Sodium in PDB 8vh8: Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 2.85 A

The structure of Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 2.85 A, PDB code: 8vh8 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)	28.76 / 2.85
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	118.57, 118.57, 262.356, 90, 90, 90
R / Rfree (%)	19.8 / 22.3

The structure of Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 2.85 A also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Manganese	(Mn)	8 atoms
Chlorine	(Cl)	18 atoms

The binding sites of Sodium atom in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 2.85 A (pdb code 8vh8). 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 2.85 A, PDB code: 8vh8:
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 2.85 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 2.85 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:67.5 occ:1.00 O A:ALA178 2.5 66.8 1.0 O A:THR181 2.6 67.1 1.0 O A:VAL184 2.7 66.1 1.0 HA A:SER182 3.1 79.3 1.0 HG2 A:ARG185 3.5 78.2 1.0 C A:ALA178 3.6 66.7 1.0 HB1 A:ALA178 3.7 78.5 1.0 C A:THR181 3.7 67.0 1.0 C A:VAL184 3.9 65.1 1.0 CA A:SER182 3.9 66.1 1.0 HA A:ARG185 4.0 78.7 1.0 H A:VAL184 4.0 79.2 1.0 HA A:ALA178 4.1 78.2 1.0 HA A:ASN179 4.1 83.8 1.0 H A:THR181 4.2 83.6 1.0 N A:SER182 4.2 66.7 1.0 HG3 A:ARG185 4.2 78.2 1.0 CA A:ALA178 4.3 65.2 1.0 CG A:ARG185 4.3 65.2 1.0 CB A:ALA178 4.4 65.5 1.0 C A:SER182 4.4 66.2 1.0 O A:HOH804 4.6 66.8 1.0 N A:ASN179 4.6 69.2 1.0 O A:SER182 4.7 66.5 1.0 N A:VAL184 4.7 66.0 1.0 HB A:VAL184 4.7 77.8 1.0 CA A:ARG185 4.7 65.6 1.0 N A:ARG185 4.7 64.8 1.0 CA A:ASN179 4.8 69.8 1.0 N A:THR181 4.8 69.7 1.0 CA A:VAL184 4.8 64.6 1.0 CA A:THR181 4.9 67.9 1.0 HG23 A:THR181 4.9 80.1 1.0 HB3 A:ALA178 4.9 78.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 2.85 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 2.85 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na705 b:64.6 occ:1.00 O B:VAL184 2.5 61.3 1.0 O B:ALA178 2.6 71.9 1.0 O B:THR181 2.8 64.4 1.0 HA B:SER182 3.0 77.2 1.0 HG2 B:ARG185 3.5 72.5 1.0 C B:ALA178 3.7 70.9 1.0 C B:VAL184 3.7 60.9 1.0 HB1 B:ALA178 3.8 82.6 1.0 C B:THR181 3.8 65.3 1.0 CA B:SER182 3.8 64.3 1.0 H B:VAL184 3.9 75.0 1.0 HA B:ARG185 3.9 71.2 1.0 HA B:ALA178 4.2 83.6 1.0 HG3 B:ARG185 4.2 72.5 1.0 N B:SER182 4.2 64.3 1.0 H B:THR181 4.3 80.1 1.0 HA B:ASN179 4.3 85.9 1.0 CG B:ARG185 4.3 60.4 1.0 C B:SER182 4.3 63.7 1.0 CA B:ALA178 4.4 69.7 1.0 O B:SER182 4.5 63.9 1.0 CB B:ALA178 4.5 68.8 1.0 N B:VAL184 4.5 62.5 1.0 N B:ARG185 4.6 59.8 1.0 HB B:VAL184 4.6 73.8 1.0 CA B:ARG185 4.6 59.4 1.0 CA B:VAL184 4.7 60.5 1.0 N B:ASN179 4.7 69.8 1.0 CA B:ASN179 4.9 71.6 1.0 N B:THR181 4.9 66.8 1.0 HB2 B:SER182 5.0 78.8 1.0 CB B:SER182 5.0 65.7 1.0 CA B:THR181 5.0 65.8 1.0 HB3 B:ALA178 5.0 82.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 2.85 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 2.85 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na705 b:72.1 occ:1.00 HA C:SER182 2.5 83.7 1.0 O C:THR181 2.5 71.1 1.0 O C:VAL184 2.6 68.3 1.0 O C:ALA178 2.7 72.2 1.0 CA C:SER182 3.4 69.8 1.0 C C:THR181 3.5 71.3 1.0 HG2 C:ARG185 3.7 79.6 1.0 H C:VAL184 3.8 83.0 1.0 N C:SER182 3.8 68.5 1.0 C C:VAL184 3.8 67.8 1.0 HB1 C:ALA178 3.8 84.3 1.0 C C:ALA178 3.9 71.7 1.0 C C:SER182 3.9 69.2 1.0 O C:SER182 4.1 69.6 1.0 HA C:ALA178 4.2 83.8 1.0 HA C:ARG185 4.2 81.6 1.0 H C:THR181 4.4 86.9 1.0 N C:VAL184 4.4 69.1 1.0 HG3 C:ARG185 4.4 79.6 1.0 CA C:ALA178 4.5 69.9 1.0 CB C:SER182 4.5 71.1 1.0 CG C:ARG185 4.5 66.3 1.0 HB2 C:SER182 4.5 85.3 1.0 HA C:ASN179 4.6 88.8 1.0 CB C:ALA178 4.6 70.2 1.0 H C:SER182 4.6 82.2 1.0 HB C:VAL184 4.7 81.7 1.0 HB3 C:SER182 4.7 85.3 1.0 CA C:VAL184 4.7 68.1 1.0 N C:LYS183 4.7 69.7 1.0 N C:ARG185 4.8 69.2 1.0 CA C:THR181 4.8 71.4 1.0 HG23 C:THR181 4.9 83.2 1.0 CA C:ARG185 4.9 68.0 1.0 N C:ASN179 4.9 72.9 1.0 N C:THR181 5.0 72.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 2.85 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 2.85 A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na705 b:62.1 occ:1.00 HA D:SER182 2.5 72.6 1.0 O D:VAL184 2.6 60.9 1.0 O D:THR181 2.6 65.3 1.0 O D:ALA178 2.7 62.2 1.0 CA D:SER182 3.4 60.5 1.0 C D:THR181 3.6 64.6 1.0 HB1 D:ALA178 3.6 71.0 1.0 H D:VAL184 3.7 72.4 1.0 HG2 D:ARG185 3.7 70.9 1.0 C D:VAL184 3.8 59.2 1.0 C D:ALA178 3.8 60.7 1.0 N D:SER182 3.9 61.0 1.0 C D:SER182 3.9 59.7 1.0 O D:SER182 4.1 60.2 1.0 HA D:ALA178 4.1 70.9 1.0 HA D:ARG185 4.2 67.9 1.0 N D:VAL184 4.4 60.3 1.0 CA D:ALA178 4.4 59.1 1.0 HG3 D:ARG185 4.4 70.9 1.0 CB D:ALA178 4.4 59.2 1.0 H D:THR181 4.4 78.3 1.0 HA D:ASN179 4.4 77.8 1.0 HB2 D:SER182 4.5 75.7 1.0 CG D:ARG185 4.5 59.1 1.0 CB D:SER182 4.5 63.1 1.0 HB D:VAL184 4.6 70.5 1.0 CA D:VAL184 4.7 58.7 1.0 H D:SER182 4.7 73.2 1.0 N D:ARG185 4.7 57.7 1.0 HB3 D:SER182 4.7 75.7 1.0 N D:LYS183 4.8 59.6 1.0 N D:ASN179 4.8 62.6 1.0 CA D:ARG185 4.8 56.6 1.0 CA D:THR181 4.9 65.0 1.0 HB3 D:ALA178 4.9 71.0 1.0 HG23 D:THR181 5.0 75.1 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