Manganese in PDB 7a15: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2224863A (Compound 42)

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2224863A (Compound 42)

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2224863A (Compound 42):
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2224863A (Compound 42), PDB code: 7a15 was solved by J.H.Thorpe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.67 / 2.15
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.282, 100.820, 99.411, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20.1

Other elements in 7a15:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2224863A (Compound 42) 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 GSK2224863A (Compound 42) (pdb code 7a15). 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 GSK2224863A (Compound 42), PDB code: 7a15:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7a15

Go back to Manganese Binding Sites List in 7a15
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2224863A (Compound 42)


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 GSK2224863A (Compound 42) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn509

b:21.1
occ:1.00
OE2 A:GLU459 2.1 17.6 1.0
OD1 A:ASP262 2.1 21.9 1.0
O A:HOH617 2.2 20.9 1.0
OD2 A:ASP251 2.2 21.6 1.0
O A:HOH827 2.3 17.4 1.0
OD1 A:ASP251 2.3 19.6 1.0
CG A:ASP251 2.6 18.1 1.0
CD A:GLU459 3.0 31.9 1.0
CG A:ASP262 3.1 23.1 1.0
OE1 A:GLU459 3.2 15.4 1.0
MN A:MN510 3.4 20.6 1.0
OD2 A:ASP262 3.5 22.3 1.0
CZ A:PHE219 3.9 18.4 1.0
NE2 A:GLN457 4.1 15.2 1.0
CB A:ASP251 4.1 15.7 1.0
O A:HOH887 4.2 26.8 1.0
O24 A:QV5508 4.2 24.9 1.0
OE2 A:GLU364 4.2 24.3 1.0
CE1 A:PHE219 4.3 18.3 1.0
O A:HOH618 4.3 17.6 1.0
O A:HOH805 4.3 17.4 1.0
CG A:GLU459 4.4 18.9 1.0
CB A:ASP262 4.4 19.2 1.0
N A:CYS263 4.6 16.6 1.0
C A:ASP262 4.6 21.6 1.0
CB A:ALA264 4.6 18.7 1.0
CA A:ASP262 4.7 17.3 1.0
CE2 A:PHE219 4.8 20.9 1.0
OE1 A:GLU364 4.8 21.0 1.0
CD A:GLU364 4.8 31.4 1.0
CB A:GLU459 4.9 18.4 1.0
N13 A:QV5508 5.0 25.4 1.0
CA A:ASP251 5.0 16.1 1.0

Manganese binding site 2 out of 2 in 7a15

Go back to Manganese Binding Sites List in 7a15
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2224863A (Compound 42)


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 GSK2224863A (Compound 42) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn510

b:20.6
occ:1.00
O24 A:QV5508 2.1 24.9 1.0
OE1 A:GLU459 2.2 15.4 1.0
OE1 A:GLU364 2.2 21.0 1.0
OD2 A:ASP262 2.2 22.3 1.0
O A:HOH617 2.2 20.9 1.0
NE2 A:HIS331 2.3 21.3 1.0
CD A:GLU364 3.1 31.4 1.0
CG A:ASP262 3.1 23.1 1.0
CE1 A:HIS331 3.2 20.7 1.0
CD2 A:HIS331 3.3 21.8 1.0
CD A:GLU459 3.3 31.9 1.0
C22 A:QV5508 3.3 26.3 1.0
MN A:MN509 3.4 21.1 1.0
OD1 A:ASP262 3.5 21.9 1.0
OE2 A:GLU364 3.5 24.3 1.0
OE2 A:GLU459 3.7 17.6 1.0
CB A:ALA362 3.9 20.4 1.0
N23 A:QV5508 3.9 25.4 1.0
O A:HOH827 4.0 17.4 1.0
CG A:GLU364 4.2 20.2 1.0
CB A:ASP262 4.3 19.2 1.0
ND1 A:HIS331 4.4 22.1 1.0
O A:HOH830 4.4 20.1 1.0
CG A:HIS331 4.4 21.6 1.0
O A:HOH805 4.4 17.4 1.0
C12 A:QV5508 4.4 24.1 1.0
CG A:GLU459 4.6 18.9 1.0
N13 A:QV5508 4.6 25.4 1.0
CB A:GLU364 4.9 18.3 1.0
CD1 A:ILE338 5.0 40.2 1.0

Reference:

D.J.Hirst, M.Brandt, G.Bruton, E.Christodoulou, L.Cutler, N.Deeks, J.D.Goodacre, T.Jack, M.Lindon, A.Miah, K.Page, N.Parr, L.Shukla, M.Sims, P.Thomas, J.Thorpe, D.S.Holmes. Structure-Based Optimisation of Orally Active & Reversible Metap-2 Inhibitors Maintaining A Tight 'Molecular Budget'. Bioorg.Med.Chem.Lett. V. 30 27533 2020.
ISSN: ESSN 1464-3405
PubMed: 32919012
DOI: 10.1016/J.BMCL.2020.127533
Page generated: Tue Dec 15 05:11:51 2020

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