Sodium in PDB 4tkx: Structure of Protease

All present enzymatic activity of Structure of Protease:
3.4.22.47;

The structure of Structure of Protease, PDB code: 4tkx was solved by M.A.Gorman, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.71 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.941, 116.941, 86.852, 90.00, 90.00, 90.00
R / Rfree (%)	12 / 14.5

The structure of Structure of Protease also contains other interesting chemical elements:

Lead	(Pb)	1 atom
Potassium	(K)	1 atom

The binding sites of Sodium atom in the Structure of Protease (pdb code 4tkx). 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 Protease, PDB code: 4tkx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Protease within 5.0Å range: probe atom residue distance (Å) B Occ L:Na705 b:11.5 occ:1.00 O L:LEU546 2.3 12.6 1.0 O L:SER549 2.4 8.1 1.0 OD1 L:ASN551 2.5 10.2 1.0 O L:TYR550 2.5 8.9 1.0 O L:THR544 2.5 10.3 1.0 O L:ALA543 2.6 9.2 1.0 C L:TYR550 3.1 9.1 1.0 C L:THR544 3.2 9.5 1.0 HB2 L:LEU546 3.3 14.3 1.0 HB2 L:TYR550 3.3 11.9 1.0 C L:LEU546 3.4 12.8 1.0 HA L:ASN551 3.4 9.6 1.0 H L:LEU546 3.5 12.8 1.0 HA L:THR544 3.5 10.8 1.0 CG L:ASN551 3.5 10.7 1.0 C L:SER549 3.6 9.6 1.0 N L:LEU546 3.6 10.6 1.0 HH12 L:ARG597 3.6 19.5 1.0 HH11 L:ARG597 3.7 19.5 1.0 C L:ALA543 3.7 9.7 1.0 NH1 L:ARG597 3.8 16.2 1.0 CA L:THR544 3.8 9.0 1.0 N L:ASN551 3.9 8.3 1.0 CA L:LEU546 3.9 11.3 1.0 CA L:TYR550 3.9 9.5 1.0 H L:SER549 3.9 17.4 0.4 CB L:TYR550 4.0 9.9 1.0 N L:PHE545 4.0 9.2 1.0 H L:SER549 4.0 17.4 0.6 CB L:LEU546 4.0 12.0 1.0 CA L:ASN551 4.0 8.0 1.0 HB3 L:TYR550 4.1 11.9 1.0 C L:PHE545 4.2 10.9 1.0 N L:TYR550 4.2 9.2 1.0 HD22 L:ASN551 4.2 14.7 1.0 N L:THR544 4.3 8.7 1.0 HA L:PHE545 4.3 12.3 1.0 ND2 L:ASN551 4.3 12.3 1.0 O L:HOH968 4.3 14.8 1.0 HB3 L:LEU546 4.4 14.3 1.0 CB L:ASN551 4.4 10.0 1.0 CA L:PHE545 4.4 10.3 1.0 HA L:GLU547 4.5 18.5 1.0 HD3 L:ARG597 4.5 18.9 1.0 CZ L:ARG597 4.5 18.8 1.0 N L:GLU547 4.5 14.1 1.0 H L:PHE545 4.6 11.0 1.0 H L:ASN551 4.6 10.0 1.0 N L:SER549 4.6 14.5 1.0 CA L:SER549 4.8 12.5 1.0 HA L:LEU546 4.8 13.6 1.0 HA L:TYR550 4.8 11.4 1.0 CA L:GLU547 4.9 15.4 1.0 O L:HOH953 4.9 14.4 1.0 HH22 L:ARG597 4.9 26.4 1.0 O L:PHE545 4.9 12.3 1.0 HA L:ALA543 5.0 12.2 1.0 C L:GLU547 5.0 16.2 1.0 HB3 L:ASN551 5.0 12.0 1.0

Sodium binding site 2 out of 2 in the Structure of Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Protease within 5.0Å range: probe atom residue distance (Å) B Occ L:Na706 b:14.7 occ:1.00 O L:VAL521 2.3 14.7 1.0 OG1 L:THR536 2.4 16.9 1.0 OD2 L:ASP542 2.4 12.3 1.0 O L:SER537 2.4 15.0 1.0 O L:HOH963 2.5 14.8 1.0 OH L:TYR402 2.5 13.2 1.0 HB L:THR536 3.2 20.9 1.0 HA3 L:GLY522 3.2 17.9 1.0 CB L:THR536 3.3 17.4 1.0 CG L:ASP542 3.4 12.1 1.0 CZ L:TYR402 3.4 13.0 1.0 H L:GLY539 3.5 14.7 1.0 C L:VAL521 3.5 14.2 1.0 C L:SER537 3.5 15.7 1.0 HA L:MET538 3.7 16.4 1.0 OD1 L:ASP542 3.7 12.0 1.0 C L:THR536 3.9 17.7 1.0 O L:THR536 3.9 17.6 1.0 HA L:PHE533 3.9 22.1 1.0 HG12 L:VAL521 4.0 20.4 1.0 HE2 L:TYR402 4.0 14.7 1.0 O L:HOH920 4.0 14.1 1.0 CA L:GLY522 4.1 14.9 1.0 N L:GLY539 4.1 12.2 1.0 CE2 L:TYR402 4.1 12.2 1.0 HG13 L:VAL521 4.1 20.4 1.0 N L:SER537 4.2 17.6 1.0 CE1 L:TYR402 4.2 12.4 1.0 HE1 L:TYR402 4.2 14.9 1.0 CA L:THR536 4.2 18.0 1.0 N L:GLY522 4.2 14.3 1.0 CA L:MET538 4.3 13.7 1.0 N L:MET538 4.4 14.6 1.0 HG21 L:THR536 4.4 21.6 1.0 O L:HOH995 4.5 27.2 1.0 HD1 L:PHE533 4.5 27.3 1.0 CG2 L:THR536 4.5 18.0 1.0 CA L:SER537 4.5 17.4 1.0 CG1 L:VAL521 4.5 17.0 1.0 HA L:VAL521 4.5 16.7 1.0 O L:PHE533 4.5 18.9 1.0 HA2 L:GLY522 4.6 17.9 1.0 H L:THR536 4.6 22.7 1.0 C L:MET538 4.6 13.6 1.0 H L:SER537 4.6 21.1 1.0 CA L:VAL521 4.6 13.9 1.0 CB L:ASP542 4.7 11.3 1.0 HA3 L:GLY539 4.7 14.5 1.0 O L:THR532 4.7 17.7 1.0 HB2 L:ASP542 4.7 13.5 1.0 CA L:PHE533 4.9 18.4 1.0 HA L:SER537 4.9 20.9 1.0 N L:THR536 4.9 18.9 1.0 HG23 L:THR536 4.9 21.6 1.0

M.A.Gorman, C.A.Seers, B.J.Michell, S.C.Feil, N.L.Huq, K.J.Cross, E.C.Reynolds, M.W.Parker. Structure of the Lysine Specific Protease Kgp From Porphyromonas Gingivalis, A Target For Improved Oral Health. Protein Sci. V. 24 162 2015.
ISSN: ESSN 1469-896X
PubMed: 25327141
DOI: 10.1002/PRO.2589