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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

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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

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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

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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: Mon Oct 7 23:59:37 2024

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