Sodium in PDB 8hfh: Cenp-E Motor Domain in Complex with Amppnp and MG2+

The structure of Cenp-E Motor Domain in Complex with Amppnp and MG2+, PDB code: 8hfh was solved by A.Shibuya, H.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.576, 46.215, 73.718, 90, 90, 90
R / Rfree (%)	16.1 / 20.6

The structure of Cenp-E Motor Domain in Complex with Amppnp and MG2+ also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Cenp-E Motor Domain in Complex with Amppnp and MG2+ (pdb code 8hfh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cenp-E Motor Domain in Complex with Amppnp and MG2+, PDB code: 8hfh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cenp-E Motor Domain in Complex with Amppnp and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cenp-E Motor Domain in Complex with Amppnp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:29.5 occ:0.50 O A:HOH701 1.7 27.2 1.0 O A:HOH710 2.1 29.7 0.5 O A:GLY43 2.3 19.4 1.0 NA A:NA603 2.7 36.8 1.0 O A:GLN40 3.2 20.5 1.0 C A:GLY43 3.5 19.9 1.0 N A:GLY43 4.3 19.6 1.0 N A:SER44 4.3 19.0 1.0 CA A:SER44 4.4 21.2 1.0 C A:GLN40 4.4 20.6 1.0 O A:VAL41 4.4 33.9 1.0 CD2 A:TYR39 4.5 21.1 1.0 CA A:GLY43 4.5 20.5 1.0 C A:SER44 4.8 20.6 1.0 CB A:TYR39 4.9 16.7 1.0 C A:VAL41 4.9 30.1 1.0 N A:GLN40 5.0 16.6 1.0 O A:LYS45 5.0 17.3 1.0

Sodium binding site 2 out of 3 in the Cenp-E Motor Domain in Complex with Amppnp and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cenp-E Motor Domain in Complex with Amppnp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:36.8 occ:1.00 O A:HOH701 1.8 27.2 1.0 NA A:NA602 2.7 29.5 0.5 O A:LYS45 2.9 17.3 1.0 O A:SER44 3.3 23.2 1.0 C A:SER44 3.4 20.6 1.0 O A:GLY43 3.5 19.4 1.0 C A:LYS45 3.5 16.3 1.0 CB A:TYR39 3.6 16.7 1.0 O A:HOH735 3.8 36.3 0.5 N A:LYS45 3.8 19.7 1.0 CA A:SER44 3.8 21.2 1.0 CB A:SER46 3.8 17.8 1.0 O A:GLN40 4.0 20.5 1.0 N A:GLN40 4.1 16.6 1.0 N A:SER46 4.2 17.2 1.0 C A:GLY43 4.3 19.9 1.0 CA A:TYR39 4.3 15.9 1.0 CA A:LYS45 4.3 18.0 1.0 OG A:SER46 4.4 19.5 1.0 N A:SER44 4.4 19.0 1.0 CA A:SER46 4.5 17.4 1.0 CG A:TYR39 4.6 17.4 1.0 C A:TYR39 4.6 16.4 1.0 CD2 A:TYR39 4.7 21.1 1.0 O A:HOH710 4.7 29.7 0.5 CB A:GLN40 4.9 18.5 1.0 CA A:GLN40 4.9 18.4 1.0 C A:GLN40 4.9 20.6 1.0

Sodium binding site 3 out of 3 in the Cenp-E Motor Domain in Complex with Amppnp and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cenp-E Motor Domain in Complex with Amppnp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:50.3 occ:1.00 O A:HOH915 2.3 37.8 1.0 O A:HOH847 2.3 18.6 1.0 O A:ILE134 3.6 10.2 1.0 CD2 A:HIS204 4.0 12.0 1.0 NE2 A:HIS204 4.0 12.3 1.0 N A:ASN136 4.0 15.9 0.5 CG1 A:ILE258 4.1 12.0 1.0 N A:ASN136 4.2 16.7 0.5 OG A:SER261 4.2 14.7 0.7 CA A:ILE258 4.4 11.1 1.0 O A:ARG202 4.4 9.1 1.0 C A:ILE134 4.5 11.0 1.0 O A:ASN257 4.5 12.4 1.0 N A:ILE258 4.5 11.8 1.0 CA A:SER203 4.6 8.9 1.0 CA A:TYR135 4.6 12.6 1.0 C A:ASN257 4.6 13.3 1.0 N A:HIS204 4.7 9.4 1.0 CG A:HIS204 4.7 10.8 1.0 CB A:SER261 4.7 11.2 0.3 CA A:ASN136 4.8 17.5 0.5 CB A:ASN257 4.8 17.6 1.0 CB A:SER261 4.8 13.1 0.7 C A:TYR135 4.8 14.7 1.0 CE1 A:HIS204 4.8 11.7 1.0 N A:GLU137 4.8 20.2 1.0 N A:TYR135 4.9 12.0 1.0 CB A:ILE258 4.9 10.9 1.0 CG2 A:ILE134 5.0 12.2 1.0 OE2 A:GLU137 5.0 31.2 1.0 C A:SER203 5.0 9.0 1.0

A.Shibuya, A.Suzuki, N.Ogo, J.I.Sawada, A.Asai, H.Yokoyama. Crystal Structure of the Motor Domain of Centromere-Associated Protein E in Complex with A Non-Hydrolyzable Atp Analogue. Febs Lett. 2023.
ISSN: ISSN 0014-5793
PubMed: 36823439
DOI: 10.1002/1873-3468.14602