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Manganese in PDB 5lyx: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline, PDB code: 5lyx 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) 44.78 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.215, 99.944, 100.930, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline (pdb code 5lyx). 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 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline, PDB code: 5lyx:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5lyx

Go back to Manganese Binding Sites List in 5lyx
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline


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 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:42.4
occ:1.00
 OD2 A:ASP262 2.1 40.0 1.0
N26 A:7BF501 2.2 44.6 1.0
OE2 A:GLU459 2.2 33.0 1.0
NE2 A:HIS331 2.3 36.1 1.0
OE2 A:GLU364 2.4 44.5 1.0
CG A:ASP262 3.1 37.4 1.0
C25 A:7BF501 3.1 47.2 1.0
CD A:GLU364 3.2 54.6 1.0
MN A:MN503 3.2 38.5 1.0
C22 A:7BF501 3.2 43.3 1.0
CE1 A:HIS331 3.3 36.6 1.0
CD A:GLU459 3.3 38.8 1.0
CD2 A:HIS331 3.4 38.2 1.0
OD1 A:ASP262 3.5 32.6 1.0
OE1 A:GLU364 3.5 38.9 1.0
OE1 A:GLU459 3.7 30.8 1.0
N19 A:7BF501 3.7 39.9 1.0
CB A:ALA362 3.8 36.5 1.0
N24 A:7BF501 4.3 46.4 1.0
CB A:ASP262 4.4 34.4 1.0
O A:HOH720 4.4 45.4 1.0
N23 A:7BF501 4.4 44.4 1.0
CG A:GLU364 4.4 47.8 1.0
ND1 A:HIS331 4.4 38.9 1.0
CG A:HIS331 4.5 38.7 1.0
CG A:GLU459 4.6 34.7 1.0
CD1 A:ILE338 5.0 38.5 1.0

Manganese binding site 2 out of 2 in 5lyx

Go back to Manganese Binding Sites List in 5lyx
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline


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 5-((R)-1-[1,2,4]Triazolo[1,5-A]Pyrimidin-7-Yl- Pyrrolidin-2-Ylmethoxy)-Isoquinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:38.5
occ:1.00
 OD1 A:ASP262 2.1 32.6 1.0
OE1 A:GLU459 2.2 30.8 1.0
OD2 A:ASP251 2.3 28.0 1.0
OD1 A:ASP251 2.3 29.2 1.0
N19 A:7BF501 2.5 39.9 1.0
CG A:ASP251 2.6 28.7 1.0
CG A:ASP262 3.0 37.4 1.0
CD A:GLU459 3.1 38.8 1.0
OE2 A:GLU459 3.2 33.0 1.0
MN A:MN502 3.2 42.4 1.0
OD2 A:ASP262 3.3 40.0 1.0
C22 A:7BF501 3.3 43.3 1.0
C20 A:7BF501 3.4 39.6 1.0
N26 A:7BF501 3.6 44.6 1.0
CZ A:PHE219 4.0 30.6 1.0
NE2 A:GLN457 4.1 29.7 1.0
CB A:ASP251 4.1 25.3 1.0
OE1 A:GLU364 4.2 38.9 1.0
O A:HOH720 4.3 45.4 1.0
O A:HOH610 4.3 36.8 1.0
CB A:ASP262 4.4 34.4 1.0
CE1 A:PHE219 4.4 31.4 1.0
CG A:GLU459 4.5 34.7 1.0
CB A:ALA264 4.6 27.1 1.0
N23 A:7BF501 4.7 44.4 1.0
C21 A:7BF501 4.7 39.7 1.0
OE2 A:GLU364 4.8 44.5 1.0
C A:ASP262 4.8 35.4 1.0
CD A:GLU364 4.8 54.6 1.0
CA A:ASP262 4.8 32.1 1.0
N A:CYS263 4.8 31.5 1.0
CE2 A:PHE219 4.9 32.7 1.0
C25 A:7BF501 4.9 47.2 1.0

Reference:

T.Heinrich, H.P.Buchstaller, B.Cezanne, F.Rohdich, J.Bomke, M.Friese-Hamim, M.Krier, T.Knochel, D.Musil, B.Leuthner, F.Zenke. Novel Reversible Methionine Aminopeptidase-2 (Metap-2) Inhibitors Based on Purine and Related Bicyclic Templates. Bioorg. Med. Chem. Lett. V. 27 551 2017.
ISSN: ESSN 1464-3405
PubMed: 27998678
DOI: 10.1016/J.BMCL.2016.12.019
Page generated: Sun Oct 6 01:53:52 2024

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