Atomistry » Sodium » PDB 5syl-5tcd » 5t0a
Atomistry »
  Sodium »
    PDB 5syl-5tcd »
      5t0a »

Sodium in PDB 5t0a: Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate

Protein crystallography data

The structure of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate, PDB code: 5t0a was solved by L.C.Pedersen, A.F.Moon, J.M.Krahn, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.84 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.775, 128.291, 178.929, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.3

Other elements in 5t0a:

The structure of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate (pdb code 5t0a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate, PDB code: 5t0a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5t0a

Go back to Sodium Binding Sites List in 5t0a
Sodium binding site 1 out of 6 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate


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 Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2026

b:53.1
occ:0.97
O3S A:GNS2003 2.3 44.1 1.0
O A:HOH2199 2.4 55.5 1.0
O1S A:IDS2004 2.7 50.4 1.0
S1 A:GNS2003 3.5 49.1 1.0
O2S A:GNS2003 3.7 40.7 1.0
S A:IDS2004 3.9 55.5 1.0
O3S A:IDS2004 3.9 51.0 1.0
O A:HOH2313 4.1 43.6 1.0
O1S A:GNS2003 4.3 46.4 1.0
O2 A:IDS2004 4.5 50.3 1.0
N A:GNS2003 4.6 45.7 1.0
NZ A:LYS1132 4.6 44.0 1.0
CD A:LYS1132 4.8 42.1 1.0

Sodium binding site 2 out of 6 in 5t0a

Go back to Sodium Binding Sites List in 5t0a
Sodium binding site 2 out of 6 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate


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 Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2027

b:41.6
occ:0.91
O A:ASN1232 2.3 44.5 1.0
O A:HOH2552 2.3 53.5 1.0
O A:ASP1235 2.3 31.6 1.0
O A:HOH2548 2.3 47.6 1.0
O A:HOH2440 2.7 45.4 1.0
C A:ASP1235 3.5 29.0 1.0
C A:ASN1232 3.5 48.1 1.0
O A:HOH2622 4.0 46.2 1.0
N A:ASP1235 4.1 30.6 1.0
CB A:TYR1231 4.3 26.9 1.0
CA A:GLY1233 4.3 44.0 1.0
N A:ASN1232 4.3 42.6 1.0
OD1 A:ASP1235 4.4 28.8 1.0
N A:GLY1233 4.4 45.0 1.0
CA A:TRP1236 4.4 28.6 1.0
N A:TRP1236 4.4 26.9 1.0
CA A:ASP1235 4.5 26.1 1.0
CA A:ASN1232 4.5 47.2 1.0
C A:GLY1233 4.5 38.7 1.0
N A:ASP1234 4.6 38.5 1.0
CD1 A:TYR1231 4.7 31.2 1.0
CG A:TYR1231 4.9 31.4 1.0
C A:TYR1231 5.0 33.9 1.0
CB A:ASN1232 5.0 49.1 1.0

Sodium binding site 3 out of 6 in 5t0a

Go back to Sodium Binding Sites List in 5t0a
Sodium binding site 3 out of 6 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2028

b:48.8
occ:0.95
O4 A:TLA2025 2.4 48.3 0.7
O6B A:BDP2002 2.8 27.5 1.0
O A:HOH2516 3.4 34.9 1.0
C4 A:TLA2025 3.4 41.1 0.7
C5 A:BDP2002 3.7 27.4 1.0
C6 A:BDP2002 3.7 35.5 1.0
O41 A:TLA2025 3.7 48.6 0.7
O4 A:BDP2002 3.7 28.1 1.0
O A:HOH2513 3.7 38.4 1.0
C3 A:GNS2001 4.1 33.5 1.0
O4 A:GNS2001 4.3 36.7 1.0
C4 A:BDP2002 4.3 26.3 1.0
C4 A:GNS2001 4.6 30.4 1.0
C5 A:GNS2001 4.6 26.0 1.0
C3 A:TLA2025 4.7 36.5 0.7
O5 A:BDP2002 4.7 34.9 1.0
O3 A:GNS2001 4.8 25.6 1.0
NH2 A:ARG1148 4.8 30.0 1.0
C1 A:GNS2001 4.9 26.3 1.0
O6A A:BDP2002 4.9 26.2 1.0
O3 A:TLA2025 4.9 38.6 0.7
C2 A:GNS2001 4.9 32.8 1.0
O6 A:GNS2003 5.0 41.5 1.0

Sodium binding site 4 out of 6 in 5t0a

Go back to Sodium Binding Sites List in 5t0a
Sodium binding site 4 out of 6 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2029

b:55.0
occ:0.94
O A:ALA1331 2.4 32.7 1.0
O A:HOH2518 2.9 40.9 1.0
O A:VAL1333 3.0 41.5 1.0
C A:ALA1331 3.4 34.9 1.0
CA A:ALA1331 4.1 30.9 1.0
C A:VAL1333 4.1 38.9 1.0
N A:VAL1333 4.4 30.8 1.0
N A:ASN1332 4.5 31.9 1.0
O A:ALA1330 4.5 23.9 1.0
C A:ASN1332 4.7 39.3 1.0
O A:HOH2160 4.7 50.4 1.0
CA A:ASN1332 4.8 33.4 1.0
CA A:VAL1333 4.9 34.7 1.0
O A:HOH2519 4.9 39.7 1.0
N A:GLU1334 4.9 41.2 1.0
CB A:ALA1331 4.9 31.8 1.0
CA A:GLU1334 5.0 38.3 1.0

Sodium binding site 5 out of 6 in 5t0a

Go back to Sodium Binding Sites List in 5t0a
Sodium binding site 5 out of 6 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1419

b:37.0
occ:0.77
O B:HOH1915 2.2 38.3 1.0
O B:ASP1235 2.3 25.2 1.0
O B:HOH1918 2.4 39.0 1.0
O B:ASN1232 2.4 35.2 1.0
O B:HOH1877 2.6 43.2 1.0
O B:HOH1715 2.8 39.9 1.0
C B:ASP1235 3.5 24.5 1.0
C B:ASN1232 3.6 36.3 1.0
O B:HOH1678 3.8 33.3 1.0
OD1 B:ASP1235 4.1 26.3 1.0
N B:ASP1235 4.2 28.1 1.0
N B:TRP1236 4.3 23.0 1.0
CA B:TRP1236 4.3 25.5 1.0
N B:ASN1232 4.4 36.7 1.0
CA B:ASP1235 4.4 24.2 1.0
CB B:TYR1231 4.4 23.6 1.0
CA B:ASN1232 4.5 42.6 1.0
N B:GLY1233 4.6 38.3 1.0
CA B:GLY1233 4.6 39.6 1.0
O B:HOH1862 4.7 50.5 1.0
CD2 B:TYR1231 4.8 27.7 1.0
N B:SER1237 4.8 24.8 0.5
C B:GLY1233 4.8 37.4 1.0
O B:HOH1641 4.8 36.7 1.0
N B:SER1237 4.8 24.8 0.6
N B:ASP1234 4.8 30.8 1.0
C B:TRP1236 4.9 23.8 1.0

Sodium binding site 6 out of 6 in 5t0a

Go back to Sodium Binding Sites List in 5t0a
Sodium binding site 6 out of 6 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and Heptasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1420

b:53.2
occ:0.83
O B:HOH1577 2.4 54.8 1.0
O B:GLN325 2.4 35.8 1.0
O B:HOH1891 2.5 52.2 1.0
O B:GLY327 2.5 39.7 1.0
O B:HOH1908 3.0 47.1 1.0
C B:GLN325 3.5 41.2 1.0
C B:GLY327 3.7 46.5 1.0
OE1 B:GLU328 3.8 64.2 1.0
O B:ALA324 4.1 41.5 1.0
CA B:GLN325 4.1 42.8 1.0
N B:GLY327 4.3 35.8 1.0
C B:LYS326 4.3 41.8 1.0
N B:LYS326 4.5 34.9 1.0
O B:LYS326 4.5 37.0 1.0
CA B:GLY327 4.6 36.6 1.0
N B:GLU328 4.6 35.0 1.0
CA B:GLU328 4.7 47.0 1.0
CA B:LYS326 4.7 38.9 1.0
CD B:GLU328 4.9 61.3 1.0
C B:ALA324 5.0 38.0 1.0

Reference:

Y.Xu, A.F.Moon, S.Xu, J.M.Krahn, J.Liu, L.C.Pedersen. Structure Based Substrate Specificity Analysis of Heparan Sulfate 6-O-Sulfotransferases. Acs Chem. Biol. V. 12 73 2017.
ISSN: ESSN 1554-8937
PubMed: 28103688
DOI: 10.1021/ACSCHEMBIO.6B00841
Page generated: Tue Dec 15 11:34:58 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