Manganese in PDB 7a12: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9)

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9)

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9):
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9), PDB code: 7a12 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) 24.76 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.424, 100.628, 99.031, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.8

Other elements in 7a12:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9) 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 GW557358X (Compound 9) (pdb code 7a12). 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 GW557358X (Compound 9), PDB code: 7a12:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7a12

Go back to Manganese Binding Sites List in 7a12
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9)


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 GW557358X (Compound 9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn511

b:23.3
occ:1.00
OD1 A:ASP262 2.0 22.7 1.0
OE2 A:GLU459 2.1 20.1 1.0
O A:HOH610 2.2 22.7 1.0
O A:HOH773 2.2 24.7 1.0
OD2 A:ASP251 2.3 19.6 1.0
OD1 A:ASP251 2.3 18.3 1.0
CG A:ASP251 2.6 19.6 1.0
CD A:GLU459 2.9 29.1 1.0
CG A:ASP262 3.0 23.3 1.0
OE1 A:GLU459 3.1 21.3 1.0
MN A:MN512 3.4 24.8 1.0
OD2 A:ASP262 3.4 22.5 1.0
CZ A:PHE219 4.0 23.1 1.0
O A:HOH780 4.1 21.1 0.5
NE2 A:GLN457 4.1 16.1 1.0
CB A:ASP251 4.1 17.1 1.0
O A:HOH742 4.1 38.8 1.0
OE2 A:GLU364 4.2 26.8 1.0
CE1 A:PHE219 4.3 23.8 1.0
O A:HOH603 4.3 38.6 1.0
O03 A:QVK510 4.3 36.9 0.5
CG A:GLU459 4.3 24.0 1.0
CB A:ASP262 4.4 22.3 1.0
O A:HOH835 4.4 48.8 1.0
N A:CYS263 4.6 20.2 1.0
CB A:ALA264 4.6 20.9 1.0
C A:ASP262 4.6 24.9 1.0
CA A:ASP262 4.7 21.1 1.0
CD A:GLU364 4.8 39.6 1.0
OE1 A:GLU364 4.8 28.8 1.0
CB A:GLU459 4.9 21.4 1.0
CE2 A:PHE219 4.9 25.3 1.0
CA A:ASP251 5.0 16.9 1.0
N05 A:QVK510 5.0 36.0 0.5

Manganese binding site 2 out of 2 in 7a12

Go back to Manganese Binding Sites List in 7a12
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9)


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 GW557358X (Compound 9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn512

b:24.8
occ:1.00
OD2 A:ASP262 2.2 22.5 1.0
O03 A:QVK510 2.2 36.9 0.5
OE1 A:GLU459 2.2 21.3 1.0
O A:HOH780 2.2 21.1 0.5
O A:HOH610 2.3 22.7 1.0
NE2 A:HIS331 2.3 29.2 1.0
OE1 A:GLU364 2.3 28.8 1.0
CG A:ASP262 3.0 23.3 1.0
CD A:GLU364 3.1 39.6 1.0
CE1 A:HIS331 3.3 29.0 1.0
C02 A:QVK510 3.3 36.1 0.5
CD A:GLU459 3.3 29.1 1.0
CD2 A:HIS331 3.3 29.4 1.0
MN A:MN511 3.4 23.3 1.0
OD1 A:ASP262 3.4 22.7 1.0
OE2 A:GLU364 3.5 26.8 1.0
OE2 A:GLU459 3.8 20.1 1.0
O A:HOH773 3.9 24.7 1.0
CB A:ALA362 3.9 25.4 1.0
N01 A:QVK510 3.9 35.1 0.5
O1 A:PO4501 4.2 70.5 1.0
CB A:ASP262 4.3 22.3 1.0
CG A:GLU364 4.3 25.9 1.0
O A:HOH742 4.3 38.8 1.0
C04 A:QVK510 4.4 36.4 0.5
ND1 A:HIS331 4.4 29.8 1.0
CG A:HIS331 4.5 28.7 1.0
N05 A:QVK510 4.5 36.0 0.5
CG A:GLU459 4.6 24.0 1.0
O3 A:PO4501 4.7 70.7 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: Tue Dec 15 05:11:20 2020

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