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Manganese in PDB 6qeg: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide, PDB code: 6qeg 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) 40.08 / 2.08
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.265, 99.853, 100.417, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide (pdb code 6qeg). 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 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide, PDB code: 6qeg:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6qeg

Go back to Manganese Binding Sites List in 6qeg
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide


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 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:34.8
occ:1.00
 OD2 A:ASP262 2.1 31.6 1.0
O23 A:K4K502 2.2 32.9 1.0
OE2 A:GLU459 2.3 33.6 1.0
OE2 A:GLU364 2.3 32.2 1.0
NE2 A:HIS331 2.3 35.0 1.0
O9 A:K4K502 2.8 34.4 1.0
CG A:ASP262 3.0 33.6 1.0
CD A:GLU364 3.1 40.5 1.0
C3 A:K4K502 3.1 34.4 1.0
C1 A:K4K502 3.2 35.9 1.0
CE1 A:HIS331 3.3 34.8 1.0
CD A:GLU459 3.3 35.7 1.0
CD2 A:HIS331 3.3 35.7 1.0
OE1 A:GLU364 3.3 25.6 1.0
MN A:MN504 3.4 28.5 1.0
OD1 A:ASP262 3.4 31.3 1.0
OE1 A:GLU459 3.7 23.1 1.0
C4 A:K4K502 3.8 33.3 1.0
CB A:ALA362 3.9 32.6 1.0
O12 A:K4K502 3.9 31.3 1.0
CB A:ASP262 4.2 27.4 1.0
CG A:GLU364 4.4 37.1 1.0
N2 A:K4K502 4.4 37.0 1.0
C6 A:K4K502 4.4 33.0 1.0
CG A:HIS331 4.4 35.2 1.0
ND1 A:HIS331 4.4 35.9 1.0
CG A:GLU459 4.6 29.4 1.0
NE2 A:HIS339 4.7 50.7 1.0
N15 A:K4K502 4.9 33.2 1.0
CB A:GLU364 5.0 31.0 1.0

Manganese binding site 2 out of 2 in 6qeg

Go back to Manganese Binding Sites List in 6qeg
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide


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 2-Oxo-1-Phenyl-Pyrrolidine-3-Carboxylic Acid (2- Thiophen-2-Yl-Ethyl)-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:28.5
occ:1.00
 OD1 A:ASP262 2.1 31.3 1.0
OE1 A:GLU459 2.1 23.1 1.0
OD1 A:ASP251 2.2 20.8 1.0
O23 A:K4K502 2.3 32.9 1.0
OD2 A:ASP251 2.3 24.3 1.0
O12 A:K4K502 2.3 31.3 1.0
CG A:ASP251 2.6 19.9 1.0
CD A:GLU459 3.1 35.7 1.0
CG A:ASP262 3.1 33.6 1.0
C4 A:K4K502 3.1 33.3 1.0
C3 A:K4K502 3.1 34.4 1.0
OE2 A:GLU459 3.3 33.6 1.0
OD2 A:ASP262 3.4 31.6 1.0
MN A:MN503 3.4 34.8 1.0
C6 A:K4K502 3.8 33.0 1.0
CZ A:PHE219 3.8 27.7 1.0
NE2 A:GLN457 4.0 25.0 1.0
CB A:ASP251 4.1 22.2 1.0
OE1 A:GLU364 4.1 25.6 1.0
CE1 A:PHE219 4.2 29.3 1.0
N15 A:K4K502 4.4 33.2 1.0
CB A:ASP262 4.4 27.4 1.0
C1 A:K4K502 4.4 35.9 1.0
CG A:GLU459 4.4 29.4 1.0
CB A:ALA264 4.5 24.2 1.0
N A:CYS263 4.6 26.0 1.0
C A:ASP262 4.7 30.6 1.0
CE2 A:PHE219 4.7 29.7 1.0
CA A:ASP262 4.8 26.5 1.0
CD A:GLU364 4.8 40.5 1.0
O9 A:K4K502 4.8 34.4 1.0
CA A:ASP251 4.9 21.8 1.0
OE2 A:GLU364 4.9 32.2 1.0
CB A:GLU459 4.9 25.7 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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