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Manganese in PDB 6qej: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide, PDB code: 6qej was solved by D.Musil, T.Heinrich, M.Lehmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.25 / 1.62
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 90.565, 99.929, 100.941, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 18.4

Other elements in 6qej:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide also contains other interesting chemical elements:

Fluorine (F) 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 Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide (pdb code 6qej). 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 Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide, PDB code: 6qej:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6qej

Go back to Manganese Binding Sites List in 6qej
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide


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 Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:15.9
occ:1.00
 OE2 A:GLU459 2.0 18.6 1.0
NE2 A:HIS331 2.1 18.6 1.0
OE2 A:GLU364 2.1 23.4 1.0
N12 A:HZT502 2.2 20.0 1.0
OD2 A:ASP262 2.2 20.4 1.0
N13 A:HZT502 3.0 20.5 1.0
CD A:GLU364 3.0 29.9 1.0
CD A:GLU459 3.1 18.0 1.0
CD2 A:HIS331 3.1 18.8 1.0
CE1 A:HIS331 3.1 17.9 1.0
CG A:ASP262 3.2 18.4 1.0
C11 A:HZT502 3.2 26.0 1.0
MN A:MN505 3.4 14.1 1.0
OE1 A:GLU364 3.5 21.0 1.0
OE1 A:GLU459 3.5 16.0 1.0
OD1 A:ASP262 3.6 16.8 1.0
C10 A:HZT502 3.6 29.3 1.0
CB A:ALA362 3.8 16.6 1.0
CG A:GLU364 4.1 22.2 1.0
C14 A:HZT502 4.2 18.3 1.0
CG A:HIS331 4.2 18.8 1.0
ND1 A:HIS331 4.2 19.3 1.0
N15 A:HZT502 4.3 23.9 1.0
O A:HOH624 4.3 32.3 1.0
CG A:GLU459 4.4 16.0 1.0
CB A:ASP262 4.4 16.3 1.0
N9 A:HZT502 4.7 35.8 1.0
CB A:GLU364 4.9 19.4 1.0
C8 A:HZT502 5.0 30.1 1.0

Manganese binding site 2 out of 2 in 6qej

Go back to Manganese Binding Sites List in 6qej
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide


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 Thiophene-2-Sulfonic Acid (4-Fluoro-Benzyl)-(4H-[1,2, 4]Triazol-3-Ylmethyl)-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:14.1
occ:1.00
 OD1 A:ASP262 2.0 16.8 1.0
OE1 A:GLU459 2.0 16.0 1.0
OD1 A:ASP251 2.0 16.3 1.0
N13 A:HZT502 2.1 20.5 1.0
OD2 A:ASP251 2.5 17.0 1.0
CG A:ASP251 2.6 13.4 1.0
CD A:GLU459 2.9 18.0 1.0
CG A:ASP262 2.9 18.4 1.0
N12 A:HZT502 2.9 20.0 1.0
C14 A:HZT502 3.1 18.3 1.0
OE2 A:GLU459 3.2 18.6 1.0
OD2 A:ASP262 3.2 20.4 1.0
MN A:MN504 3.4 15.9 1.0
CZ A:PHE219 3.7 16.7 1.0
CB A:ASP251 4.1 12.5 1.0
C11 A:HZT502 4.1 26.0 1.0
CE1 A:PHE219 4.1 16.5 1.0
N15 A:HZT502 4.2 23.9 1.0
CG A:GLU459 4.2 16.0 1.0
NE2 A:GLN457 4.2 14.4 1.0
CB A:ASP262 4.3 16.3 1.0
OE1 A:GLU364 4.3 21.0 1.0
N A:CYS263 4.4 13.9 1.0
C A:ASP262 4.5 16.0 1.0
CB A:ALA264 4.5 13.3 1.0
O A:HOH606 4.5 24.1 1.0
CE2 A:PHE219 4.6 18.3 1.0
CA A:ASP262 4.6 14.3 1.0
CB A:GLU459 4.7 14.2 1.0
OE2 A:GLU364 4.7 23.4 1.0
CA A:ASP251 4.8 11.1 1.0
CD A:GLU364 4.8 29.9 1.0
O A:HOH624 4.8 32.3 1.0
O A:CYS263 4.8 13.8 1.0
C A:CYS263 4.9 14.5 1.0
C A:ASP251 5.0 13.2 1.0

Reference:

T.Heinrich, J.Seenisamy, B.Blume, J.Bomke, M.Calderini, U.Eckert, M.Friese-Hamim, R.Kohl, M.Lehmann, B.Leuthner, D.Musil, F.Rohdich, F.T.Zenke. Discovery and Structure-Based Optimization of Next-Generation Reversible Methionine Aminopeptidase-2 (Metap-2) Inhibitors. J.Med.Chem. V. 62 5025 2019.
ISSN: ISSN 0022-2623
PubMed: 30939017
DOI: 10.1021/ACS.JMEDCHEM.9B00041
Page generated: Sun Oct 6 05:56:22 2024

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