Sodium in PDB 4gly: Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504

All present enzymatic activity of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504:
3.4.21.73;

The structure of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504, PDB code: 4gly was solved by S.A.Buth, P.G.Leiman, S.Chen, C.Heinis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.13 / 1.52
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	120.800, 120.800, 43.080, 90.00, 90.00, 120.00
R / Rfree (%)	12.8 / 20.4

The structure of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504 (pdb code 4gly). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504, PDB code: 4gly:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:27.8 occ:1.00 O A:HOH593 2.2 56.4 1.0 OG A:SER48 2.9 20.9 1.0 N A:CYS50 3.2 13.7 1.0 CB A:SER48 3.4 16.1 1.0 CB A:CYS50 3.7 17.9 1.0 N A:PRO49 3.7 14.1 1.0 CD A:PRO49 3.7 19.7 1.0 CD1 A:TRP51 3.7 19.3 1.0 SG A:CYS50 3.8 23.1 1.0 O A:HOH591 3.8 63.1 1.0 CA A:CYS50 3.9 14.0 1.0 C A:SER48 4.1 14.6 1.0 C A:PRO49 4.1 13.6 1.0 CA A:PRO49 4.2 15.6 1.0 CB A:PRO49 4.3 17.9 1.0 CA A:SER48 4.4 13.2 1.0 O A:HOH584 4.4 71.0 1.0 NE1 A:TRP51 4.4 16.9 1.0 CG A:PRO49 4.4 23.6 1.0 N A:TRP51 4.5 10.7 1.0 C A:CYS50 4.6 12.3 1.0 O A:SER48 4.6 13.4 1.0 O A:HOH562 4.7 49.5 1.0 CG A:TRP51 4.8 13.2 1.0 O A:HOH508 5.0 42.0 1.0

Sodium binding site 2 out of 2 in the Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:38.2 occ:1.00 O A:HOH563 2.8 53.0 1.0 O A:HOH462 3.0 22.7 1.0 OE1 A:GLU25 3.1 10.8 1.0 OG A:SER71 3.1 12.3 1.0 OE2 A:GLU25 3.1 14.1 1.0 CD A:GLU25 3.5 10.6 1.0 CG2 A:THR77 3.5 8.6 1.0 CG2 A:ILE24 3.7 8.1 1.0 O A:HOH594 4.0 29.0 1.0 CB A:THR23 4.1 8.9 1.0 CB A:SER71 4.2 9.6 1.0 N A:ILE24 4.4 7.2 1.0 CG2 A:THR117 4.6 13.1 1.0 CG2 A:THR23 4.6 13.2 1.0 OG1 A:THR23 4.7 13.1 1.0 O A:HOH654 4.7 32.7 1.0 CB A:ILE24 4.8 7.9 1.0 CB A:THR77 4.9 10.5 1.0 CG A:GLU25 4.9 10.4 1.0 N A:GLU25 5.0 7.0 1.0

S.Chen, I.Rentero Rebollo, S.A.Buth, J.Morales-Sanfrutos, J.Touati, P.G.Leiman, C.Heinis. Bicyclic Peptide Ligands Pulled Out of Cysteine-Rich Peptide Libraries. J.Am.Chem.Soc. V. 135 6562 2013.
ISSN: ISSN 0002-7863
PubMed: 23560397
DOI: 10.1021/JA400461H