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Manganese in PDB 7a16: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43)

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43)

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43):
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43), PDB code: 7a16 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) 26.32 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.891, 100.891, 99.608, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.6

Other elements in 7a16:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43) also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43) (pdb code 7a16). 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 GSK2229238A (Compound 43), PDB code: 7a16:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7a16

Go back to Manganese Binding Sites List in 7a16
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43)


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 GSK2229238A (Compound 43) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn509

b:20.6
occ:1.00
OD1 A:ASP262 2.1 20.7 1.0
OE2 A:GLU459 2.1 17.4 1.0
O A:HOH603 2.2 18.7 1.0
OD2 A:ASP251 2.2 19.9 1.0
O A:HOH850 2.3 20.1 1.0
OD1 A:ASP251 2.4 18.3 1.0
CG A:ASP251 2.6 18.9 1.0
CD A:GLU459 3.0 27.8 1.0
CG A:ASP262 3.1 20.1 1.0
OE1 A:GLU459 3.2 18.3 1.0
OD2 A:ASP262 3.4 22.2 1.0
MN A:MN510 3.4 22.4 1.0
CZ A:PHE219 3.9 17.6 1.0
NE2 A:GLN457 4.1 18.8 1.0
O12 A:HZE508 4.1 22.8 1.0
OE2 A:GLU364 4.1 22.1 1.0
CB A:ASP251 4.1 17.3 1.0
O A:HOH889 4.2 21.6 1.0
O A:HOH615 4.3 20.5 1.0
O A:HOH819 4.3 20.6 1.0
CE1 A:PHE219 4.3 18.1 1.0
CG A:GLU459 4.3 21.7 1.0
CB A:ASP262 4.4 19.6 1.0
CB A:ALA264 4.6 16.8 1.0
N A:CYS263 4.6 18.5 1.0
C A:ASP262 4.7 21.6 1.0
CE2 A:PHE219 4.7 20.1 1.0
CA A:ASP262 4.8 17.8 1.0
CD A:GLU364 4.8 30.7 1.0
OE1 A:GLU364 4.8 19.7 1.0
CB A:GLU459 4.9 18.1 1.0

Manganese binding site 2 out of 2 in 7a16

Go back to Manganese Binding Sites List in 7a16
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43)


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 GSK2229238A (Compound 43) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn510

b:22.4
occ:1.00
O12 A:HZE508 2.1 22.8 1.0
OD2 A:ASP262 2.2 22.2 1.0
OE1 A:GLU459 2.2 18.3 1.0
OE1 A:GLU364 2.3 19.7 1.0
NE2 A:HIS331 2.3 24.4 1.0
O A:HOH603 2.4 18.7 1.0
CD A:GLU364 3.1 30.7 1.0
CG A:ASP262 3.1 20.1 1.0
C10 A:HZE508 3.3 21.8 1.0
CD2 A:HIS331 3.3 24.9 1.0
CD A:GLU459 3.3 27.8 1.0
CE1 A:HIS331 3.3 24.6 1.0
OE2 A:GLU364 3.4 22.1 1.0
MN A:MN509 3.4 20.6 1.0
OD1 A:ASP262 3.5 20.7 1.0
OE2 A:GLU459 3.7 17.4 1.0
N11 A:HZE508 3.8 21.5 1.0
CB A:ALA362 3.8 20.6 1.0
O A:HOH850 3.9 20.1 1.0
CG A:GLU364 4.2 20.5 1.0
CB A:ASP262 4.4 19.6 1.0
O A:HOH819 4.4 20.6 1.0
CG A:HIS331 4.4 24.6 1.0
C8 A:HZE508 4.5 23.2 1.0
ND1 A:HIS331 4.5 25.5 1.0
O A:HOH879 4.5 23.1 1.0
CG A:GLU459 4.6 21.7 1.0
N7 A:HZE508 4.7 22.5 1.0
CB A:GLU364 4.9 18.6 1.0
O A:HOH640 5.0 35.5 1.0
CD1 A:ILE338 5.0 34.1 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: Sun Oct 6 08:02:40 2024

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