Sodium in PDB 4qrv: Crystal Structure of I86F Mutant of Papain

All present enzymatic activity of Crystal Structure of I86F Mutant of Papain:
3.4.22.2;

The structure of Crystal Structure of I86F Mutant of Papain, PDB code: 4qrv was solved by S.Dutta, D.Choudhury, S.Roy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.13 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.670, 74.267, 116.326, 90.00, 92.85, 90.00
R / Rfree (%)	19.8 / 24.9

The structure of Crystal Structure of I86F Mutant of Papain also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of I86F Mutant of Papain (pdb code 4qrv). 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 I86F Mutant of Papain, PDB code: 4qrv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of I86F Mutant of Papain


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 I86F Mutant of Papain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:52.2 occ:1.00 CL A:CL401 2.5 74.9 1.0 O A:CYS260 2.6 26.9 1.0 N A:CYS307 2.8 20.1 1.0 SG A:CYS260 3.2 29.8 1.0 C A:CYS260 3.6 22.2 1.0 CA A:CYS307 3.6 21.1 1.0 CA A:VAL306 3.6 20.7 1.0 C A:VAL306 3.7 21.4 1.0 CG1 A:VAL306 4.1 23.1 1.0 O A:HOH715 4.1 51.4 1.0 O A:GLY261 4.2 27.1 1.0 CB A:CYS260 4.3 28.7 1.0 CA A:CYS260 4.3 26.1 1.0 N A:CYS260 4.3 21.6 1.0 O A:GLY305 4.3 25.6 1.0 CB A:VAL306 4.4 23.0 1.0 N A:GLY261 4.5 22.4 1.0 N A:GLY308 4.6 19.9 1.0 ND2 A:ASN262 4.6 30.1 1.0 C A:CYS307 4.6 23.1 1.0 C A:GLY261 4.6 26.9 1.0 SG A:CYS307 4.6 28.1 1.0 CA A:GLY261 4.7 21.4 1.0 CB A:CYS307 4.7 21.9 1.0 N A:VAL306 4.8 23.0 1.0 O A:VAL306 4.8 21.8 1.0 ND2 A:ASN302 4.9 37.4 1.0 CG2 A:VAL306 5.0 26.7 1.0 C A:GLY305 5.0 22.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of I86F Mutant of Papain


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 I86F Mutant of Papain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:60.6 occ:1.00 OE1 B:GLU38 3.2 73.5 1.0 OE2 B:GLU38 3.7 79.5 1.0 CD B:GLU38 3.9 73.8 1.0 CE2 B:TYR41 4.4 52.1 1.0 NH2 B:ARG42 4.4 46.0 1.0 CD2 B:TYR41 4.5 48.6 1.0 OE2 B:GLU77 4.8 87.2 1.0

S.Dutta, D.Choudhury, S.Roy, S.Biswas. Pro-Peptide Regulates the Substrate Specificity and Zymogen Activation Process of Papain: A Structural and Mechanistic Insight To Be Published.