Manganese in PDB 5lyw: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine, PDB code: 5lyw was solved by D.Musil, T.Heinrich, T.Knoechel, M.Lehmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.13 / 1.69
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.780, 100.230, 100.380, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine (pdb code 5lyw). 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 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine, PDB code: 5lyw:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5lyw

Go back to Manganese Binding Sites List in 5lyw
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine


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 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:27.5
occ:1.00
OD2 A:ASP262 2.0 28.5 1.0
NE2 A:HIS331 2.2 25.4 1.0
OE2 A:GLU459 2.2 27.2 1.0
N15 A:7BH501 2.3 27.6 1.0
OE2 A:GLU364 2.4 35.1 1.0
CG A:ASP262 3.0 24.8 1.0
CE1 A:HIS331 3.1 26.1 1.0
C16 A:7BH501 3.1 36.0 1.0
CD A:GLU364 3.3 42.9 1.0
CD2 A:HIS331 3.3 28.2 1.0
C18 A:7BH501 3.3 32.0 1.0
CD A:GLU459 3.3 29.2 1.0
MN A:MN503 3.4 23.7 1.0
OD1 A:ASP262 3.4 24.7 1.0
OE1 A:GLU364 3.6 33.3 1.0
N22 A:7BH501 3.7 24.9 1.0
OE1 A:GLU459 3.7 20.4 1.0
CB A:ALA362 3.9 28.2 1.0
ND1 A:HIS331 4.3 28.2 1.0
CB A:ASP262 4.3 24.7 1.0
O A:HOH788 4.3 58.1 1.0
CG A:HIS331 4.4 27.9 1.0
O A:HOH822 4.4 32.8 1.0
CG A:GLU364 4.4 35.0 1.0
N17 A:7BH501 4.5 36.7 1.0
CG A:GLU459 4.6 27.2 1.0
C19 A:7BH501 4.6 32.4 1.0

Manganese binding site 2 out of 2 in 5lyw

Go back to Manganese Binding Sites List in 5lyw
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine


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 6-((R)-2-O-Tolyloxymethyl-Pyrrolidin-1-Yl)-9H- Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:23.7
occ:1.00
OD1 A:ASP262 2.0 24.7 1.0
OD1 A:ASP251 2.1 21.1 1.0
OE1 A:GLU459 2.1 20.4 1.0
N22 A:7BH501 2.3 24.9 1.0
OD2 A:ASP251 2.3 21.7 1.0
CG A:ASP251 2.5 19.7 1.0
CD A:GLU459 3.0 29.2 1.0
CG A:ASP262 3.0 24.8 1.0
OE2 A:GLU459 3.2 27.2 1.0
C18 A:7BH501 3.3 32.0 1.0
C21 A:7BH501 3.3 31.4 1.0
OD2 A:ASP262 3.3 28.5 1.0
MN A:MN502 3.4 27.5 1.0
N15 A:7BH501 3.6 27.6 1.0
CB A:ASP251 4.0 17.3 1.0
CZ A:PHE219 4.0 23.8 1.0
NE2 A:GLN457 4.1 26.0 1.0
OE1 A:GLU364 4.2 33.3 1.0
O A:HOH822 4.3 32.8 1.0
CE1 A:PHE219 4.4 22.6 1.0
O A:HOH613 4.4 33.7 1.0
CG A:GLU459 4.4 27.2 1.0
CB A:ASP262 4.4 24.7 1.0
C19 A:7BH501 4.4 32.4 1.0
N20 A:7BH501 4.4 31.1 1.0
CB A:ALA264 4.5 21.6 1.0
N A:CYS263 4.7 23.1 1.0
C A:ASP262 4.7 26.3 1.0
OE2 A:GLU364 4.8 35.1 1.0
CA A:ASP262 4.8 23.4 1.0
CA A:ASP251 4.9 18.5 1.0
CD A:GLU364 4.9 42.9 1.0
CE2 A:PHE219 4.9 25.7 1.0
CB A:GLU459 4.9 23.3 1.0
C16 A:7BH501 4.9 36.0 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: Tue Dec 15 04:43:44 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy