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Sodium in PDB 5mc0: Crystal Structure of DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand

Enzymatic activity of Crystal Structure of DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand

All present enzymatic activity of Crystal Structure of DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand:
3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand, PDB code: 5mc0 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) 43.26 / 1.56
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 103.943, 108.113, 211.927, 90.00, 90.00, 90.00
R / Rfree (%) 11.6 / 15.3

Other elements in 5mc0:

The structure of Crystal Structure of DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand (pdb code 5mc0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand, PDB code: 5mc0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5mc0

Go back to Sodium Binding Sites List in 5mc0
Sodium binding site 1 out of 2 in the Crystal Structure of DELTYR231 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 DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na511

b:24.1
occ:1.00
O A:GLY317 2.3 20.8 1.0
O A:HOH1036 2.3 37.1 0.9
O A:HOH700 2.3 28.9 1.0
O A:HOH708 2.4 19.6 1.0
O A:HOH1144 3.1 50.1 1.0
C A:GLY317 3.3 18.5 1.0
CA A:GLY317 4.0 18.5 1.0
O A:MET319 4.0 21.5 1.0
N A:ALA318 4.3 18.4 1.0
O A:MET316 4.5 18.3 1.0
CA A:GLY460 4.6 25.1 1.0
CA A:ALA318 4.6 17.6 1.0
C A:ALA318 4.6 19.3 1.0
O A:SER459 4.6 34.7 1.0
N A:MET319 4.8 19.1 1.0
C A:MET319 4.9 19.9 1.0
O A:ALA318 5.0 22.6 1.0

Sodium binding site 2 out of 2 in 5mc0

Go back to Sodium Binding Sites List in 5mc0
Sodium binding site 2 out of 2 in the Crystal Structure of DELTYR231 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 DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na515

b:31.2
occ:1.00
O B:HOH611 2.5 29.8 1.0
O B:HOH1100 2.8 30.6 1.0
O B:VAL213 2.8 24.1 1.0
O B:MET210 2.8 20.6 1.0
O B:HOH1057 3.0 41.3 1.0
O B:LYS211 3.2 22.9 1.0
O B:MET478 3.5 29.2 1.0
CG2 B:VAL213 3.5 26.9 0.3
C B:LYS211 3.6 21.8 1.0
CG1 B:VAL213 3.6 30.1 0.7
O B:HOH649 3.7 30.7 1.0
CE B:MET478 3.8 21.5 1.0
N B:VAL213 3.8 22.7 1.0
C B:VAL213 3.8 22.7 1.0
C B:MET210 3.9 18.4 1.0
CB B:MET478 4.0 24.5 1.0
CA B:LYS211 4.1 21.7 1.0
CA B:MET478 4.2 26.0 1.0
N B:ALA212 4.2 21.9 1.0
C B:ALA212 4.2 23.9 1.0
CA B:VAL213 4.2 23.5 0.3
CA B:VAL213 4.2 24.9 0.7
C B:MET478 4.2 27.5 1.0
O B:HOH1166 4.3 54.8 1.0
CB B:VAL213 4.5 24.8 0.3
N B:LYS211 4.5 17.8 1.0
CG B:MET478 4.5 23.2 1.0
CB B:VAL213 4.6 29.5 0.7
CA B:ALA212 4.6 22.5 1.0
O B:ALA212 4.7 26.4 1.0
O B:HOH1065 4.9 53.1 1.0

Reference:

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
Page generated: Mon Oct 7 22:32:27 2024

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