Sodium in PDB 6s98: Crystal Structure of the Catalytic Domain of UBE2S Wt.

All present enzymatic activity of Crystal Structure of the Catalytic Domain of UBE2S Wt.:
2.3.2.23;

The structure of Crystal Structure of the Catalytic Domain of UBE2S Wt., PDB code: 6s98 was solved by A.K.L.Liess, S.Lorenz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.15 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.812, 49.050, 71.926, 90.00, 106.03, 90.00
R / Rfree (%)	16.1 / 18.4

The binding sites of Sodium atom in the Crystal Structure of the Catalytic Domain of UBE2S Wt. (pdb code 6s98). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Catalytic Domain of UBE2S Wt., PDB code: 6s98:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of UBE2S Wt.


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 the Catalytic Domain of UBE2S Wt. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:17.7 occ:1.00 OD1 A:ASN124 2.2 15.7 1.0 OD1 B:ASN124 2.3 17.6 1.0 O B:PRO123 2.3 15.5 1.0 O A:PRO123 2.3 15.2 1.0 O B:HOH345 2.5 17.2 1.0 HA A:ASN124 2.9 18.3 1.0 HA B:ASN124 2.9 18.1 1.0 C A:PRO123 3.3 16.8 1.0 C B:PRO123 3.3 15.9 1.0 HB3 A:HIS122 3.4 15.9 1.0 HB3 B:HIS122 3.4 15.2 1.0 CG A:ASN124 3.4 15.0 1.0 CG B:ASN124 3.4 18.7 1.0 O A:HIS122 3.5 15.2 1.0 CA A:ASN124 3.7 15.3 1.0 CA B:ASN124 3.7 15.0 1.0 O B:HIS122 3.7 15.6 1.0 N A:ASN124 3.8 14.4 1.0 HD2 B:PRO125 3.8 21.2 1.0 HD2 A:PRO125 3.8 23.5 1.0 N B:ASN124 3.8 13.1 1.0 C A:HIS122 3.9 15.8 1.0 O A:HOH319 3.9 16.9 1.0 O B:HOH349 4.0 20.1 1.0 CB A:ASN124 4.1 14.1 1.0 CB B:ASN124 4.1 16.1 1.0 C B:HIS122 4.1 15.7 1.0 CB A:HIS122 4.2 13.2 1.0 CB B:HIS122 4.3 12.7 1.0 HB3 B:ASN124 4.3 19.4 1.0 HB3 A:ASN124 4.4 17.0 1.0 HB2 A:HIS122 4.4 15.9 1.0 N A:PRO123 4.4 15.1 1.0 CA A:PRO123 4.4 15.4 1.0 ND2 A:ASN124 4.5 18.2 1.0 HB2 B:HIS122 4.5 15.2 1.0 HD3 B:PRO125 4.5 21.2 1.0 ND2 B:ASN124 4.5 19.1 1.0 CA B:PRO123 4.5 11.5 1.0 HD3 A:PRO125 4.5 23.5 1.0 N B:PRO123 4.5 12.7 1.0 HD21 A:ASN124 4.5 21.9 1.0 HD21 B:ASN124 4.6 22.9 1.0 CD B:PRO125 4.6 17.7 1.0 CD A:PRO125 4.6 19.5 1.0 CA A:HIS122 4.6 13.3 1.0 H A:ASN124 4.6 17.3 1.0 H B:ASN124 4.6 15.7 1.0 CA B:HIS122 4.7 13.0 1.0 HA A:HIS122 4.7 16.0 1.0 OE1 B:GLU126 4.7 19.9 1.0 OE2 A:GLU126 4.8 18.5 1.0 HA B:HIS122 4.8 15.6 1.0 HB2 A:ASN124 4.9 17.0 1.0 HB2 B:ASN124 4.9 19.4 1.0 HA A:PRO123 4.9 18.5 1.0 C B:ASN124 5.0 16.4 1.0 C A:ASN124 5.0 19.1 1.0 OE1 A:GLU126 5.0 21.8 1.0 HA B:PRO123 5.0 13.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of UBE2S Wt.


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 the Catalytic Domain of UBE2S Wt. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:36.5 occ:1.00 O A:HOH369 2.6 28.8 1.0 HB2 A:ARG101 2.7 17.9 1.0 O B:HOH365 2.7 16.9 1.0 O A:VAL98 2.8 23.4 1.0 HE1 B:HIS122 2.8 15.8 1.0 HG13 A:VAL98 3.1 53.2 1.0 O B:HOH301 3.3 12.4 1.0 HD2 A:ARG101 3.3 24.2 1.0 HG21 A:THR115 3.4 20.0 1.0 CE1 B:HIS122 3.5 13.1 1.0 HG23 A:THR115 3.5 20.0 1.0 CB A:ARG101 3.6 15.0 1.0 C A:VAL98 3.8 25.8 1.0 HG12 A:VAL98 3.8 53.2 1.0 HB3 A:ARG101 3.8 17.9 1.0 ND1 B:HIS122 3.9 14.1 1.0 HG22 B:ILE121 3.9 16.6 1.0 CG1 A:VAL98 3.9 44.3 1.0 O B:HOH342 3.9 18.2 1.0 CG2 A:THR115 3.9 16.6 1.0 HD3 A:ARG101 4.0 24.2 1.0 CD A:ARG101 4.0 20.3 1.0 HG23 B:ILE121 4.0 16.6 1.0 O A:ARG101 4.1 16.0 1.0 H A:ARG101 4.1 19.4 1.0 O B:ILE121 4.2 13.1 1.0 HA A:LEU99 4.2 23.1 1.0 HA A:VAL98 4.3 32.1 1.0 HG22 A:THR115 4.3 20.0 1.0 CG A:ARG101 4.4 18.0 1.0 CG2 B:ILE121 4.4 13.8 1.0 HG11 A:VAL98 4.5 53.2 1.0 HH11 A:ARG101 4.5 32.2 1.0 CA A:ARG101 4.5 14.2 1.0 NE2 B:HIS122 4.6 15.6 1.0 CA A:VAL98 4.6 26.8 1.0 N A:ARG101 4.6 16.1 1.0 HG3 A:ARG101 4.6 21.5 1.0 O A:HOH336 4.6 24.6 1.0 HG21 B:ILE121 4.7 16.6 1.0 C A:ARG101 4.7 15.8 1.0 N A:LEU99 4.7 21.7 1.0 O B:HOH334 4.8 17.9 1.0 CA A:LEU99 4.8 19.2 1.0 HE2 B:HIS122 4.9 18.7 1.0 HD21 A:ASN124 4.9 21.9 1.0 CB A:VAL98 4.9 40.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of UBE2S Wt.


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 the Catalytic Domain of UBE2S Wt. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:78.0 occ:1.00 O A:ILE121 2.2 14.9 1.0 O B:HOH387 2.3 33.4 1.0 O A:HOH352 2.4 23.7 1.0 O A:HOH301 2.6 28.2 1.0 O B:HOH361 2.6 19.0 1.0 C A:ILE121 3.4 12.9 1.0 HG23 A:ILE121 3.7 20.9 1.0 HG22 A:ILE121 3.7 20.9 1.0 HA A:ILE121 3.7 15.8 1.0 O A:HOH349 3.8 19.8 1.0 HD3 B:ARG101 3.8 63.2 1.0 HG22 A:THR53 3.8 23.4 1.0 HH11 B:ARG101 3.8 59.1 1.0 HB3 B:ARG101 3.9 37.4 1.0 HB2 B:ARG101 3.9 37.4 1.0 HD2 B:ARG101 4.0 63.2 1.0 HA A:HIS122 4.0 16.0 1.0 OD2 B:ASP102 4.0 29.0 1.0 OH A:TYR141 4.1 28.6 1.0 CA A:ILE121 4.1 13.1 1.0 CG2 A:ILE121 4.1 17.4 1.0 HH A:TYR141 4.2 34.4 1.0 HD3 A:PRO123 4.3 17.8 1.0 ND1 A:HIS122 4.3 16.3 1.0 CD B:ARG101 4.3 52.7 1.0 CB B:ARG101 4.4 31.1 1.0 HD2 A:PRO123 4.5 17.8 1.0 N A:HIS122 4.5 13.5 1.0 HA A:THR53 4.5 24.4 1.0 O A:GLY52 4.5 26.4 1.0 HE1 A:HIS122 4.6 22.7 1.0 HD3 A:PRO54 4.7 27.7 1.0 CE1 A:HIS122 4.7 18.9 1.0 NH1 B:ARG101 4.7 49.3 1.0 CG2 A:THR53 4.7 19.5 1.0 CA A:HIS122 4.7 13.3 1.0 CB A:ILE121 4.8 15.2 1.0 O B:ARG101 4.8 24.9 1.0 HB A:THR53 4.8 22.0 1.0 CD A:PRO123 4.8 14.8 1.0 HG21 A:THR53 4.9 23.4 1.0 HG21 A:ILE121 4.9 20.9 1.0

A.K.L.Liess, A.Kucerova, K.Schweimer, D.Schlesinger, O.Dybkov, H.Urlaub, J.Mansfeld, S.Lorenz. Dimerization Regulates the Human Apc/C-Associated Ubiquitin-Conjugating Enzyme UBE2S. Sci.Signal. V. 13 2020.
ISSN: ESSN 1937-9145
PubMed: 33082289
DOI: 10.1126/SCISIGNAL.ABA8208