Sodium in PDB 6nsv: Crystal Structure of the Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide

All present enzymatic activity of Crystal Structure of the Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide:
2.3.2.27;

The structure of Crystal Structure of the Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide, PDB code: 6nsv was solved by K.Basu, M.Ravalin, M.-F.Bohn, C.S.Craik, J.E.Gestwicki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.74 / 1.31
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.219, 71.920, 77.790, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 24.3

The structure of Crystal Structure of the Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide (pdb code 6nsv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide, PDB code: 6nsv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide


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 Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:30.0 occ:1.00 HE2 A:HIS76 1.5 30.3 1.0 OE1 A:GLU106 2.1 32.8 0.4 OE2 B:GLU106 2.1 16.2 0.6 OE1 A:GLN74 2.1 33.8 1.0 OE1 B:GLU106 2.2 13.1 0.6 O A:HOH302 2.3 20.5 1.0 NE2 A:HIS76 2.3 25.2 1.0 CD B:GLU106 2.5 18.6 0.6 HE1 A:HIS76 2.9 40.1 1.0 CE1 A:HIS76 2.9 33.4 1.0 CD A:GLU106 3.0 27.4 0.4 HE22 A:GLN74 3.0 24.8 1.0 CD A:GLN74 3.0 27.1 1.0 HG3 A:GLU106 3.3 25.3 0.6 NE2 A:GLN74 3.4 20.6 1.0 OE2 A:GLU106 3.4 32.8 0.4 HA A:GLN74 3.5 16.9 1.0 CD2 A:HIS76 3.5 20.5 1.0 CD A:GLU106 3.7 34.7 0.6 HB3 A:GLU106 3.7 25.0 0.4 OE2 A:GLU106 3.8 23.4 0.6 OE1 B:GLU106 3.8 12.1 0.4 HB3 A:GLU106 3.8 20.3 0.6 HD2 A:HIS76 3.9 24.6 1.0 CG A:GLU106 3.9 21.1 0.6 HG2 B:GLU106 4.0 18.3 0.4 CG B:GLU106 4.0 18.4 0.6 OE1 A:GLU106 4.0 38.0 0.6 HE21 A:GLN74 4.2 24.8 1.0 ND1 A:HIS76 4.2 21.5 1.0 CG A:GLU106 4.2 27.0 0.4 HB3 A:GLN74 4.3 18.8 1.0 HG2 B:GLU106 4.3 22.1 0.6 CB A:GLU106 4.3 17.0 0.6 CG A:GLN74 4.3 15.5 1.0 CB A:GLU106 4.3 20.8 0.4 O B:HOH347 4.4 29.3 1.0 CA A:GLN74 4.4 14.1 1.0 HG3 B:GLU106 4.4 22.1 0.6 CD B:GLU106 4.4 14.4 0.4 CG A:HIS76 4.5 15.4 1.0 O A:LEU71 4.5 16.2 1.0 HB2 A:GLU106 4.5 25.0 0.4 CB A:GLN74 4.6 15.6 1.0 HB2 A:GLU106 4.6 20.3 0.6 HA B:GLU106 4.6 20.2 1.0 HB3 B:GLU106 4.6 23.1 0.4 CG B:GLU106 4.6 15.2 0.4 HG2 A:GLU106 4.7 32.4 0.4 HG2 A:GLU106 4.7 25.3 0.6 HG2 A:GLN74 4.8 18.6 1.0 HG3 A:GLU106 4.8 32.4 0.4 HB3 B:GLU106 4.9 23.6 0.6 NA B:NA201 4.9 11.2 1.0 H A:GLN74 4.9 17.7 1.0 HG3 A:GLN74 5.0 18.6 1.0 CB B:GLU106 5.0 19.6 0.6 H132 A:1PE203 5.0 35.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide


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 Human Chip Tpr Domain in Complex with A 5MER Acetylated Optimized Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:11.2 occ:1.00 OE1 B:GLU106 2.0 12.1 0.4 NE2 B:GLN74 2.0 20.2 1.0 NE2 B:HIS76 2.2 18.5 1.0 OE2 A:GLU106 2.2 23.4 0.6 OE1 A:GLU106 2.3 38.0 0.6 O B:HOH305 2.3 19.7 1.0 HE21 B:GLN74 2.4 24.2 1.0 CD A:GLU106 2.6 34.7 0.6 CE1 B:HIS76 2.9 24.6 1.0 HE1 B:HIS76 2.9 29.5 1.0 CD B:GLU106 3.0 14.4 0.4 CD B:GLN74 3.1 24.7 1.0 HG3 B:GLU106 3.2 22.1 0.6 CD2 B:HIS76 3.3 22.7 1.0 OE2 B:GLU106 3.4 10.1 0.4 HA B:GLN74 3.4 24.2 1.0 OE1 B:GLN74 3.5 24.1 1.0 CD B:GLU106 3.6 18.6 0.6 HD2 B:HIS76 3.6 27.2 1.0 HB3 B:GLU106 3.7 23.1 0.4 OE1 A:GLU106 3.7 32.8 0.4 OE2 B:GLU106 3.7 16.2 0.6 HB3 B:GLU106 3.8 23.6 0.6 CG B:GLU106 3.8 18.4 0.6 OE1 B:GLU106 4.1 13.1 0.6 CG A:GLU106 4.1 21.1 0.6 HG2 A:GLU106 4.1 32.4 0.4 ND1 B:HIS76 4.1 25.0 1.0 CG B:GLU106 4.2 15.2 0.4 CB B:GLU106 4.3 19.6 0.6 HB3 B:GLN74 4.3 24.4 1.0 CA B:GLN74 4.3 20.2 1.0 CB B:GLU106 4.3 19.3 0.4 CG B:HIS76 4.4 19.4 1.0 CD A:GLU106 4.4 27.4 0.4 CG B:GLN74 4.4 18.9 1.0 HG2 A:GLU106 4.4 25.3 0.6 O A:HOH339 4.5 32.2 1.0 HB2 B:GLU106 4.5 23.6 0.6 O B:LEU71 4.5 16.3 1.0 HG3 A:GLU106 4.5 25.3 0.6 HB3 A:GLU106 4.5 25.0 0.4 HB2 B:GLU106 4.6 23.1 0.4 CB B:GLN74 4.6 20.3 1.0 HG2 B:GLU106 4.6 18.3 0.4 HA A:GLU106 4.6 25.5 1.0 CG A:GLU106 4.7 27.0 0.4 HG2 B:GLU106 4.7 22.1 0.6 HD1 B:HIS76 4.8 30.0 1.0 HB3 A:GLU106 4.8 20.3 0.6 HG3 B:GLU106 4.9 18.3 0.4 NA A:NA202 4.9 30.0 1.0 H B:GLN74 4.9 19.1 1.0 HG2 B:GLN74 4.9 22.7 1.0 HG3 B:GLN74 5.0 22.7 1.0 CB A:GLU106 5.0 17.0 0.6

M.Ravalin, P.Theofilas, K.Basu, K.A.Opoku-Nsiah, V.A.Assimon, D.Medina-Cleghorn, Y.F.Chen, M.F.Bohn, M.Arkin, L.T.Grinberg, C.S.Craik, J.E.Gestwicki. Specificity For Latent C Termini Links the E3 Ubiquitin Ligase Chip to Caspases. Nat.Chem.Biol. V. 15 786 2019.
ISSN: ESSN 1552-4469
PubMed: 31320752
DOI: 10.1038/S41589-019-0322-6