Manganese 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:

Sodium

(Na)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Heparosan Synthase 2 From Pasteurella Multocida at 1.98 A, PDB code: 8vh7:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn701 b:31.1 occ:1.00 O1B A:UDP702 2.0 33.5 1.0 O A:HOH857 2.1 26.2 1.0 O2A A:UDP702 2.1 31.7 1.0 OD2 A:ASP481 2.2 25.0 1.0 O A:HOH993 2.4 34.6 1.0 O A:HOH1132 2.5 36.8 1.0 CG A:ASP481 3.1 28.9 1.0 PB A:UDP702 3.2 36.4 1.0 OD1 A:ASP481 3.3 28.0 1.0 PA A:UDP702 3.3 34.9 1.0 H12 A:EDO705 3.4 53.5 1.0 H11 A:EDO705 3.5 53.5 1.0 O3A A:UDP702 3.5 31.0 1.0 HH12 A:ARG403 3.6 38.3 1.0 O3B A:UDP702 3.7 45.0 1.0 HH22 A:ARG403 3.8 42.6 1.0 C1 A:EDO705 4.0 44.6 1.0 H5'1 A:UDP702 4.0 34.7 1.0 O A:HOH1109 4.2 36.5 1.0 O1A A:UDP702 4.2 37.4 1.0 NH1 A:ARG403 4.3 31.9 1.0 HO1 A:EDO705 4.3 63.0 1.0 OD2 A:ASP479 4.4 36.6 1.0 NH2 A:ARG403 4.4 35.5 1.0 O5' A:UDP702 4.4 33.6 1.0 O2B A:UDP702 4.5 35.7 1.0 CB A:ASP481 4.5 31.3 1.0 HB3 A:ASP479 4.5 30.6 1.0 H3' A:UDP702 4.6 36.0 1.0 HB3 A:ASP481 4.7 37.6 1.0 O A:HOH1170 4.7 47.9 1.0 O1 A:EDO705 4.7 52.5 1.0 HB2 A:ASP481 4.7 37.6 1.0 C5' A:UDP702 4.8 28.9 1.0 CZ A:ARG403 4.8 37.1 1.0 HH11 A:ARG403 4.8 38.3 1.0 O A:HOH810 5.0 52.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn703 b:22.1 occ:1.00 O3B A:UDP704 2.1 20.5 1.0 O2A A:UDP704 2.1 22.8 1.0 O A:HOH832 2.2 23.8 1.0 O A:HOH821 2.3 17.1 1.0 OD2 A:ASP217 2.3 17.1 1.0 OD1 A:ASP217 2.6 20.1 1.0 CG A:ASP217 2.8 23.1 1.0 PB A:UDP704 3.2 22.1 1.0 PA A:UDP704 3.2 20.5 1.0 O3A A:UDP704 3.3 17.9 1.0 HH21 A:ARG320 3.5 33.6 1.0 HH12 A:ARG247 3.6 27.5 1.0 H5'1 A:UDP704 3.6 23.6 1.0 HE A:ARG320 3.7 32.2 1.0 OD1 A:ASP218 3.8 19.4 1.0 OD2 A:ASP218 4.0 21.9 1.0 H3' A:UDP704 4.0 22.9 1.0 O1B A:UDP704 4.0 21.1 1.0 HB3 A:ASP215 4.2 22.2 1.0 HB2 A:SER323 4.2 25.9 1.0 O1A A:UDP704 4.3 20.9 1.0 CG A:ASP218 4.3 18.4 1.0 CB A:ASP217 4.3 17.2 1.0 OD1 A:ASN317 4.3 28.3 1.0 HB2 A:ASP215 4.3 22.2 1.0 NH1 A:ARG247 4.3 22.9 1.0 O2B A:UDP704 4.3 20.5 1.0 O A:THR318 4.3 21.7 1.0 NH2 A:ARG320 4.4 28.0 1.0 O5' A:UDP704 4.4 24.2 1.0 OD2 A:ASP215 4.4 20.0 1.0 C5' A:UDP704 4.5 19.6 1.0 NE A:ARG320 4.5 26.8 1.0 HH11 A:ARG247 4.6 27.5 1.0 HB2 A:ASP217 4.6 20.7 1.0 CB A:ASP215 4.6 18.5 1.0 HB3 A:ASP217 4.7 20.7 1.0 H A:ASP217 4.7 20.7 1.0 O A:HOH880 4.8 30.1 1.0 HG A:SER323 4.8 31.4 1.0 HB A:THR318 4.8 32.6 1.0 HH22 A:ARG247 4.8 27.9 1.0 H A:THR318 4.8 24.8 1.0 HG2 A:ARG320 4.9 29.9 1.0 CZ A:ARG320 5.0 30.4 1.0 HH22 A:ARG320 5.0 33.6 1.0 CB A:SER323 5.0 21.6 1.0 CG A:ASP215 5.0 25.7 1.0

Manganese 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 Manganese with other atoms in the Mn 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 B:Mn701 b:32.0 occ:1.00 O1B B:UDP702 2.1 30.8 1.0 OD2 B:ASP481 2.1 29.5 1.0 O B:HOH860 2.1 25.3 1.0 O2A B:UDP702 2.2 29.3 1.0 O B:HOH992 2.3 37.4 1.0 O B:HOH1092 2.4 32.5 1.0 CG B:ASP481 3.1 29.1 1.0 PB B:UDP702 3.2 38.2 1.0 PA B:UDP702 3.3 31.4 1.0 OD1 B:ASP481 3.3 28.4 1.0 HO2 B:EDO711 3.5 58.9 1.0 O3A B:UDP702 3.5 30.9 1.0 HH12 B:ARG403 3.5 41.6 1.0 O3B B:UDP702 3.7 43.9 1.0 HH22 B:ARG403 3.8 39.0 1.0 O B:HOH1097 4.0 36.3 1.0 H5'1 B:UDP702 4.0 39.0 1.0 O1A B:UDP702 4.2 32.9 1.0 O2 B:EDO711 4.2 49.0 1.0 NH1 B:ARG403 4.2 34.6 1.0 OD1 B:ASN597 4.3 61.2 1.0 H21 B:EDO711 4.4 41.6 1.0 OD2 B:ASP479 4.4 32.5 1.0 NH2 B:ARG403 4.4 32.5 1.0 CB B:ASP481 4.4 31.8 1.0 O5' B:UDP702 4.5 31.9 1.0 O2B B:UDP702 4.5 41.4 1.0 HB3 B:ASP479 4.5 29.2 1.0 HD21 B:ASN597 4.6 75.9 1.0 HB3 B:ASP481 4.7 38.2 1.0 HB2 B:ASP481 4.7 38.2 1.0 H3' B:UDP702 4.7 35.8 1.0 CZ B:ARG403 4.8 37.5 1.0 HH11 B:ARG403 4.8 41.6 1.0 C5' B:UDP702 4.8 32.5 1.0 C2 B:EDO711 4.8 34.7 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn703 b:22.9 occ:1.00 O3B B:UDP704 2.1 24.6 1.0 O B:HOH847 2.2 19.7 1.0 O2A B:UDP704 2.2 20.1 1.0 OD2 B:ASP217 2.3 20.4 1.0 O B:HOH815 2.4 18.1 1.0 OD1 B:ASP217 2.5 20.9 1.0 CG B:ASP217 2.7 21.7 1.0 PA B:UDP704 3.3 22.2 1.0 O3A B:UDP704 3.3 21.6 1.0 PB B:UDP704 3.3 21.4 1.0 HH21 B:ARG320 3.6 28.4 1.0 HH12 B:ARG247 3.6 32.5 1.0 HE B:ARG320 3.6 33.4 1.0 H5'1 B:UDP704 3.6 20.0 1.0 OD1 B:ASP218 3.8 23.3 1.0 OD2 B:ASP218 4.0 19.1 1.0 H3' B:UDP704 4.0 24.1 1.0 HB3 B:ASP215 4.1 19.9 1.0 O1B B:UDP704 4.2 24.8 1.0 HB2 B:ASP215 4.2 19.9 1.0 CG B:ASP218 4.2 22.4 1.0 CB B:ASP217 4.2 21.1 1.0 O B:THR318 4.3 24.5 1.0 HB2 B:SER323 4.3 32.8 1.0 O1A B:UDP704 4.3 22.7 1.0 O2B B:UDP704 4.3 22.2 1.0 OD1 B:ASN317 4.3 29.6 1.0 NH1 B:ARG247 4.3 27.1 1.0 O5' B:UDP704 4.4 19.3 1.0 OD2 B:ASP215 4.4 20.5 1.0 NH2 B:ARG320 4.4 23.7 1.0 NE B:ARG320 4.4 27.9 1.0 C5' B:UDP704 4.5 16.7 1.0 CB B:ASP215 4.6 16.6 1.0 HB2 B:ASP217 4.6 25.3 1.0 HB3 B:ASP217 4.6 25.3 1.0 HH11 B:ARG247 4.6 32.5 1.0 H B:ASP217 4.6 22.6 1.0 HG B:SER323 4.7 33.0 1.0 HB B:THR318 4.7 35.2 1.0 HH22 B:ARG247 4.8 30.6 1.0 O B:HOH876 4.9 31.5 1.0 HG2 B:ARG320 4.9 35.5 1.0 H B:THR318 4.9 27.0 1.0 CG B:ASP215 4.9 23.9 1.0 CZ B:ARG320 5.0 35.0 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