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Manganese in PDB 7a14: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2218325A (Compound 32)

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2218325A (Compound 32)

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2218325A (Compound 32):
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2218325A (Compound 32), PDB code: 7a14 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) 29.90 / 2.14
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 87.343, 100.812, 99.047, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.5

Other elements in 7a14:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2218325A (Compound 32) 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 GSK2218325A (Compound 32) (pdb code 7a14). 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 GSK2218325A (Compound 32), PDB code: 7a14:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7a14

Go back to Manganese Binding Sites List in 7a14
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2218325A (Compound 32)


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 GSK2218325A (Compound 32) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn509

b:25.0
occ:1.00
OD1 A:ASP262 2.0 28.1 1.0
OE2 A:GLU459 2.1 25.7 1.0
O A:HOH623 2.1 21.3 1.0
O A:HOH787 2.2 20.8 1.0
OD2 A:ASP251 2.3 25.5 1.0
OD1 A:ASP251 2.4 24.3 1.0
CG A:ASP251 2.7 24.6 1.0
CG A:ASP262 3.0 27.4 1.0
CD A:GLU459 3.0 27.4 1.0
OE1 A:GLU459 3.2 27.4 1.0
OD2 A:ASP262 3.3 28.0 1.0
MN A:MN510 3.3 28.6 1.0
CZ A:PHE219 4.0 25.1 1.0
NE2 A:GLN457 4.1 23.9 1.0
OE2 A:GLU364 4.1 27.8 1.0
O A:HOH835 4.2 26.9 1.0
CB A:ASP251 4.2 23.2 1.0
O A:HOH784 4.2 28.0 1.0
O24 A:QVB508 4.3 35.8 1.0
CE1 A:PHE219 4.3 25.3 1.0
O A:HOH641 4.3 27.9 1.0
CB A:ASP262 4.3 25.6 1.0
CG A:GLU459 4.4 24.9 1.0
N A:CYS263 4.6 25.4 1.0
C A:ASP262 4.7 25.9 1.0
CB A:ALA264 4.7 26.2 1.0
CA A:ASP262 4.7 25.5 1.0
CD A:GLU364 4.8 29.2 1.0
CE2 A:PHE219 4.9 25.3 1.0
OE1 A:GLU364 4.9 30.3 1.0
CB A:GLU459 4.9 24.4 1.0
N13 A:QVB508 5.0 35.2 1.0

Manganese binding site 2 out of 2 in 7a14

Go back to Manganese Binding Sites List in 7a14
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2218325A (Compound 32)


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 GSK2218325A (Compound 32) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn510

b:28.6
occ:1.00
OD2 A:ASP262 2.1 28.0 1.0
OE1 A:GLU459 2.2 27.4 1.0
O24 A:QVB508 2.2 35.8 1.0
O A:HOH623 2.3 21.3 1.0
NE2 A:HIS331 2.3 31.5 1.0
OE1 A:GLU364 2.4 30.3 1.0
CG A:ASP262 3.0 27.4 1.0
CD A:GLU364 3.1 29.2 1.0
CD A:GLU459 3.3 27.4 1.0
CE1 A:HIS331 3.3 31.4 1.0
CD2 A:HIS331 3.3 30.7 1.0
OE2 A:GLU364 3.3 27.8 1.0
MN A:MN509 3.3 25.0 1.0
C22 A:QVB508 3.4 35.6 1.0
OD1 A:ASP262 3.5 28.1 1.0
OE2 A:GLU459 3.7 25.7 1.0
O A:HOH787 3.9 20.8 1.0
CB A:ALA362 4.0 28.9 1.0
N23 A:QVB508 4.1 35.8 1.0
O A:HOH784 4.3 28.0 1.0
CB A:ASP262 4.3 25.6 1.0
CG A:GLU364 4.3 27.3 1.0
CG A:HIS331 4.4 30.1 1.0
ND1 A:HIS331 4.4 31.1 1.0
C12 A:QVB508 4.5 35.3 1.0
CG A:GLU459 4.6 24.9 1.0
N13 A:QVB508 4.6 35.2 1.0
CD1 A:ILE338 4.9 36.6 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 08:02:34 2024

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