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Manganese in PDB 5mc5: Crystal Structure of DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand

Enzymatic activity of Crystal Structure of DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand

All present enzymatic activity of Crystal Structure of DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand:
3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand, PDB code: 5mc5 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) 46.58 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 103.779, 108.043, 211.341, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 18.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand (pdb code 5mc5). 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 DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand, PDB code: 5mc5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5mc5

Go back to Manganese Binding Sites List in 5mc5
Manganese binding site 1 out of 4 in the Crystal Structure of DELGLU452 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 DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn499

b:52.6
occ:0.97
 O A:OH501 2.3 46.7 1.0
NE2 A:HIS370 2.4 22.4 1.0
OD2 A:ASP287 2.5 28.0 1.0
OE2 A:GLU412 2.5 28.8 1.0
O A:GLY503 2.5 43.4 1.0
OE2 A:GLU452 2.6 22.5 1.0
C A:GLY503 3.1 43.4 1.0
MN A:MN500 3.2 81.2 0.3
CD A:GLU412 3.3 30.5 1.0
CG A:ASP287 3.3 23.5 1.0
CE1 A:HIS370 3.4 21.5 1.0
CD2 A:HIS370 3.4 23.0 1.0
CD A:GLU452 3.5 25.8 1.0
OE1 A:GLU412 3.5 30.6 1.0
OE1 A:GLU452 3.7 28.6 1.0
N A:GLY503 3.8 43.5 1.0
N A:PRO504 3.8 43.5 1.0
OD1 A:ASP287 3.8 31.3 1.0
CA A:PRO504 3.9 43.5 1.0
CA A:GLY503 3.9 43.5 1.0
CG2 A:THR410 4.2 21.8 1.0
OG1 A:THR410 4.2 21.3 1.0
NE2 A:HIS377 4.4 24.5 1.0
CB A:ASP287 4.4 21.1 1.0
CB A:THR410 4.5 21.2 1.0
ND1 A:HIS370 4.5 22.8 1.0
CG A:HIS370 4.5 21.8 1.0
CG A:GLU412 4.6 22.1 1.0
C A:PRO504 4.7 43.7 1.0
CD2 A:HIS377 4.7 22.2 1.0
CG A:GLU452 4.8 21.7 1.0
CD A:PRO504 4.9 44.3 1.0
CG2 A:VAL376 5.0 26.6 1.0

Manganese binding site 2 out of 4 in 5mc5

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Manganese binding site 2 out of 4 in the Crystal Structure of DELGLU452 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 DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:81.2
occ:0.31
 O A:OH501 1.8 46.7 1.0
OD1 A:ASP276 2.1 26.0 1.0
OD2 A:ASP276 2.3 28.9 1.0
OD1 A:ASP287 2.4 31.3 1.0
N A:GLY503 2.5 43.5 1.0
CG A:ASP276 2.5 27.1 1.0
OD2 A:ASP287 2.8 28.0 1.0
CA A:GLY503 2.9 43.5 1.0
OE1 A:GLU452 2.9 28.6 1.0
CG A:ASP287 2.9 23.5 1.0
MN A:MN499 3.2 52.6 1.0
OH A:TYR241 3.4 26.5 1.0
C A:GLY503 3.5 43.4 1.0
CZ A:TYR241 3.7 33.4 1.0
CD A:GLU452 3.8 25.8 1.0
O A:GLY503 3.8 43.4 1.0
OE2 A:GLU452 3.8 22.5 1.0
OG1 A:THR289 4.0 22.5 1.0
CE2 A:TYR241 4.0 26.6 1.0
CB A:ASP276 4.0 26.3 1.0
N A:PRO504 4.2 43.5 1.0
CE1 A:TYR241 4.4 26.7 1.0
CB A:ASP287 4.5 21.1 1.0
CD A:PRO504 4.6 44.3 1.0
CD1 A:ILE244 4.7 34.6 1.0
OE1 A:GLU412 4.8 30.6 1.0
CA A:ASP276 4.8 25.6 1.0
CD2 A:TYR241 4.9 29.4 1.0
NH2 A:ARG450 4.9 22.2 1.0
C A:ASP276 4.9 25.1 1.0
NE A:ARG450 5.0 21.5 1.0

Manganese binding site 3 out of 4 in 5mc5

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Manganese binding site 3 out of 4 in the Crystal Structure of DELGLU452 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 DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn499

b:50.6
occ:1.00
 NE2 B:HIS370 2.3 22.3 1.0
OE2 B:GLU412 2.3 23.7 1.0
OD2 B:ASP287 2.5 25.4 1.0
OE2 B:GLU452 2.5 25.8 1.0
O B:OH501 2.7 41.9 1.0
O B:GLY503 2.8 44.4 1.0
CD B:GLU412 3.2 28.7 1.0
CE1 B:HIS370 3.2 22.6 1.0
MN B:MN500 3.3 0.8 0.6
CD2 B:HIS370 3.3 22.4 1.0
CG B:ASP287 3.3 26.7 1.0
C B:GLY503 3.4 44.0 1.0
OE1 B:GLU412 3.4 27.2 1.0
CD B:GLU452 3.4 28.0 1.0
OE1 B:GLU452 3.7 31.5 1.0
OD1 B:ASP287 3.9 32.7 1.0
N B:GLY503 3.9 44.4 1.0
N B:PRO504 4.0 44.3 1.0
OG1 B:THR410 4.0 23.1 1.0
CG2 B:THR410 4.0 22.8 1.0
CA B:PRO504 4.1 44.1 1.0
CA B:GLY503 4.1 44.3 1.0
CB B:THR410 4.3 22.8 1.0
CB B:ASP287 4.4 22.8 1.0
ND1 B:HIS370 4.4 22.0 1.0
CG B:HIS370 4.5 22.8 1.0
NE2 B:HIS377 4.5 24.3 1.0
CG B:GLU412 4.5 22.3 1.0
CG B:GLU452 4.7 24.8 1.0
C B:PRO504 4.8 44.1 1.0
CD2 B:HIS377 4.9 22.4 1.0
OD2 B:ASP276 5.0 23.8 1.0

Manganese binding site 4 out of 4 in 5mc5

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Manganese binding site 4 out of 4 in the Crystal Structure of DELGLU452 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 DELGLU452 Mutant of Human Prolidase with Mn Ions and Glypro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn500

b:0.8
occ:0.64
 O B:OH501 1.4 41.9 1.0
OD1 B:ASP276 2.1 23.8 1.0
OD2 B:ASP276 2.2 23.8 1.0
OD1 B:ASP287 2.3 32.7 1.0
CG B:ASP276 2.4 22.3 1.0
OE1 B:GLU452 2.6 31.5 1.0
N B:GLY503 2.8 44.4 1.0
OD2 B:ASP287 2.8 25.4 1.0
CG B:ASP287 2.9 26.7 1.0
CA B:GLY503 3.1 44.3 1.0
MN B:MN499 3.3 50.6 1.0
CD B:GLU452 3.5 28.0 1.0
OH B:TYR241 3.6 37.2 1.0
OE2 B:GLU452 3.6 25.8 1.0
C B:GLY503 3.6 44.0 1.0
OG1 B:THR289 3.7 20.9 1.0
CB B:ASP276 3.9 21.2 1.0
CZ B:TYR241 4.0 31.8 1.0
O B:GLY503 4.0 44.4 1.0
CE2 B:TYR241 4.2 28.0 1.0
N B:PRO504 4.3 44.3 1.0
OE1 B:GLU412 4.3 27.2 1.0
CB B:ASP287 4.4 22.8 1.0
CD B:PRO504 4.6 44.8 1.0
CE1 B:TYR241 4.7 28.6 1.0
CA B:ASP276 4.7 21.1 1.0
CG B:GLU452 4.9 24.8 1.0
OE2 B:GLU412 4.9 23.7 1.0
NE B:ARG450 4.9 24.2 1.0
NH2 B:ARG450 4.9 25.9 1.0
O B:ILE288 4.9 21.6 1.0
C B:ASP276 4.9 22.2 1.0
CD B:GLU412 5.0 28.7 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: Sun Oct 6 01:57:25 2024

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