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Sodium in PDB 5t05: Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate

Protein crystallography data

The structure of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate, PDB code: 5t05 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) 38.49 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.785, 128.161, 178.711, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.2

Other elements in 5t05:

The structure of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate (pdb code 5t05). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate, PDB code: 5t05:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5t05

Go back to Sodium Binding Sites List in 5t05
Sodium binding site 1 out of 7 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1425

b:48.0
occ:1.00
 O A:ASP1235 2.3 29.7 1.0
O A:HOH1990 2.4 47.2 1.0
O A:HOH1954 2.4 48.2 1.0
O A:ASN1232 2.4 43.0 1.0
O A:HOH1883 2.7 47.7 1.0
O A:HOH1920 3.0 45.7 1.0
C A:ASP1235 3.5 29.4 1.0
C A:ASN1232 3.6 45.4 1.0
O A:HOH1940 4.1 44.6 1.0
N A:ASP1235 4.3 30.2 1.0
CB A:TYR1231 4.3 27.5 1.0
CA A:TRP1236 4.3 25.5 1.0
N A:TRP1236 4.4 25.3 1.0
OD1 A:ASP1235 4.4 28.7 1.0
N A:ASN1232 4.4 41.4 1.0
CA A:GLY1233 4.5 41.2 1.0
N A:GLY1233 4.5 43.6 1.0
CA A:ASP1235 4.5 26.8 1.0
CA A:ASN1232 4.6 47.1 1.0
C A:GLY1233 4.7 36.7 1.0
CD1 A:TYR1231 4.8 30.2 1.0
N A:ASP1234 4.8 38.1 1.0
CG A:TYR1231 5.0 30.6 1.0
N A:SER1237 5.0 28.8 1.0
C A:TYR1231 5.0 35.4 1.0

Sodium binding site 2 out of 7 in 5t05

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Sodium binding site 2 out of 7 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1426

b:50.6
occ:1.00
 O A:HOH1923 2.3 51.1 1.0
O A:HOH1850 2.3 53.8 1.0
O3S A:GNS1404 2.4 37.2 1.0
O1S A:IDS1405 2.4 41.3 1.0
O A:HOH1964 2.9 50.3 1.0
S1 A:GNS1404 3.5 38.4 1.0
S A:IDS1405 3.6 44.1 1.0
O2S A:GNS1404 3.7 34.6 1.0
O3S A:IDS1405 3.7 41.9 1.0
O2 A:IDS1405 4.2 38.6 1.0
O A:HOH1699 4.4 36.7 1.0
O1S A:GNS1404 4.4 39.0 1.0
N A:GNS1404 4.5 32.3 1.0
NZ A:LYS1132 4.6 38.5 1.0
O2S A:IDS1405 4.7 45.7 1.0
CD A:LYS1132 4.9 35.1 1.0
C2 A:IDS1405 5.0 35.8 1.0

Sodium binding site 3 out of 7 in 5t05

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Sodium binding site 3 out of 7 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1427

b:36.1
occ:0.67
 O11 A:TLA1430 2.1 31.1 0.7
O A:HOH1811 2.6 35.8 1.0
C1 A:TLA1430 3.2 33.5 0.7
NZ A:LYS1104 3.4 19.8 1.0
O2 A:EDO1420 3.4 30.4 1.0
O A:HOH1715 3.5 21.9 1.0
NH2 A:ARG1206 3.5 23.8 1.0
CE1 A:HIS1203 3.6 25.9 1.0
C3 A:TLA1430 3.7 26.3 0.7
C2 A:TLA1430 3.7 39.3 0.7
O A:HOH1786 3.8 29.9 1.0
ND1 A:HIS1203 4.0 20.9 1.0
NE2 A:HIS1203 4.1 21.9 1.0
O1 A:TLA1430 4.3 31.5 0.7
O4 A:GNS1402 4.3 24.5 1.0
O4P A:A3P1401 4.3 19.6 1.0
O3 A:TLA1430 4.5 27.3 0.7
O41 A:TLA1430 4.7 38.0 0.7
C4 A:TLA1430 4.7 34.1 0.7
CZ A:ARG1206 4.8 26.5 1.0
C2 A:EDO1420 4.8 39.8 1.0
CG A:HIS1203 4.8 23.7 1.0
CE A:LYS1104 4.8 19.9 1.0
CD2 A:HIS1203 4.9 23.8 1.0

Sodium binding site 4 out of 7 in 5t05

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Sodium binding site 4 out of 7 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1428

b:35.2
occ:0.71
 O4 A:TLA1430 2.3 34.9 0.7
O6B A:BDP1403 2.7 25.0 1.0
C4 A:TLA1430 3.2 34.1 0.7
O41 A:TLA1430 3.5 38.0 0.7
O A:HOH1877 3.5 30.9 1.0
C6 A:BDP1403 3.6 30.4 1.0
C5 A:BDP1403 3.7 25.2 1.0
O4 A:BDP1403 3.8 23.5 1.0
O A:HOH1896 3.9 29.7 1.0
O A:HOH1925 4.1 46.4 1.0
C3 A:GNS1402 4.2 28.0 1.0
O4 A:GNS1402 4.4 24.5 1.0
C4 A:BDP1403 4.4 24.6 1.0
C3 A:TLA1430 4.5 26.3 0.7
C5 A:GNS1402 4.6 22.7 1.0
C4 A:GNS1402 4.6 25.2 1.0
NH2 A:ARG1148 4.6 25.5 1.0
O3 A:TLA1430 4.7 27.3 0.7
O6A A:BDP1403 4.8 24.4 1.0
O5 A:BDP1403 4.8 28.5 1.0
O3 A:GNS1402 4.9 22.5 1.0
C1 A:GNS1402 4.9 23.0 1.0

Sodium binding site 5 out of 7 in 5t05

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Sodium binding site 5 out of 7 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1429

b:43.5
occ:0.76
 O A:ALA1331 2.2 31.6 1.0
O A:HOH1935 2.4 43.4 0.8
O A:HOH1928 2.8 40.2 1.0
O A:VAL1333 2.9 41.9 1.0
C A:ALA1331 3.1 35.6 1.0
CA A:ALA1331 3.8 29.2 1.0
C A:VAL1333 3.9 38.1 1.0
N A:ASN1332 4.2 31.3 1.0
O A:ALA1330 4.2 26.1 1.0
N A:VAL1333 4.3 31.8 1.0
C A:ASN1332 4.4 43.0 1.0
CA A:ASN1332 4.5 33.5 1.0
CA A:VAL1333 4.7 33.5 1.0
CB A:ALA1331 4.8 28.3 1.0
N A:GLU1334 4.8 42.2 1.0
CA A:GLU1334 4.9 37.1 1.0
N A:ALA1331 4.9 25.7 1.0
O A:ASN1332 4.9 38.2 1.0
O A:HOH1947 5.0 36.4 1.0

Sodium binding site 6 out of 7 in 5t05

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Sodium binding site 6 out of 7 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide 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 IDOA2S Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1420

b:44.1
occ:1.00
 O B:HOH1941 2.3 36.0 1.0
O B:ASP1235 2.4 25.4 1.0
O B:HOH1942 2.4 40.7 1.0
O B:ASN1232 2.4 33.9 1.0
O B:HOH1881 2.6 38.3 1.0
O B:HOH1772 3.0 39.6 1.0
C B:ASP1235 3.5 24.1 1.0
C B:ASN1232 3.6 36.8 1.0
O B:HOH1744 3.9 33.2 1.0
OD1 B:ASP1235 4.2 26.4 1.0
N B:ASP1235 4.2 26.4 1.0
CA B:TRP1236 4.4 24.0 1.0
N B:TRP1236 4.4 22.7 1.0
N B:ASN1232 4.4 36.4 1.0
CA B:ASP1235 4.5 24.4 1.0
CB B:TYR1231 4.5 25.1 1.0
CA B:GLY1233 4.5 41.1 1.0
N B:GLY1233 4.5 43.1 1.0
CA B:ASN1232 4.6 42.7 1.0
C B:GLY1233 4.7 36.5 1.0
N B:ASP1234 4.8 32.8 1.0
CD2 B:TYR1231 4.8 29.0 1.0
O B:HOH1572 4.8 34.9 1.0
N B:SER1237 4.8 24.2 0.5
N B:SER1237 4.9 24.1 0.5
C B:TRP1236 4.9 22.9 1.0

Sodium binding site 7 out of 7 in 5t05

Go back to Sodium Binding Sites List in 5t05
Sodium binding site 7 out of 7 in the Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with Bound Pap and IDOA2S Containing Hexasaccharide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1421

b:53.9
occ:0.86
 O B:GLY327 2.3 38.9 1.0
O B:HOH1874 2.3 47.2 1.0
O B:HOH1940 2.4 49.4 0.8
O B:GLN325 2.4 37.3 1.0
C B:GLN325 3.4 39.4 1.0
C B:GLY327 3.5 42.8 1.0
O B:HOH1915 3.5 47.3 1.0
O B:ALA324 3.8 38.7 1.0
CA B:GLN325 4.0 44.0 1.0
N B:GLY327 4.1 35.8 1.0
C B:LYS326 4.2 39.3 1.0
N B:LYS326 4.3 35.7 1.0
N B:GLU328 4.4 36.7 1.0
CA B:GLY327 4.4 34.0 1.0
CA B:GLU328 4.4 43.3 1.0
O B:LYS326 4.5 34.9 1.0
CA B:LYS326 4.7 38.7 1.0
C B:ALA324 4.8 38.6 1.0
N B:GLN325 4.9 38.1 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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