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Manganese in PDB 7a13: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK1978537A (Compound 27)

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK1978537A (Compound 27)

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK1978537A (Compound 27):
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK1978537A (Compound 27), PDB code: 7a13 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) 29.97 / 2.04
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.195, 100.770, 99.396, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.7

Other elements in 7a13:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK1978537A (Compound 27) also contains other interesting chemical elements:

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 GSK1978537A (Compound 27) (pdb code 7a13). 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 GSK1978537A (Compound 27), PDB code: 7a13:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7a13

Go back to Manganese Binding Sites List in 7a13
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK1978537A (Compound 27)


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 GSK1978537A (Compound 27) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn509

b:19.5
occ:1.00
OD1 A:ASP262 2.0 20.0 1.0
OE2 A:GLU459 2.1 19.6 1.0
O A:HOH656 2.2 28.8 1.0
OD1 A:ASP251 2.2 14.6 1.0
OD2 A:ASP251 2.3 16.3 1.0
O A:HOH789 2.3 24.9 1.0
CG A:ASP251 2.6 17.4 1.0
CD A:GLU459 2.9 27.4 1.0
CG A:ASP262 3.0 22.4 1.0
OE1 A:GLU459 3.1 16.4 1.0
MN A:MN510 3.4 21.4 1.0
OD2 A:ASP262 3.4 19.6 1.0
CZ A:PHE219 4.0 18.8 1.0
CB A:ASP251 4.1 15.3 1.0
O A:HOH875 4.1 42.5 1.0
NE2 A:GLN457 4.1 14.5 1.0
O A:HOH817 4.2 32.4 1.0
OE2 A:GLU364 4.2 23.5 1.0
O21 A:QW5508 4.3 39.2 1.0
CE1 A:PHE219 4.3 19.3 1.0
CG A:GLU459 4.3 23.7 1.0
O A:HOH613 4.3 36.0 1.0
CB A:ASP262 4.4 19.9 1.0
N A:CYS263 4.6 17.4 1.0
CB A:ALA264 4.6 17.8 1.0
C A:ASP262 4.6 21.1 1.0
CA A:ASP262 4.7 17.9 1.0
OE1 A:GLU364 4.8 28.1 1.0
CD A:GLU364 4.8 35.5 1.0
CE2 A:PHE219 4.8 22.1 1.0
CB A:GLU459 4.9 18.6 1.0
CA A:ASP251 4.9 14.9 1.0

Manganese binding site 2 out of 2 in 7a13

Go back to Manganese Binding Sites List in 7a13
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK1978537A (Compound 27)


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 GSK1978537A (Compound 27) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn510

b:21.4
occ:1.00
OD2 A:ASP262 2.1 19.6 1.0
OE1 A:GLU459 2.1 16.4 1.0
O21 A:QW5508 2.2 39.2 1.0
O A:HOH656 2.2 28.8 1.0
NE2 A:HIS331 2.3 25.5 1.0
OE1 A:GLU364 2.4 28.1 1.0
CG A:ASP262 3.0 22.4 1.0
CD A:GLU364 3.2 35.5 1.0
CD A:GLU459 3.2 27.4 1.0
CE1 A:HIS331 3.3 25.4 1.0
CD2 A:HIS331 3.3 25.8 1.0
C19 A:QW5508 3.3 41.9 1.0
MN A:MN509 3.4 19.5 1.0
OD1 A:ASP262 3.4 20.0 1.0
OE2 A:GLU364 3.6 23.5 1.0
OE2 A:GLU459 3.7 19.6 1.0
O A:HOH789 3.8 24.9 1.0
CB A:ALA362 3.9 20.5 1.0
N20 A:QW5508 4.0 40.5 1.0
CB A:ASP262 4.2 19.9 1.0
O A:HOH817 4.3 32.4 1.0
O1 A:PO4501 4.3 74.1 1.0
CG A:GLU364 4.4 27.7 1.0
ND1 A:HIS331 4.4 25.9 1.0
CG A:HIS331 4.4 24.9 1.0
C10 A:QW5508 4.5 43.1 1.0
CG A:GLU459 4.5 23.7 1.0
N11 A:QW5508 4.6 42.8 1.0
O3 A:PO4501 4.8 72.6 1.0
CD1 A:ILE338 5.0 37.7 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 08:01:15 2024

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