252 4.5 35.7 1.0
C4 C:GNS1 4.5 53.3 1.0
C2 C:GNS1 4.5 52.3 1.0
CG2 A:THR256 4.6 47.0 1.0
CB A:ASP252 4.6 37.0 1.0
CG A:GLN255 4.7 40.1 1.0
N2 C:GNS1 4.7 51.4 1.0
C A:GLN255 4.8 42.1 1.0
O4 C:GNS1 4.9 49.4 1.0
C1 C:IDS2 4.9 46.5 1.0
I A:IOD504 4.9 59.7 0.5
N A:TYR253 5.0 33.1 1.0
S1 C:GNS1 5.0 61.3 1.0

Sodium binding site 2 out of 2 in 6xl8

Go back to Sodium Binding Sites List in 6xl8
Sodium binding site 2 out of 2 in the Crystal Structure of 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation


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 3-O-Sulfotransferase Isoform 3 in Complex with 8MER Oligosaccharide with No 6S Sulfation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:26.4
occ:1.00
 OG1 B:THR256 2.4 42.0 1.0
OD1 B:ASP252 2.4 32.7 1.0
O1S D:GNS2 2.6 42.0 1.0
O B:ASP252 2.6 34.0 1.0
O3 D:GNS2 2.6 43.5 1.0
O6A D:IDS3 3.0 46.2 1.0
C B:ASP252 3.6 33.2 1.0
CG B:ASP252 3.6 34.1 1.0
CB B:THR256 3.6 40.6 1.0
N B:THR256 3.6 34.4 1.0
S1 D:GNS2 3.6 42.6 1.0
NZ B:LYS161 3.7 34.6 1.0
N2 D:GNS2 3.9 39.3 1.0
C3 D:GNS2 3.9 42.4 1.0
C6 D:IDS3 4.0 45.5 1.0
CA B:THR256 4.1 36.5 1.0
O3S D:GNS2 4.1 39.5 1.0
CA B:ASP252 4.2 30.8 1.0
CB B:GLN255 4.2 32.3 1.0
CE B:LYS161 4.3 33.2 1.0
O B:HOH625 4.3 37.8 1.0
C2 D:GNS2 4.4 38.7 1.0
CG B:GLN255 4.4 33.8 1.0
CB B:ASP252 4.4 29.2 1.0
OD2 B:ASP252 4.4 35.0 1.0
O5 D:IDS3 4.4 39.5 1.0
C B:GLN255 4.6 35.5 1.0
N B:TYR253 4.6 31.5 1.0
CG2 B:THR256 4.8 40.6 1.0
O6B D:IDS3 4.8 40.0 1.0
O2S D:GNS2 4.8 45.2 1.0
C5 D:IDS3 4.8 42.1 1.0
CA B:TYR253 4.9 29.8 1.0
CA B:GLN255 4.9 29.4 1.0

Reference:

R.Wander, A.M.Kaminski, Y.Xu, V.Pagadala, J.M.Krahn, T.Q.Pham, J.Liu, L.C.Pedersen. Deciphering the Substrate Recognition Mechanisms of the Heparan Sulfate 3-O-Sulfotransferase-3 Rsc Chem Biol 2021.
ISSN: ESSN 2633-0679
DOI: 10.1039/D1CB00079A
Page generated: Mon Jul 12 15:50:05 2021

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