Sodium in PDB 8q8h: Crystal Structure of Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2)

All present enzymatic activity of Crystal Structure of Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2):
3.2.1.53;

The structure of Crystal Structure of Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2), PDB code: 8q8h was solved by J.P.Morth, E.S.Moreno Prieto, S.Siebenhaar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.29 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	173.64, 195.57, 82.04, 90, 90, 90
R / Rfree (%)	18.8 / 23.2

The binding sites of Sodium atom in the Crystal Structure of Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2) (pdb code 8q8h). 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 Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2), PDB code: 8q8h:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2)


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 Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:73.9 occ:1.00 O A:HOH725 1.9 74.8 1.0 NE2 A:HIS272 2.1 78.8 1.0 OD1 A:ASP338 2.2 90.8 1.0 OD1 A:ASP366 2.3 85.3 1.0 CD2 A:HIS272 3.0 78.3 1.0 CG A:ASP338 3.0 95.9 1.0 HD2 A:HIS272 3.0 93.9 1.0 HD1 A:HIS335 3.1 88.1 1.0 CE1 A:HIS272 3.2 74.6 1.0 H A:ALA367 3.3 110.1 1.0 HA A:ASP366 3.3 110.1 1.0 CG A:ASP366 3.4 88.8 1.0 ND1 A:HIS335 3.4 73.4 1.0 OD2 A:ASP338 3.4 93.2 1.0 HE1 A:HIS272 3.5 89.5 1.0 HB3 A:HIS335 3.6 87.1 1.0 HA A:ASP338 3.6 122.5 1.0 HH2 A:TRP179 3.9 76.0 1.0 CG A:HIS335 4.1 70.4 1.0 CE1 A:HIS335 4.1 71.2 1.0 HB3 A:ASP366 4.1 112.2 1.0 CB A:ASP338 4.1 101.9 1.0 C A:SER337 4.1 95.0 1.0 N A:ASP338 4.1 98.5 1.0 CB A:ASP366 4.1 93.5 1.0 CA A:ASP366 4.1 91.7 1.0 CA A:ASP338 4.1 102.1 1.0 HZ2 A:TRP179 4.1 76.8 1.0 N A:ALA367 4.1 91.8 1.0 CG A:HIS272 4.2 72.9 1.0 HE1 A:HIS335 4.2 85.5 1.0 ND1 A:HIS272 4.3 72.7 1.0 O A:SER337 4.3 98.8 1.0 CB A:HIS335 4.3 72.5 1.0 HB3 A:ALA367 4.4 112.3 1.0 HA A:SER337 4.4 108.0 1.0 OD2 A:ASP366 4.4 89.4 1.0 HB2 A:ASP338 4.5 122.3 1.0 H A:ASP338 4.5 118.2 1.0 CH2 A:TRP179 4.6 63.3 1.0 O A:MET365 4.6 80.9 1.0 HB2 A:ALA367 4.6 112.3 1.0 H A:LEU336 4.7 94.0 1.0 CA A:SER337 4.7 90.0 1.0 CZ2 A:TRP179 4.7 64.0 1.0 C A:ASP366 4.7 92.4 1.0 H A:SER337 4.8 102.4 1.0 HB3 A:ASP338 4.8 122.3 1.0 N A:SER337 4.8 85.3 1.0 HD12 A:ILE383 4.9 89.2 1.0 CB A:ALA367 4.9 93.6 1.0 NE2 A:HIS335 4.9 65.7 1.0 CD2 A:HIS335 4.9 67.8 1.0 HA A:HIS335 4.9 86.7 1.0 HB2 A:HIS335 5.0 87.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2)


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 Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:66.3 occ:1.00 O B:HOH734 2.1 69.2 1.0 NE2 B:HIS272 2.2 70.5 1.0 OD1 B:ASP366 2.2 72.9 1.0 OD1 B:ASP338 2.2 92.4 1.0 HD1 B:HIS335 2.8 80.1 1.0 HA B:ASP366 3.0 98.1 1.0 CD2 B:HIS272 3.0 66.5 1.0 HD2 B:HIS272 3.1 79.8 1.0 CG B:ASP338 3.2 101.3 1.0 HB3 B:HIS335 3.2 74.9 1.0 CG B:ASP366 3.2 76.9 1.0 CE1 B:HIS272 3.2 67.5 1.0 H B:ALA367 3.3 102.9 1.0 ND1 B:HIS335 3.3 66.8 1.0 HE1 B:HIS272 3.5 81.0 1.0 HB3 B:ASP366 3.6 97.6 1.0 OD2 B:ASP338 3.7 96.2 1.0 HA B:ASP338 3.7 117.4 1.0 CA B:ASP366 3.7 81.8 1.0 CB B:ASP366 3.7 81.3 1.0 CG B:HIS335 3.9 63.8 1.0 C B:SER337 4.0 81.6 1.0 O B:SER337 4.0 82.5 1.0 CB B:HIS335 4.0 62.4 1.0 N B:ALA367 4.0 85.8 1.0 CE1 B:HIS335 4.1 65.6 1.0 N B:ASP338 4.1 99.3 1.0 HH2 B:TRP179 4.2 68.7 1.0 CA B:ASP338 4.2 97.8 1.0 O B:MET365 4.2 75.5 1.0 CG B:HIS272 4.2 61.6 1.0 CB B:ASP338 4.3 101.5 1.0 OD2 B:ASP366 4.3 75.8 1.0 ND1 B:HIS272 4.3 62.7 1.0 HE1 B:HIS335 4.3 78.7 1.0 HZ2 B:TRP179 4.3 68.8 1.0 HA B:SER337 4.3 91.7 1.0 C B:ASP366 4.5 84.1 1.0 H B:LEU336 4.5 79.7 1.0 H B:ASP338 4.5 119.1 1.0 HB3 B:ALA367 4.6 104.8 1.0 CA B:SER337 4.6 76.4 1.0 H B:SER337 4.6 86.8 1.0 N B:SER337 4.6 72.3 1.0 HB2 B:HIS335 4.6 74.9 1.0 HA B:HIS335 4.7 76.2 1.0 HB2 B:ASP366 4.7 97.6 1.0 HB2 B:ASP338 4.8 121.8 1.0 HB2 B:ALA367 4.8 104.8 1.0 N B:ASP366 4.8 78.8 1.0 CH2 B:TRP179 4.8 57.2 1.0 CZ2 B:TRP179 4.9 57.3 1.0 CA B:HIS335 4.9 63.5 1.0 CD2 B:HIS335 4.9 61.5 1.0 HD12 B:ILE383 4.9 85.3 1.0 HB3 B:ASP338 4.9 121.8 1.0 C B:MET365 5.0 79.5 1.0 N B:LEU336 5.0 66.4 1.0 NE2 B:HIS335 5.0 60.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2)


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 Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na605 b:52.9 occ:1.00 NE2 C:HIS272 2.2 61.1 1.0 OD1 C:ASP338 2.2 61.9 1.0 O C:HOH729 2.3 51.3 1.0 HD1 C:HIS335 2.4 71.9 1.0 OD1 C:ASP366 2.4 65.5 1.0 CG C:ASP338 2.9 66.1 1.0 ND1 C:HIS335 3.0 60.0 1.0 CD2 C:HIS272 3.0 59.5 1.0 HD2 C:HIS272 3.1 71.3 1.0 HA C:ASP366 3.1 83.2 1.0 CE1 C:HIS272 3.2 55.8 1.0 OD2 C:ASP338 3.3 67.2 1.0 HB3 C:HIS335 3.3 66.6 1.0 H C:ALA367 3.4 82.8 1.0 HE1 C:HIS272 3.5 66.9 1.0 CG C:ASP366 3.5 68.6 1.0 CE1 C:HIS335 3.7 57.4 1.0 CG C:HIS335 3.8 56.2 1.0 HA C:ASP338 3.8 82.6 1.0 HE1 C:HIS335 3.9 68.9 1.0 HB3 C:ASP366 3.9 83.7 1.0 HH2 C:TRP179 3.9 61.6 1.0 CA C:ASP366 3.9 69.3 1.0 CB C:ASP366 4.0 69.7 1.0 CB C:HIS335 4.0 55.5 1.0 CB C:ASP338 4.1 68.8 1.0 O C:MET365 4.2 61.7 1.0 HZ2 C:TRP179 4.2 62.4 1.0 N C:ASP338 4.2 68.1 1.0 N C:ALA367 4.2 69.0 1.0 C C:SER337 4.2 67.4 1.0 CG C:HIS272 4.2 55.5 1.0 CA C:ASP338 4.2 68.8 1.0 ND1 C:HIS272 4.3 56.0 1.0 HA C:SER337 4.4 79.0 1.0 O C:SER337 4.4 69.4 1.0 H C:ASP338 4.5 81.8 1.0 HB2 C:ASP338 4.6 82.5 1.0 HA C:HIS335 4.6 65.3 1.0 CH2 C:TRP179 4.6 51.4 1.0 H C:LEU336 4.6 71.6 1.0 C C:ASP366 4.6 73.9 1.0 HB3 C:ALA367 4.7 76.0 1.0 OD2 C:ASP366 4.7 69.1 1.0 HB2 C:HIS335 4.7 66.6 1.0 NE2 C:HIS335 4.7 55.2 1.0 CZ2 C:TRP179 4.7 52.0 1.0 CA C:SER337 4.7 65.9 1.0 CD2 C:HIS335 4.8 56.3 1.0 H C:SER337 4.8 75.0 1.0 HB3 C:ASP338 4.8 82.5 1.0 N C:SER337 4.8 62.5 1.0 CA C:HIS335 4.9 54.4 1.0 HB2 C:ALA367 4.9 76.0 1.0 HD12 C:ILE383 4.9 73.1 1.0 HB2 C:ASP366 4.9 83.7 1.0 N C:ASP366 5.0 69.5 1.0 C C:MET365 5.0 62.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2)


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 Apo Beta-D-Galnacase From Niabella Aurantiaca (Structure 2) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:69.2 occ:1.00 O D:HOH727 2.0 62.4 1.0 NE2 D:HIS272 2.1 72.4 1.0 OD1 D:ASP338 2.2 84.7 1.0 OD1 D:ASP366 2.4 72.6 1.0 HD1 D:HIS335 2.6 80.4 1.0 CD2 D:HIS272 2.9 68.8 1.0 HD2 D:HIS272 3.0 82.6 1.0 CG D:ASP338 3.1 93.6 1.0 HA D:ASP366 3.1 88.3 1.0 ND1 D:HIS335 3.2 67.0 1.0 CE1 D:HIS272 3.2 68.7 1.0 H D:ALA367 3.3 89.6 1.0 CG D:ASP366 3.4 75.6 1.0 HB3 D:HIS335 3.5 75.1 1.0 HE1 D:HIS272 3.5 82.4 1.0 OD2 D:ASP338 3.6 87.6 1.0 HA D:ASP338 3.6 111.2 1.0 HB3 D:ASP366 3.7 92.7 1.0 CB D:ASP366 3.9 77.2 1.0 CA D:ASP366 3.9 73.6 1.0 C D:SER337 3.9 82.0 1.0 CE1 D:HIS335 4.0 65.3 1.0 CG D:HIS335 4.0 62.9 1.0 O D:SER337 4.0 82.1 1.0 HE1 D:HIS335 4.1 78.4 1.0 HH2 D:TRP179 4.1 73.0 1.0 N D:ASP338 4.1 89.7 1.0 N D:ALA367 4.1 74.6 1.0 CA D:ASP338 4.1 92.7 1.0 CG D:HIS272 4.1 63.6 1.0 CB D:HIS335 4.2 62.6 1.0 CB D:ASP338 4.2 97.9 1.0 HZ2 D:TRP179 4.2 72.5 1.0 ND1 D:HIS272 4.3 67.9 1.0 HA D:SER337 4.3 92.6 1.0 O D:MET365 4.4 70.2 1.0 H D:LEU336 4.5 85.3 1.0 OD2 D:ASP366 4.5 74.1 1.0 H D:ASP338 4.5 107.6 1.0 HB3 D:ALA367 4.5 93.8 1.0 CA D:SER337 4.5 77.2 1.0 H D:SER337 4.5 87.3 1.0 C D:ASP366 4.6 73.3 1.0 N D:SER337 4.6 72.8 1.0 HA D:HIS335 4.6 77.1 1.0 HB2 D:ASP338 4.7 117.5 1.0 CH2 D:TRP179 4.8 60.9 1.0 HB2 D:ALA367 4.8 93.8 1.0 HB2 D:ASP366 4.8 92.7 1.0 CZ2 D:TRP179 4.8 60.5 1.0 HB3 D:ASP338 4.9 117.5 1.0 HB2 D:HIS335 4.9 75.1 1.0 CA D:HIS335 5.0 64.3 1.0 NE2 D:HIS335 5.0 61.0 1.0 HD12 D:ILE383 5.0 81.3 1.0 N D:LEU336 5.0 71.1 1.0

E.S.Moreno Prieto, S.Fjermedal, S.Siebenhaar, M.Vuillemin, J.Holck, R.Vincentelli, G.P.Gippert, C.Wilkens, J.P.Morth, B.Henrissat. Characterization and Structural Study of A Novel Beta-N-Acetylgalactosaminidase From Niabella Aurantiaca. Febs J. V. 291 1439 2024.
ISSN: ISSN 1742-464X
PubMed: 38129294
DOI: 10.1111/FEBS.17042