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Manganese 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:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of DELTYR231 Mutant of Human Prolidase with Mn Ions and Glypro Ligand, PDB code: 5mc0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5mc0

Go back to Manganese Binding Sites List in 5mc0
Manganese binding site 1 out of 4 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 Manganese with other atoms in the Mn 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:Mn499

b:28.0
occ:0.73
OD2 A:ASP286 2.3 24.9 1.0
OE2 A:GLU411 2.3 20.9 1.0
O A:OH501 2.4 20.2 0.7
NE2 A:HIS369 2.4 15.6 1.0
OE2 A:GLU451 2.5 20.9 1.0
O A:GLY503 2.5 26.7 1.0
CD A:GLU411 3.1 23.8 1.0
CG A:ASP286 3.2 23.7 1.0
MN A:MN500 3.2 33.5 0.2
C A:GLY503 3.2 29.6 1.0
OE1 A:GLU411 3.3 29.2 1.0
CE1 A:HIS369 3.4 16.5 1.0
CD2 A:HIS369 3.4 15.9 1.0
CD A:GLU451 3.4 24.0 1.0
OD1 A:ASP286 3.6 25.3 1.0
OE1 A:GLU451 3.6 29.2 1.0
N A:PRO504 3.8 30.8 1.0
N A:GLY503 3.8 34.2 1.0
CA A:GLY503 4.0 32.6 1.0
CA A:PRO504 4.0 34.1 1.0
OG1 A:THR409 4.1 15.2 1.0
CG2 A:THR409 4.2 16.2 1.0
CB A:ASP286 4.3 18.5 1.0
CB A:THR409 4.4 15.2 1.0
NE2 A:HIS376 4.4 17.4 1.0
CG A:GLU411 4.5 20.9 1.0
ND1 A:HIS369 4.5 15.0 1.0
CG A:HIS369 4.5 14.9 1.0
CG A:GLU451 4.7 17.3 1.0
C A:PRO504 4.8 37.8 1.0
CD2 A:HIS376 4.8 16.4 1.0
CD A:PRO504 4.9 35.7 1.0
OD2 A:ASP275 4.9 18.8 1.0

Manganese binding site 2 out of 4 in 5mc0

Go back to Manganese Binding Sites List in 5mc0
Manganese binding site 2 out of 4 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 Manganese with other atoms in the Mn 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
A:Mn500

b:33.5
occ:0.24
O A:OH501 1.8 20.2 0.7
OD1 A:ASP275 2.1 20.0 1.0
OD2 A:ASP275 2.1 18.8 1.0
OD1 A:ASP286 2.2 25.3 1.0
OE1 A:GLU451 2.4 29.2 1.0
CG A:ASP275 2.4 16.9 1.0
N A:GLY503 3.0 34.2 1.0
CG A:ASP286 3.0 23.7 1.0
OD2 A:ASP286 3.1 24.9 1.0
CA A:GLY503 3.1 32.6 1.0
MN A:MN499 3.2 28.0 0.7
CD A:GLU451 3.3 24.0 1.0
OE2 A:GLU451 3.4 20.9 1.0
OG1 A:THR288 3.6 17.9 1.0
C A:GLY503 3.6 29.6 1.0
OH A:TYR240 3.8 19.2 1.0
CB A:ASP275 3.9 15.3 1.0
O A:GLY503 3.9 26.7 1.0
OE1 A:GLU411 4.0 29.2 1.0
N A:PRO504 4.2 30.8 1.0
CZ A:TYR240 4.3 16.8 1.0
CB A:ASP286 4.4 18.5 1.0
CE2 A:TYR240 4.5 16.9 1.0
CD A:PRO504 4.5 35.7 1.0
NE A:ARG449 4.6 17.7 1.0
CG A:GLU451 4.7 17.3 1.0
CD A:GLU411 4.7 23.8 1.0
OE2 A:GLU411 4.7 20.9 1.0
CA A:ASP275 4.7 14.3 1.0
NH2 A:ARG449 4.7 17.9 1.0
C A:ASP286 4.9 15.8 1.0
N A:ILE287 4.9 17.2 1.0
O A:ILE287 4.9 14.7 1.0
CA A:ASP286 5.0 15.1 1.0
CB A:THR288 5.0 16.0 1.0
CE1 A:TYR240 5.0 15.2 1.0

Manganese binding site 3 out of 4 in 5mc0

Go back to Manganese Binding Sites List in 5mc0
Manganese binding site 3 out of 4 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 Manganese with other atoms in the Mn binding site number 3 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:Mn499

b:28.9
occ:0.70
OD2 B:ASP286 2.3 27.0 1.0
O B:OH501 2.3 18.7 0.7
OE2 B:GLU411 2.3 21.6 1.0
NE2 B:HIS369 2.4 16.2 1.0
OE2 B:GLU451 2.4 20.8 1.0
O B:GLY503 2.6 30.7 1.0
CD B:GLU411 3.1 23.1 1.0
CG B:ASP286 3.1 23.6 1.0
MN B:MN500 3.2 33.5 0.2
OE1 B:GLU411 3.3 26.1 1.0
C B:GLY503 3.3 32.3 1.0
CD B:GLU451 3.3 20.6 1.0
CD2 B:HIS369 3.4 15.9 1.0
CE1 B:HIS369 3.4 16.3 1.0
OD1 B:ASP286 3.6 26.6 1.0
OE1 B:GLU451 3.6 26.5 1.0
N B:GLY503 3.8 35.9 1.0
N B:PRO504 3.9 30.2 1.0
CA B:GLY503 4.0 33.9 1.0
CA B:PRO504 4.1 29.9 1.0
OG1 B:THR409 4.1 16.2 1.0
CG2 B:THR409 4.1 14.7 1.0
CB B:ASP286 4.2 17.9 1.0
CB B:THR409 4.4 14.3 1.0
ND1 B:HIS369 4.5 15.4 1.0
CG B:GLU411 4.5 19.8 1.0
CG B:HIS369 4.5 14.4 1.0
NE2 B:HIS376 4.5 18.2 1.0
CG B:GLU451 4.7 17.8 1.0
C B:PRO504 4.8 32.0 1.0
CD2 B:HIS376 4.9 16.4 1.0
OD2 B:ASP275 4.9 18.5 1.0
CD B:PRO504 5.0 32.7 1.0

Manganese binding site 4 out of 4 in 5mc0

Go back to Manganese Binding Sites List in 5mc0
Manganese binding site 4 out of 4 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 Manganese with other atoms in the Mn binding site number 4 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:Mn500

b:33.5
occ:0.25
O B:OH501 1.8 18.7 0.7
OD2 B:ASP275 2.1 18.5 1.0
OD1 B:ASP275 2.1 19.6 1.0
OD1 B:ASP286 2.2 26.6 1.0
CG B:ASP275 2.3 18.1 1.0
OE1 B:GLU451 2.4 26.5 1.0
N B:GLY503 2.9 35.9 1.0
CG B:ASP286 3.0 23.6 1.0
OD2 B:ASP286 3.1 27.0 1.0
CA B:GLY503 3.2 33.9 1.0
MN B:MN499 3.2 28.9 0.7
CD B:GLU451 3.3 20.6 1.0
OE2 B:GLU451 3.5 20.8 1.0
OG1 B:THR288 3.6 15.3 1.0
C B:GLY503 3.7 32.3 1.0
OH B:TYR240 3.8 17.9 1.0
CB B:ASP275 3.8 15.7 1.0
O B:GLY503 3.9 30.7 1.0
OE1 B:GLU411 4.1 26.1 1.0
CZ B:TYR240 4.2 17.0 1.0
N B:PRO504 4.3 30.2 1.0
CB B:ASP286 4.5 17.9 1.0
CE2 B:TYR240 4.5 18.4 1.0
CD B:PRO504 4.5 32.7 1.0
NE B:ARG449 4.6 19.1 1.0
CA B:ASP275 4.7 13.7 1.0
CG B:GLU451 4.7 17.8 1.0
NH2 B:ARG449 4.7 18.2 1.0
CD B:GLU411 4.8 23.1 1.0
OE2 B:GLU411 4.8 21.6 1.0
C B:ASP286 4.9 14.6 1.0
CE1 B:TYR240 4.9 16.9 1.0
O B:ILE287 4.9 14.8 1.0
N B:ILE287 4.9 14.7 1.0
CA B:ASP286 5.0 15.4 1.0
CB B:THR288 5.0 15.6 1.0
C B:ASP275 5.0 15.2 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: Tue Dec 15 04:44:07 2020

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