Sodium in PDB 6qci: Structure of Xiap-BIR1 V86E Mutant

All present enzymatic activity of Structure of Xiap-BIR1 V86E Mutant:
2.3.2.27;

The structure of Structure of Xiap-BIR1 V86E Mutant, PDB code: 6qci was solved by L.Sorrentino, F.Cossu, M.Milani, E.Mastrangelo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.35 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.530, 72.700, 70.180, 90.00, 96.16, 90.00
R / Rfree (%)	26.4 / 30.3

The structure of Structure of Xiap-BIR1 V86E Mutant also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Structure of Xiap-BIR1 V86E Mutant (pdb code 6qci). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Xiap-BIR1 V86E Mutant, PDB code: 6qci:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Xiap-BIR1 V86E Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Xiap-BIR1 V86E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:30.0 occ:1.00 O B:ALA69 2.1 35.1 1.0 O A:ALA69 2.2 25.6 1.0 OE2 A:GLU86 2.2 18.7 1.0 OE1 A:GLU86 2.2 25.8 1.0 O B:HOH1602 2.5 30.0 1.0 CD A:GLU86 2.6 25.3 1.0 OE2 B:GLU86 2.6 27.2 1.0 OE1 B:GLU86 2.6 36.2 1.0 CD B:GLU86 2.9 29.2 1.0 C B:ALA69 3.3 26.2 1.0 C A:ALA69 3.4 20.7 1.0 CG A:GLU86 4.1 26.8 1.0 N B:ALA69 4.1 26.6 1.0 CA B:ALA69 4.2 26.5 1.0 N B:VAL70 4.3 27.4 1.0 N A:ALA69 4.3 24.5 1.0 N A:VAL70 4.3 21.5 1.0 CA A:VAL70 4.4 25.8 1.0 CA A:ALA69 4.4 21.4 1.0 CG B:GLU86 4.4 25.7 1.0 CA B:VAL70 4.5 25.5 1.0 CB B:ALA69 4.6 26.3 1.0 CG2 A:VAL70 4.7 26.0 1.0 CB A:ALA69 4.8 21.5 1.0 CG2 B:VAL70 4.8 25.0 1.0 CB A:GLU86 4.9 29.9 1.0

Sodium binding site 2 out of 2 in the Structure of Xiap-BIR1 V86E Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Xiap-BIR1 V86E Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Na102 b:30.0 occ:1.00 OE2 D:GLU86 2.2 46.6 1.0 O1 C:PEG102 2.4 56.7 1.0 O C:ALA69 2.4 41.6 1.0 O D:ALA69 2.4 44.1 1.0 O D:HOH213 2.7 27.8 1.0 O C:HOH204 3.0 45.7 1.0 CD D:GLU86 3.2 54.2 1.0 OE1 D:GLU86 3.5 55.1 1.0 C C:ALA69 3.6 43.2 1.0 C D:ALA69 3.6 44.7 1.0 C1 C:PEG102 3.6 57.8 1.0 CA C:VAL70 4.0 40.8 1.0 N C:VAL70 4.2 43.3 1.0 CA D:VAL70 4.4 37.2 1.0 N D:VAL70 4.4 40.7 1.0 CG2 C:VAL70 4.4 39.9 1.0 CG C:GLU86 4.5 56.9 1.0 CG D:GLU86 4.5 52.3 1.0 CA D:ALA69 4.6 46.1 1.0 CB C:VAL70 4.6 42.0 1.0 C2 C:PEG102 4.7 56.7 1.0 O D:HOH206 4.7 35.2 1.0 CA C:ALA69 4.8 45.7 1.0 CB D:ALA69 4.8 49.5 1.0 N D:ALA69 4.9 49.8 1.0 CG1 C:VAL70 4.9 42.5 1.0 N C:ALA69 4.9 51.0 1.0 CB C:GLU86 5.0 57.6 1.0 CG2 D:VAL70 5.0 36.3 1.0

L.Sorrentino, F.Cossu, M.Milani, B.Malkoc, W.C.Huang, S.C.Tsay, J.Ru Hwu, E.Mastrangelo. Structure-Activity Relationship of NF023 Derivatives Binding to Xiap-BIR1. Chemistryopen V. 8 476 2019.
ISSN: ESSN 2191-1363
PubMed: 31011505
DOI: 10.1002/OPEN.201900059