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Manganese in PDB 6qef: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide, PDB code: 6qef was solved by D.Musil, T.Heinrich, M.Lehmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.45 / 1.79
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.360, 99.400, 100.600, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.5

Other elements in 6qef:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide (pdb code 6qef). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide, PDB code: 6qef:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6qef

Go back to Manganese Binding Sites List in 6qef
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide


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 Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn508

b:28.0
occ:1.00
 OD2 A:ASP262 2.1 27.0 1.0
O13 A:HZW507 2.1 29.9 1.0
OE2 A:GLU459 2.2 24.3 1.0
NE2 A:HIS331 2.2 25.5 1.0
OE2 A:GLU364 2.3 30.6 1.0
O12 A:HZW507 2.7 36.2 1.0
C7 A:HZW507 3.1 34.1 1.0
CG A:ASP262 3.1 25.8 1.0
C6 A:HZW507 3.1 35.6 1.0
CD A:GLU364 3.1 40.6 1.0
CE1 A:HIS331 3.2 24.5 1.0
CD2 A:HIS331 3.2 27.5 1.0
CD A:GLU459 3.2 31.8 1.0
MN A:MN509 3.4 23.8 1.0
OE1 A:GLU364 3.4 30.6 1.0
OD1 A:ASP262 3.5 23.7 1.0
OE1 A:GLU459 3.6 22.0 1.0
CB A:ALA362 3.8 28.4 1.0
C4 A:HZW507 3.8 35.5 1.0
O5 A:HZW507 4.0 32.8 1.0
N8 A:HZW507 4.2 37.0 1.0
ND1 A:HIS331 4.3 26.1 1.0
CG A:HIS331 4.3 27.5 1.0
CB A:ASP262 4.4 23.4 1.0
CG A:GLU364 4.4 34.5 1.0
C10 A:HZW507 4.4 37.0 1.0
CG A:GLU459 4.5 22.8 1.0
NE2 A:HIS339 4.7 39.8 1.0
N3 A:HZW507 4.8 37.4 1.0
C14 A:HZW507 4.8 40.1 1.0
CB A:GLU364 5.0 27.5 1.0

Manganese binding site 2 out of 2 in 6qef

Go back to Manganese Binding Sites List in 6qef
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide


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 Human Methionine Aminopeptidase-2 in Complex with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro-Benzylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn509

b:23.8
occ:1.00
 OD1 A:ASP262 2.0 23.7 1.0
OE1 A:GLU459 2.1 22.0 1.0
OD1 A:ASP251 2.1 20.2 1.0
OD2 A:ASP251 2.2 24.7 1.0
O13 A:HZW507 2.2 29.9 1.0
O5 A:HZW507 2.3 32.8 1.0
CG A:ASP251 2.5 22.2 1.0
C4 A:HZW507 3.0 35.5 1.0
CG A:ASP262 3.0 25.8 1.0
C6 A:HZW507 3.0 35.6 1.0
CD A:GLU459 3.0 31.8 1.0
OE2 A:GLU459 3.2 24.3 1.0
OD2 A:ASP262 3.3 27.0 1.0
MN A:MN508 3.4 28.0 1.0
C10 A:HZW507 3.8 37.0 1.0
NE2 A:GLN457 4.0 24.0 1.0
CZ A:PHE219 4.0 25.1 1.0
CB A:ASP251 4.0 18.5 1.0
OE1 A:GLU364 4.1 30.6 1.0
N3 A:HZW507 4.3 37.4 1.0
C7 A:HZW507 4.3 34.1 1.0
CE1 A:PHE219 4.3 24.2 1.0
CB A:ASP262 4.3 23.4 1.0
CG A:GLU459 4.4 22.8 1.0
CB A:ALA264 4.4 21.7 1.0
N A:CYS263 4.6 21.1 1.0
C A:ASP262 4.6 25.5 1.0
O12 A:HZW507 4.7 36.2 1.0
CA A:ASP262 4.7 22.1 1.0
CD A:GLU364 4.7 40.6 1.0
OE2 A:GLU364 4.8 30.6 1.0
CA A:ASP251 4.9 19.6 1.0
CB A:GLU459 4.9 21.1 1.0
CE2 A:PHE219 4.9 25.7 1.0
O A:CYS263 5.0 22.6 1.0
C A:CYS263 5.0 24.5 1.0

Reference:

T.Heinrich, J.Seenisamy, B.Blume, J.Bomke, M.Calderini, U.Eckert, M.Friese-Hamim, R.Kohl, M.Lehmann, B.Leuthner, D.Musil, F.Rohdich, F.T.Zenke. Discovery and Structure-Based Optimization of Next-Generation Reversible Methionine Aminopeptidase-2 (Metap-2) Inhibitors. J.Med.Chem. V. 62 5025 2019.
ISSN: ISSN 0022-2623
PubMed: 30939017
DOI: 10.1021/ACS.JMEDCHEM.9B00041
Page generated: Sun Oct 6 05:56:22 2024

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