Sodium in PDB 7nuz: Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel

All present enzymatic activity of Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel:
3.4.21.64;

The structure of Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel, PDB code: 7nuz was solved by J.A.Gavira, F.Artusio, A.Castellvi, R.Pisano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.77 / 1.09
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.829, 67.829, 106.999, 90, 90, 90
R / Rfree (%)	17.1 / 19.1

The structure of Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel (pdb code 7nuz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel, PDB code: 7nuz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:11.3 occ:1.00 OG A:SER130 2.7 7.6 1.0 OG A:SER132 2.8 5.8 1.0 O A:HOH464 2.8 7.4 1.0 CB A:SER130 3.3 7.1 1.0 CB A:CYS73 3.4 6.1 1.0 CB A:SER132 3.5 6.1 1.0 O A:SER130 3.7 6.3 1.0 C A:SER130 3.7 5.9 1.0 N A:SER132 3.7 5.7 1.0 SG A:CYS73 4.0 6.8 1.0 CD A:PRO228 4.0 5.5 1.0 CG1 A:VAL37 4.1 8.3 1.0 CA A:SER130 4.1 6.3 1.0 CB A:PRO228 4.1 6.3 1.0 N A:LEU131 4.1 6.1 1.0 CA A:SER132 4.2 6.3 1.0 CG A:PRO228 4.3 6.5 1.0 OD2 A:ASP39 4.5 8.2 1.0 C A:LEU131 4.5 5.6 1.0 N A:PRO228 4.5 5.2 1.0 O A:SER224 4.6 6.4 1.0 CG2 A:THR227 4.6 6.5 1.0 CA A:PRO228 4.6 6.1 1.0 CA A:CYS73 4.7 6.1 1.0 CA A:LEU131 4.7 6.2 1.0 C A:CYS73 4.9 6.5 1.0 CB A:THR227 4.9 6.6 1.0 O A:CYS73 5.0 6.1 1.0

Sodium binding site 2 out of 2 in the Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Proteinase K Structure at Atomic Resolution From Crystals Grown in Agarose Gel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:24.6 occ:1.00 O A:LEU261 2.9 16.4 1.0 N A:ILE264 3.0 13.0 1.0 C3 A:GOL303 3.1 30.3 1.0 N A:ASN263 3.3 13.8 1.0 CB A:ILE264 3.4 12.2 1.0 C1 A:GOL303 3.4 33.7 1.0 CA A:SER262 3.4 14.9 0.1 CA A:SER262 3.4 14.9 0.9 O3 A:GOL303 3.5 39.9 1.0 C A:SER262 3.5 13.2 0.9 C A:SER262 3.5 13.2 0.1 C2 A:GOL303 3.6 23.2 1.0 O2 A:GOL303 3.7 23.5 1.0 CA A:ILE264 3.7 12.6 1.0 O A:HOH688 3.7 28.1 1.0 CG1 A:ILE264 3.7 12.9 1.0 O A:ILE264 3.8 14.5 1.0 C A:LEU261 3.8 12.7 1.0 ND2 A:ASN270 3.9 13.9 1.0 C A:ASN263 4.1 13.1 1.0 N A:SER262 4.1 13.9 0.1 N A:SER262 4.1 13.8 0.9 O A:HOH671 4.1 32.4 1.0 CA A:ASN263 4.1 15.3 1.0 C A:ILE264 4.2 13.3 1.0 O A:SER262 4.3 13.8 0.9 O A:SER262 4.3 13.8 0.1 O A:HOH794 4.4 42.5 1.0 O A:HOH473 4.4 22.2 1.0 O1 A:GOL303 4.6 34.8 1.0 CB A:SER262 4.7 15.7 0.1 CB A:SER262 4.7 15.4 0.9 CG2 A:ILE264 4.7 14.4 1.0

F.Artusio, A.Castellvi, R.Pisano, J.A.Gavira. Tuning Transport Phenomena in Agarose Gels For the Control of Protein Nucleation Density and Crystal Form Crystals 2021.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST11050466