Sodium in PDB 8vh7: Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A

The structure of Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A, PDB code: 8vh7 was solved by L.C.Pedersen, J.Liu, E.Stancanelli, J.M.Krahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.70 / 1.98
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.178, 163.177, 84.273, 90, 90, 90
R / Rfree (%)	20.8 / 24.9

The structure of Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A (pdb code 8vh7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A, PDB code: 8vh7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A


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 Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na707 b:27.2 occ:1.00 O A:HOH1123 2.2 45.4 1.0 NE2 A:HIS296 2.4 35.3 1.0 OD1 A:ASP292 2.4 26.4 1.0 O A:HOH1187 2.5 46.8 1.0 O A:HOH1182 2.7 49.5 1.0 O A:HOH976 2.8 43.5 1.0 CG A:ASP292 3.2 23.6 1.0 HZ A:PHE267 3.2 25.6 1.0 CD2 A:HIS296 3.2 32.1 1.0 OD2 A:ASP292 3.2 32.7 1.0 HD2 A:HIS296 3.2 38.5 1.0 CE1 A:HIS296 3.4 31.1 1.0 HE1 A:HIS296 3.7 37.4 1.0 CZ A:PHE267 4.0 21.3 1.0 O A:HOH1237 4.0 44.6 1.0 CG A:HIS296 4.4 35.4 1.0 ND1 A:HIS296 4.5 36.1 1.0 HE1 A:PHE267 4.6 26.2 1.0 CB A:ASP292 4.6 21.2 1.0 HZ A:PHE352 4.7 30.8 1.0 O A:HOH1156 4.7 47.4 1.0 CE1 A:PHE267 4.7 21.8 1.0 HE2 A:PHE267 4.7 27.1 1.0 HA A:ASP292 4.7 21.9 1.0 HD2 A:PHE295 4.8 27.3 1.0 CE2 A:PHE267 4.8 22.6 1.0 HE21 A:GLN353 4.9 57.5 1.0 O A:HOH1107 4.9 37.6 1.0 HB2 A:ASP292 4.9 25.5 1.0 O A:ASP292 5.0 17.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A


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 Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na708 b:44.0 occ:1.00 HD22 A:ASN388 2.2 29.8 1.0 O A:HOH1209 2.3 44.6 1.0 O A:LEU386 2.6 17.9 1.0 ND2 A:ASN388 3.0 24.9 1.0 HB2 A:ASN388 3.3 28.9 1.0 HD21 A:ASN388 3.4 29.8 1.0 O A:HOH957 3.5 50.0 1.0 C A:LEU386 3.7 21.5 1.0 O A:SER384 3.9 20.6 1.0 CG A:ASN388 4.0 25.8 1.0 CB A:ASN388 4.1 24.1 1.0 HB3 A:SER384 4.1 23.8 1.0 N A:LEU386 4.1 17.9 1.0 OG A:SER384 4.2 22.5 1.0 H A:LEU386 4.2 21.4 1.0 HA A:LYS385 4.2 22.6 1.0 O A:HOH964 4.3 34.3 1.0 HB2 A:LEU386 4.3 22.1 1.0 C A:LYS385 4.4 17.6 1.0 C A:SER384 4.4 18.8 1.0 O A:SER387 4.5 18.9 1.0 CA A:LEU386 4.5 21.1 1.0 C A:SER387 4.5 21.8 1.0 HA A:SER387 4.6 28.5 1.0 CB A:SER384 4.6 19.8 1.0 HB3 A:ASN388 4.7 28.9 1.0 CA A:LYS385 4.7 18.8 1.0 N A:ASN388 4.7 18.7 1.0 N A:SER387 4.7 19.3 1.0 O A:HOH1077 4.8 27.0 1.0 HA A:GLN381 4.8 37.0 1.0 N A:LYS385 4.8 19.9 1.0 HG A:SER384 4.8 27.0 1.0 CA A:SER387 4.9 23.7 1.0 O A:LYS385 4.9 19.0 1.0 CG A:GLN381 4.9 53.8 1.0 CB A:LEU386 4.9 18.4 1.0 H A:ASN388 5.0 22.5 1.0 O A:HOH933 5.0 38.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A


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 Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na709 b:58.5 occ:1.00 O A:HOH1232 2.7 61.6 1.0 O A:HOH1191 3.4 47.8 1.0 HB3 A:ASP168 3.5 31.9 1.0 HG A:SER167 3.5 47.6 1.0 OG A:SER167 3.6 39.6 1.0 HB3 A:ASN137 3.7 26.0 1.0 CG A:ASN137 4.0 24.6 1.0 ND2 A:ASN137 4.0 24.1 1.0 HD22 A:ASN137 4.2 28.9 1.0 HD21 A:ASN137 4.2 28.9 1.0 O A:HOH1184 4.2 50.7 1.0 OD1 A:ASN137 4.3 23.9 1.0 CB A:ASN137 4.3 21.7 1.0 H A:ASP168 4.4 24.6 1.0 CB A:ASP168 4.4 26.6 1.0 N A:ASP168 4.6 20.5 1.0 HB2 A:ASN137 4.9 26.0 1.0 CB A:SER167 4.9 29.1 1.0 HB2 A:ASP168 5.0 31.9 1.0 CA A:ASP168 5.0 28.0 1.0 HA A:ASP168 5.0 33.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A


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 Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na705 b:25.2 occ:1.00 O B:HOH1076 2.2 41.8 1.0 OD1 B:ASP292 2.4 30.4 1.0 NE2 B:HIS296 2.4 32.0 1.0 O B:HOH1164 2.5 41.0 1.0 O B:HOH1140 2.5 34.0 1.0 O B:HOH1068 2.6 32.9 1.0 OD2 B:ASP292 3.1 33.4 1.0 CG B:ASP292 3.1 23.0 1.0 HZ B:PHE267 3.1 30.0 1.0 CD2 B:HIS296 3.3 23.7 1.0 HD2 B:HIS296 3.4 28.4 1.0 CE1 B:HIS296 3.5 31.7 1.0 HE1 B:HIS296 3.6 38.0 1.0 O B:HOH1169 3.7 50.2 1.0 CZ B:PHE267 3.9 25.0 1.0 HE2 B:PHE267 4.5 29.3 1.0 CB B:ASP292 4.5 22.6 1.0 CG B:HIS296 4.5 29.5 1.0 ND1 B:HIS296 4.6 34.3 1.0 CE2 B:PHE267 4.6 24.4 1.0 HD2 B:PHE295 4.7 27.4 1.0 HE1 B:PHE267 4.7 30.6 1.0 HA B:ASP292 4.8 28.6 1.0 CE1 B:PHE267 4.8 25.5 1.0 HB2 B:ASP292 4.8 27.1 1.0 HZ B:PHE352 4.9 36.5 1.0 O B:HOH1168 4.9 50.2 1.0 O B:HOH1119 5.0 41.5 1.0

E.Stancanelli, J.A.Krahn, E.Viverette, R.Dutcher, V.Pagadala, M.J.Borgnia, J.Liu, L.C.Pedersen. Structural and Functional Analysis of Heparosan Synthase 2 From Pasteurella Multocida to Improve the Synthesis of Heparin Acs Catalysis V. 14 6577 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.4C00677