Sodium in PDB 5m4j: Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand

All present enzymatic activity of Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand:
3.4.13.9;

The structure of Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand, PDB code: 5m4j was solved by P.Wilk, M.S.Weiss, U.Mueller, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.94 / 1.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.554, 106.942, 216.524, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 16.8

The binding sites of Sodium atom in the Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand (pdb code 5m4j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand, PDB code: 5m4j:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand


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 Wild-Type Human Prolidase with Glypro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na499 b:19.8 occ:1.00 NA A:NA500 2.3 29.1 1.0 OD2 A:ASP287 2.4 21.7 1.0 OE2 A:GLU412 2.4 21.4 1.0 OE2 A:GLU452 2.4 19.3 1.0 NE2 A:HIS370 2.5 17.2 1.0 O A:GLY503 2.6 25.7 1.0 CG A:ASP287 3.2 21.4 1.0 CD A:GLU412 3.2 21.2 1.0 C A:GLY503 3.2 25.7 1.0 CD A:GLU452 3.3 20.8 1.0 OE1 A:GLU412 3.3 23.6 1.0 CD2 A:HIS370 3.4 16.9 1.0 CE1 A:HIS370 3.5 17.3 1.0 OE1 A:GLU452 3.5 24.8 1.0 OD1 A:ASP287 3.7 27.8 1.0 N A:GLY503 3.8 28.5 1.0 N A:PRO504 3.9 26.0 1.0 CA A:GLY503 4.0 26.5 1.0 CA A:PRO504 4.1 25.9 1.0 CG2 A:THR410 4.1 16.6 1.0 OG1 A:THR410 4.1 17.6 1.0 CB A:ASP287 4.2 16.0 1.0 CB A:THR410 4.4 16.1 1.0 CG A:GLU412 4.5 18.2 1.0 NE2 A:HIS377 4.6 19.0 1.0 ND1 A:HIS370 4.6 17.1 1.0 CG A:HIS370 4.6 17.2 1.0 CG A:GLU452 4.7 17.9 1.0 C A:PRO504 4.8 26.5 1.0 OD2 A:ASP276 4.9 18.7 1.0 CD2 A:HIS377 4.9 18.1 1.0 CG2 A:VAL376 5.0 19.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand


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 Wild-Type Human Prolidase with Glypro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na500 b:29.1 occ:1.00 NA A:NA499 2.3 19.8 1.0 OE1 A:GLU412 2.5 23.6 1.0 OE1 A:GLU452 2.6 24.8 1.0 OD2 A:ASP276 2.7 18.7 1.0 C A:GLY503 2.8 25.7 1.0 CA A:GLY503 3.1 26.5 1.0 N A:PRO504 3.1 26.0 1.0 O A:GLY503 3.1 25.7 1.0 OE2 A:GLU452 3.2 19.3 1.0 CD A:GLU452 3.2 20.8 1.0 CD A:GLU412 3.2 21.2 1.0 OD2 A:ASP287 3.3 21.7 1.0 OE2 A:GLU412 3.3 21.4 1.0 N A:GLY503 3.5 28.5 1.0 OD1 A:ASP287 3.5 27.8 1.0 CG A:ASP276 3.5 18.0 1.0 CD A:PRO504 3.6 26.0 1.0 OD1 A:ASP276 3.6 17.5 1.0 CG A:ASP287 3.7 21.4 1.0 CA A:PRO504 3.8 25.9 1.0 NE A:ARG450 4.0 17.6 1.0 CG A:PRO504 4.0 25.8 1.0 OG1 A:THR289 4.0 18.1 1.0 CB A:PRO504 4.5 25.6 1.0 CG A:GLU452 4.5 17.9 1.0 CD A:ARG450 4.6 17.6 1.0 CG A:GLU412 4.6 18.2 1.0 NH2 A:ARG450 4.7 19.4 1.0 CZ A:ARG450 4.7 18.3 1.0 NE2 A:HIS370 4.7 17.2 1.0 CB A:GLU412 4.9 15.7 1.0 CB A:ASP276 4.9 16.7 1.0 CB A:GLU452 4.9 16.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na499 b:20.4 occ:1.00 OD2 B:ASP287 2.3 23.0 1.0 NE2 B:HIS370 2.4 16.2 1.0 NA B:NA500 2.5 32.0 1.0 OE2 B:GLU412 2.5 19.1 1.0 OE2 B:GLU452 2.5 19.9 1.0 O B:GLY503 2.5 26.6 1.0 CG B:ASP287 3.1 22.8 1.0 C B:GLY503 3.2 26.6 1.0 CD B:GLU412 3.2 20.9 1.0 OE1 B:GLU412 3.4 25.3 1.0 CD2 B:HIS370 3.4 15.7 1.0 CE1 B:HIS370 3.4 16.1 1.0 CD B:GLU452 3.4 21.8 1.0 OE1 B:GLU452 3.6 26.9 1.0 OD1 B:ASP287 3.7 25.6 1.0 N B:GLY503 3.8 26.7 1.0 N B:PRO504 3.9 27.0 1.0 CA B:GLY503 4.0 26.7 1.0 CA B:PRO504 4.0 27.5 1.0 OG1 B:THR410 4.1 16.0 1.0 CG2 B:THR410 4.2 15.5 1.0 CB B:ASP287 4.2 18.4 1.0 CB B:THR410 4.4 15.3 1.0 NE2 B:HIS377 4.5 18.1 1.0 ND1 B:HIS370 4.5 15.2 1.0 CG B:HIS370 4.5 15.1 1.0 CG B:GLU412 4.6 17.7 1.0 CG B:GLU452 4.8 17.3 1.0 CD2 B:HIS377 4.8 17.3 1.0 C B:PRO504 4.8 27.4 1.0 OD2 B:ASP276 4.9 19.3 1.0 CG2 B:VAL376 4.9 24.1 1.0 CD B:PRO504 5.0 28.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Wild-Type Human Prolidase with Glypro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na500 b:32.0 occ:1.00 NA B:NA499 2.5 20.4 1.0 OE1 B:GLU412 2.5 25.3 1.0 OD2 B:ASP276 2.6 19.3 1.0 OE1 B:GLU452 2.7 26.9 1.0 C B:GLY503 2.8 26.6 1.0 N B:PRO504 3.1 27.0 1.0 CA B:GLY503 3.1 26.7 1.0 O B:GLY503 3.2 26.6 1.0 CD B:GLU452 3.2 21.8 1.0 OE2 B:GLU452 3.3 19.9 1.0 CD B:GLU412 3.3 20.9 1.0 CG B:ASP276 3.4 18.7 1.0 OD2 B:ASP287 3.4 23.0 1.0 N B:GLY503 3.4 26.7 1.0 OD1 B:ASP287 3.4 25.6 1.0 OE2 B:GLU412 3.5 19.1 1.0 CD B:PRO504 3.5 28.8 1.0 OD1 B:ASP276 3.5 19.8 1.0 CA B:PRO504 3.8 27.5 1.0 CG B:ASP287 3.8 22.8 1.0 NE B:ARG450 3.9 16.6 1.0 OG1 B:THR289 4.0 16.2 1.0 CG B:PRO504 4.1 29.9 1.0 CB B:PRO504 4.4 29.3 1.0 CD B:ARG450 4.5 15.6 1.0 NH2 B:ARG450 4.6 18.0 1.0 CZ B:ARG450 4.6 17.5 1.0 CG B:GLU452 4.6 17.3 1.0 CG B:GLU412 4.7 17.7 1.0 CB B:ASP276 4.8 16.8 1.0 NE2 B:HIS370 4.8 16.2 1.0 CB B:GLU412 4.9 16.3 1.0 CB B:GLU452 4.9 14.8 1.0

P.Wilk, M.Uehlein, J.Kalms, H.Dobbek, U.Mueller, M.S.Weiss. Substrate Specificity and Reaction Mechanism of Human Prolidase. Febs J. V. 284 2870 2017.
ISSN: ISSN 1742-4658
PubMed: 28677335
DOI: 10.1111/FEBS.14158