Sodium in PDB 6fhj: Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.

The structure of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native., PDB code: 6fhj was solved by O.V.Moroz, P.F.Jensen, S.P.Mcdonald, N.Mcgregor, E.Blagova, G.Comamala, D.R.Segura, L.Anderson, S.M.Vasu, V.P.Rao, L.Giger, R.N.Monrad, A.Svendsen, J.E.Nielsen, B.Henrissat, G.J.Davies, H.Brumer, K.Rand, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.50 / 2.04
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.350, 103.350, 212.500, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 21

The structure of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native. also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	5 atoms

The binding sites of Sodium atom in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native. (pdb code 6fhj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native., PDB code: 6fhj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2406 b:31.9 occ:1.00 O A:HOH3049 2.3 37.7 1.0 O A:HOH2939 2.3 28.4 1.0 O A:HOH2988 2.4 24.9 1.0 OD2 A:ASP476 2.4 28.1 1.0 O A:PHE474 2.5 25.2 1.0 OD1 A:ASN473 2.5 34.2 1.0 CG A:ASP476 3.4 27.4 1.0 N A:PHE474 3.5 26.2 1.0 C A:PHE474 3.5 24.9 1.0 CG A:ASN473 3.6 31.3 1.0 OD1 A:ASP476 3.8 28.3 1.0 C A:ASN473 4.1 26.9 1.0 CA A:PHE474 4.2 25.6 1.0 CA A:ASN473 4.2 27.9 1.0 OD2 A:ASP521 4.2 24.7 1.0 O A:HOH2898 4.2 29.3 1.0 CB A:ASN473 4.5 29.8 1.0 CB A:ASP476 4.5 26.5 1.0 ND2 A:ASN473 4.6 31.2 1.0 O A:HOH3184 4.6 44.2 1.0 N A:ASP476 4.6 23.6 1.0 N A:THR475 4.6 23.1 1.0 O A:HOH3227 4.8 52.9 1.0 CD1 A:ILE464 4.8 24.4 1.0 O A:HOH2952 4.9 42.5 1.0 CA A:THR475 4.9 22.8 1.0 C A:THR475 5.0 22.9 1.0

Sodium binding site 2 out of 3 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2407 b:37.4 occ:1.00 OD2 A:ASP846 2.2 39.9 1.0 OD2 A:ASP901 2.3 32.9 1.0 O A:THR818 2.3 36.8 1.0 O A:HOH2591 2.6 40.1 1.0 O A:HOH2670 2.6 32.9 1.0 CG A:ASP846 3.2 41.5 1.0 OD1 A:ASP846 3.4 43.0 1.0 CG A:ASP901 3.5 30.7 1.0 C A:THR818 3.5 36.8 1.0 CB A:GLN850 4.0 46.4 1.0 N A:THR818 4.0 38.1 1.0 CG A:GLN850 4.2 46.0 1.0 CD A:PRO820 4.2 31.9 1.0 CB A:ASP901 4.3 30.1 1.0 N A:PRO820 4.3 33.2 1.0 OD1 A:ASP901 4.4 29.5 1.0 C A:ALA819 4.4 34.1 1.0 N A:ALA819 4.4 35.0 1.0 CA A:THR818 4.4 38.3 1.0 CA A:ALA819 4.5 34.1 1.0 CB A:ASP846 4.6 41.2 1.0 OG1 A:THR904 4.7 27.5 1.0 CG2 A:THR904 4.8 29.5 1.0 C A:GLY817 4.8 38.0 1.0 O A:ALA819 5.0 34.5 1.0

Sodium binding site 3 out of 3 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2408 b:45.5 occ:1.00 O A:THR699 2.4 53.3 1.0 OD1 A:ASP807 2.5 45.7 1.0 O A:ASP807 2.5 42.9 1.0 O A:ASP663 2.6 44.5 1.0 C A:ASP807 3.5 42.9 1.0 C A:THR699 3.6 53.7 1.0 CG A:ASP807 3.6 44.8 1.0 C A:ASP663 3.6 43.5 1.0 O A:HOH2647 3.7 49.4 1.0 CG2 A:THR699 3.8 56.3 1.0 CA A:ASP807 4.0 43.9 1.0 N A:THR699 4.1 56.8 1.0 CA A:ASP663 4.2 41.1 1.0 CA A:THR699 4.3 56.6 1.0 CB A:ASP663 4.4 41.5 1.0 CB A:ASP807 4.4 44.3 1.0 OD2 A:ASP807 4.6 44.2 1.0 CB A:THR699 4.6 58.0 1.0 N A:VAL700 4.6 52.8 1.0 N A:GLU808 4.7 41.2 1.0 N A:PHE664 4.7 44.8 1.0 CB A:PHE664 4.8 46.8 1.0 OE2 A:GLU808 4.8 45.9 1.0 CA A:VAL700 5.0 50.2 1.0

O.V.Moroz, P.F.Jensen, S.P.Mcdonald, N.Mcgregor, E.Blagova, G.Comamala, D.R.Segura, L.Anderson, S.M.Vasu, V.P.Rao, L.Giger, R.N.Monrad, A.Svendsen, J.E.Nielsen, B.Henrissat, G.J.Davies, H.Brumer, K.Rand, K.S.Wilson. Structural Dynamics and Catalytic Properties of A Multimodular Xanthanase Acs Catalysis 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B00666