Sodium in PDB 5mc1: Crystal Structure of ASP276ASN Mutant of Human Prolidase with Mn Ions and Glypro Ligand

All present enzymatic activity of Crystal Structure of ASP276ASN Mutant of Human Prolidase with Mn Ions and Glypro Ligand:
3.4.13.9;

The structure of Crystal Structure of ASP276ASN Mutant of Human Prolidase with Mn Ions and Glypro Ligand, PDB code: 5mc1 was solved by P.Wilk, U.Mueller, H.Dobbek, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 1.43
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.419, 106.848, 216.299, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 15.7

The structure of Crystal Structure of ASP276ASN Mutant of Human Prolidase with Mn Ions and Glypro Ligand also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of ASP276ASN Mutant of Human Prolidase with Mn Ions and Glypro Ligand (pdb code 5mc1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of ASP276ASN Mutant of Human Prolidase with Mn Ions and Glypro Ligand, PDB code: 5mc1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of ASP276ASN Mutant of Human Prolidase with Mn Ions and 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 ASP276ASN Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na500 b:29.0 occ:0.89 MN A:MN499 2.4 21.2 0.5 OE1 A:GLU412 2.5 21.5 1.0 OD1 A:ASN276 2.7 17.0 1.0 C A:GLY503 2.7 19.6 1.0 OE1 A:GLU452 2.8 18.6 1.0 CA A:GLY503 2.8 26.2 1.0 N A:PRO504 3.1 18.7 1.0 O A:GLY503 3.1 18.4 1.0 N A:GLY503 3.2 21.6 1.0 OE2 A:GLU452 3.3 16.5 1.0 CD A:GLU452 3.3 19.8 1.0 CD A:GLU412 3.3 19.8 1.0 OD2 A:ASP287 3.4 18.9 1.0 CG A:ASN276 3.4 14.5 1.0 CD A:PRO504 3.4 24.2 1.0 OD1 A:ASP287 3.5 16.1 1.0 ND2 A:ASN276 3.5 15.7 1.0 OE2 A:GLU412 3.5 17.5 1.0 CG A:ASP287 3.8 15.7 1.0 CA A:PRO504 3.9 19.0 1.0 NE A:ARG450 4.1 15.2 1.0 CG A:PRO504 4.1 27.0 1.0 OG1 A:THR289 4.1 13.6 1.0 NH2 A:ARG450 4.6 17.8 1.0 CB A:PRO504 4.7 21.1 1.0 NE2 A:HIS370 4.7 12.9 1.0 CD A:ARG450 4.7 14.8 1.0 CG A:GLU412 4.7 16.2 1.0 CZ A:ARG450 4.7 15.8 1.0 CG A:GLU452 4.7 14.3 1.0 CB A:ASN276 4.9 13.9 1.0 CB A:GLU412 5.0 16.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of ASP276ASN Mutant of Human Prolidase with Mn Ions and 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 ASP276ASN Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:35.7 occ:1.00 O A:HOH1114 2.3 31.5 0.4 O A:HOH1101 2.3 58.4 1.0 O A:HOH1073 2.4 22.8 1.0 O B:HOH1122 2.4 34.9 0.5 O A:HOH749 2.5 30.0 1.0 OE1 A:GLU227 2.6 18.9 1.0 O A:HOH857 3.1 31.6 1.0 O A:HOH1114 3.1 30.8 0.6 O B:HOH1133 3.2 25.1 0.4 CD A:GLU227 3.3 18.6 1.0 O B:HOH706 3.5 20.5 0.8 OE2 A:GLU227 3.7 17.3 1.0 O A:HOH786 3.9 22.2 1.0 O A:HOH985 4.2 21.4 1.0 O A:ARG237 4.3 14.3 1.0 O A:HOH736 4.3 26.2 1.0 O B:HOH786 4.4 21.2 1.0 CG A:GLU227 4.4 15.0 1.0 CB A:GLU227 4.4 14.4 1.0 O A:HOH1191 4.6 34.7 1.0 O B:HOH1133 4.7 26.5 0.6 O B:HOH981 4.7 41.2 1.0 O A:HOH777 4.8 18.4 1.0 O B:HOH702 5.0 24.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of ASP276ASN Mutant of Human Prolidase with Mn Ions and 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 ASP276ASN Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na500 b:28.5 occ:0.97 MN B:MN499 2.3 15.6 0.4 OE1 B:GLU412 2.5 18.0 1.0 OE1 B:GLU452 2.7 18.0 1.0 OD1 B:ASN276 2.7 17.8 1.0 C B:GLY503 2.7 19.3 1.0 CA B:GLY503 2.8 25.3 1.0 O B:GLY503 3.1 19.1 1.0 N B:PRO504 3.2 19.7 1.0 OE2 B:GLU452 3.2 15.0 1.0 CD B:GLU452 3.3 15.3 1.0 CD B:GLU412 3.3 17.9 1.0 OD2 B:ASP287 3.3 18.1 1.0 OE2 B:GLU412 3.3 19.2 1.0 N B:GLY503 3.4 24.7 1.0 OD1 B:ASP287 3.4 15.2 1.0 CD B:PRO504 3.5 21.7 1.0 CG B:ASN276 3.5 16.2 1.0 ND2 B:ASN276 3.5 13.7 1.0 CG B:ASP287 3.7 14.9 1.0 CA B:PRO504 4.0 19.0 1.0 NE B:ARG450 4.1 15.6 1.0 OG1 B:THR289 4.1 15.9 1.0 CG B:PRO504 4.2 26.5 1.0 NE2 B:HIS370 4.6 15.0 1.0 CG B:GLU412 4.6 14.7 1.0 CG B:GLU452 4.6 14.0 1.0 NH2 B:ARG450 4.7 17.1 1.0 CD B:ARG450 4.7 14.8 1.0 CZ B:ARG450 4.7 14.5 1.0 CB B:PRO504 4.8 20.5 1.0 CB B:GLU412 4.9 13.0 1.0 CB B:ASN276 4.9 12.6 1.0

P.Wilk, M.Uehlein, R.Piwowarczyk, H.Dobbek, U.Mueller, M.S.Weiss. Structural Basis For Prolidase Deficiency Disease Mechanisms. Febs J. V. 285 3422 2018.
ISSN: ISSN 1742-4658
PubMed: 30066404
DOI: 10.1111/FEBS.14620