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Magnesium in PDB 5m4l: Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand

Enzymatic activity of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand

All present enzymatic activity of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand:
3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand, PDB code: 5m4l 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) 46.75 / 1.49
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 103.605, 106.839, 216.990, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17.1

Other elements in 5m4l:

The structure of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand (pdb code 5m4l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand, PDB code: 5m4l:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5m4l

Go back to Magnesium Binding Sites List in 5m4l
Magnesium binding site 1 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg499

b:15.8
occ:0.60
 OD2 A:ASP287 2.3 22.8 1.0
NE2 A:HIS370 2.3 17.8 1.0
OE2 A:GLU452 2.3 20.2 1.0
O A:OH501 2.4 36.2 1.0
OE2 A:GLU412 2.4 25.7 1.0
O A:LEU503 2.7 36.6 1.0
CD A:GLU412 3.1 24.8 1.0
CG A:ASP287 3.2 20.5 1.0
OE1 A:GLU412 3.2 26.1 1.0
MG A:MG500 3.2 13.9 0.4
C A:LEU503 3.3 36.7 1.0
CD2 A:HIS370 3.3 16.7 1.0
CE1 A:HIS370 3.3 17.5 1.0
CD A:GLU452 3.4 19.4 1.0
N A:LEU503 3.5 41.8 1.0
OD1 A:ASP287 3.6 24.3 1.0
OE1 A:GLU452 3.7 21.9 1.0
OG1 A:THR410 3.9 17.0 1.0
CG2 A:THR410 3.9 16.0 1.0
CA A:LEU503 4.0 44.4 1.0
N A:PRO504 4.0 36.6 1.0
CB A:THR410 4.2 15.9 1.0
CA A:PRO504 4.3 36.5 1.0
CB A:ASP287 4.3 16.0 1.0
ND1 A:HIS370 4.4 17.4 1.0
CG A:HIS370 4.4 17.1 1.0
CG A:GLU412 4.5 21.1 1.0
CG A:GLU452 4.6 15.9 1.0
NE2 A:HIS377 4.7 19.9 1.0
CG2 A:VAL376 4.9 17.3 1.0
CD2 A:HIS377 4.9 18.4 1.0

Magnesium binding site 2 out of 4 in 5m4l

Go back to Magnesium Binding Sites List in 5m4l
Magnesium binding site 2 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:13.9
occ:0.40
 O A:OH501 1.8 36.2 1.0
OD1 A:ASP287 2.0 24.3 1.0
OE1 A:GLU452 2.2 21.9 1.0
OD1 A:ASP276 2.2 19.3 1.0
N A:LEU503 2.3 41.8 1.0
OD2 A:ASP276 2.3 19.7 1.0
CG A:ASP276 2.6 19.5 1.0
CG A:ASP287 2.8 20.5 1.0
CD A:GLU452 3.0 19.4 1.0
OD2 A:ASP287 3.1 22.8 1.0
CA A:LEU503 3.1 44.4 1.0
OE2 A:GLU452 3.2 20.2 1.0
MG A:MG499 3.2 15.8 0.6
OG1 A:THR289 3.6 17.6 1.0
OH A:TYR241 3.7 21.5 1.0
C A:LEU503 3.7 36.7 1.0
CB A:ASP276 4.0 16.6 1.0
OE1 A:GLU412 4.1 26.1 1.0
O A:LEU503 4.1 36.6 1.0
CZ A:TYR241 4.1 20.6 1.0
CB A:ASP287 4.2 16.0 1.0
CG A:GLU452 4.4 15.9 1.0
CB A:LEU503 4.5 45.8 1.0
N A:PRO504 4.5 36.6 1.0
CE2 A:TYR241 4.5 21.6 1.0
C A:ASP287 4.5 15.8 1.0
N A:ILE288 4.6 15.6 1.0
CA A:ASP287 4.7 14.5 1.0
CD A:PRO504 4.7 36.6 1.0
NE A:ARG450 4.8 19.4 1.0
CE1 A:TYR241 4.8 19.7 1.0
CD A:GLU412 4.8 24.8 1.0
CA A:ASP276 4.8 15.2 1.0
O A:ASP287 4.8 16.1 1.0
O A:ILE288 4.8 14.5 1.0
C A:ILE288 4.9 15.0 1.0
OE2 A:GLU412 4.9 25.7 1.0
CB A:GLU452 4.9 15.1 1.0
NH2 A:ARG450 5.0 19.6 1.0
CB A:THR289 5.0 16.3 1.0

Magnesium binding site 3 out of 4 in 5m4l

Go back to Magnesium Binding Sites List in 5m4l
Magnesium binding site 3 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg499

b:17.2
occ:0.66
 NE2 B:HIS370 2.3 16.1 1.0
OD2 B:ASP287 2.3 23.5 1.0
OE2 B:GLU412 2.3 23.4 1.0
O B:OH501 2.4 30.6 1.0
OE2 B:GLU452 2.4 21.0 1.0
O B:LEU503 2.6 40.6 1.0
CD B:GLU412 3.1 24.9 1.0
C B:LEU503 3.2 40.6 1.0
CG B:ASP287 3.2 21.4 1.0
OE1 B:GLU412 3.2 27.8 1.0
CD2 B:HIS370 3.2 16.3 1.0
CE1 B:HIS370 3.3 16.3 1.0
MG B:MG500 3.3 17.1 0.5
CD B:GLU452 3.4 20.9 1.0
N B:LEU503 3.5 40.7 1.0
OD1 B:ASP287 3.6 22.8 1.0
OE1 B:GLU452 3.8 22.9 1.0
N B:PRO504 3.9 40.6 1.0
CA B:LEU503 3.9 40.7 1.0
OG1 B:THR410 3.9 15.8 1.0
CG2 B:THR410 4.0 16.9 1.0
CA B:PRO504 4.1 40.5 1.0
CB B:THR410 4.2 16.4 1.0
CB B:ASP287 4.4 17.6 1.0
ND1 B:HIS370 4.4 16.9 1.0
CG B:HIS370 4.4 16.2 1.0
CG B:GLU412 4.4 20.7 1.0
NE2 B:HIS377 4.6 18.4 1.0
CG B:GLU452 4.7 17.0 1.0
CD2 B:HIS377 4.9 16.4 1.0
C B:PRO504 4.9 40.5 1.0
CG2 B:VAL376 4.9 19.6 1.0
CD B:PRO504 4.9 40.7 1.0
OD2 B:ASP276 5.0 17.8 1.0

Magnesium binding site 4 out of 4 in 5m4l

Go back to Magnesium Binding Sites List in 5m4l
Magnesium binding site 4 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg500

b:17.1
occ:0.48
 O B:OH501 1.8 30.6 1.0
OD1 B:ASP287 2.0 22.8 1.0
OD1 B:ASP276 2.1 20.0 1.0
OD2 B:ASP276 2.2 17.8 1.0
OE1 B:GLU452 2.2 22.9 1.0
N B:LEU503 2.4 40.7 1.0
CG B:ASP276 2.4 17.3 1.0
CG B:ASP287 3.0 21.4 1.0
CD B:GLU452 3.1 20.9 1.0
CA B:LEU503 3.1 40.7 1.0
OD2 B:ASP287 3.3 23.5 1.0
OE2 B:GLU452 3.3 21.0 1.0
MG B:MG499 3.3 17.2 0.7
OG1 B:THR289 3.5 15.8 1.0
C B:LEU503 3.7 40.6 1.0
OH B:TYR241 3.8 22.5 1.0
CB B:ASP276 3.9 15.0 1.0
OE1 B:GLU412 4.1 27.8 1.0
O B:LEU503 4.1 40.6 1.0
CZ B:TYR241 4.2 22.5 1.0
CB B:ASP287 4.4 17.6 1.0
N B:PRO504 4.4 40.6 1.0
CB B:LEU503 4.5 40.7 1.0
CG B:GLU452 4.5 17.0 1.0
CE2 B:TYR241 4.5 20.9 1.0
C B:ASP287 4.6 16.1 1.0
CD B:PRO504 4.6 40.7 1.0
N B:ILE288 4.6 15.6 1.0
NE B:ARG450 4.7 16.9 1.0
CA B:ASP276 4.7 13.9 1.0
O B:ILE288 4.7 15.1 1.0
CA B:ASP287 4.8 16.0 1.0
CD B:GLU412 4.8 24.9 1.0
C B:ILE288 4.8 15.8 1.0
NH2 B:ARG450 4.9 19.3 1.0
CE1 B:TYR241 4.9 21.7 1.0
CB B:GLU452 4.9 16.4 1.0
OE2 B:GLU412 4.9 23.4 1.0
CB B:THR289 4.9 15.7 1.0
O B:ASP287 4.9 17.1 1.0
C B:ASP276 5.0 14.6 1.0

Reference:

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
Page generated: Tue Aug 12 14:49:05 2025

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