Manganese in PDB 4fli: Human METAP1 with Bengamide Analog Y16, in Mn Form

All present enzymatic activity of Human METAP1 with Bengamide Analog Y16, in Mn Form:
3.4.11.18;

The structure of Human METAP1 with Bengamide Analog Y16, in Mn Form, PDB code: 4fli was solved by Q.Z.Ye, W.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.41 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.771, 77.562, 48.811, 90.00, 90.18, 90.00
R / Rfree (%)	18.3 / 21.1

The structure of Human METAP1 with Bengamide Analog Y16, in Mn Form also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Human METAP1 with Bengamide Analog Y16, in Mn Form (pdb code 4fli). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human METAP1 with Bengamide Analog Y16, in Mn Form, PDB code: 4fli:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human METAP1 with Bengamide Analog Y16, in Mn Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human METAP1 with Bengamide Analog Y16, in Mn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:14.1 occ:1.00 NE2 A:HIS303 2.1 8.6 1.0 O2 A:Y16503 2.2 18.1 1.0 OD2 A:ASP240 2.2 16.1 1.0 OE1 A:GLU336 2.2 15.1 1.0 OE2 A:GLU367 2.2 13.3 1.0 O3 A:Y16503 2.3 13.8 1.0 CD2 A:HIS303 3.1 18.4 1.0 CD A:GLU336 3.1 14.5 1.0 CE1 A:HIS303 3.1 16.9 1.0 CG A:ASP240 3.2 16.5 1.0 C06 A:Y16503 3.2 13.7 1.0 C05 A:Y16503 3.2 14.7 1.0 OE2 A:GLU336 3.3 13.8 1.0 CD A:GLU367 3.3 15.5 1.0 MN A:MN502 3.5 13.5 1.0 OE1 A:GLU367 3.7 13.5 1.0 OD1 A:ASP240 3.7 13.5 1.0 OG1 A:THR334 3.9 16.8 1.0 C07 A:Y16503 3.9 15.5 1.0 C04 A:Y16503 3.9 16.7 1.0 CG2 A:THR334 4.2 14.1 1.0 CG A:HIS303 4.2 14.2 1.0 ND1 A:HIS303 4.2 16.0 1.0 O1 A:Y16503 4.3 17.8 1.0 CB A:ASP240 4.3 13.8 1.0 NE2 A:HIS310 4.4 15.6 1.0 CG A:GLU336 4.4 11.9 1.0 CB A:THR334 4.5 12.6 1.0 CG A:GLU367 4.6 14.7 1.0 N1 A:Y16503 4.7 16.6 1.0 C11 A:Y16503 4.8 15.4 1.0 CD2 A:HIS310 4.8 20.2 1.0 O6 A:Y16503 4.9 16.8 1.0 CE1 A:PHE309 4.9 13.2 1.0

Manganese binding site 2 out of 2 in the Human METAP1 with Bengamide Analog Y16, in Mn Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human METAP1 with Bengamide Analog Y16, in Mn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:13.5 occ:1.00 OD1 A:ASP240 2.1 13.5 1.0 OD1 A:ASP229 2.1 12.6 1.0 OE1 A:GLU367 2.1 13.5 1.0 O1 A:Y16503 2.2 17.8 1.0 O3 A:Y16503 2.3 13.8 1.0 OD2 A:ASP229 2.4 16.3 1.0 CG A:ASP229 2.5 13.5 1.0 CG A:ASP240 3.0 16.5 1.0 CD A:GLU367 3.1 15.5 1.0 C04 A:Y16503 3.2 16.7 1.0 C05 A:Y16503 3.2 14.7 1.0 OD2 A:ASP240 3.3 16.1 1.0 OE2 A:GLU367 3.3 13.3 1.0 MN A:MN501 3.5 14.1 1.0 OE2 A:GLU336 4.0 13.8 1.0 O A:HOH655 4.0 19.4 1.0 CB A:ASP229 4.0 11.9 1.0 OG1 A:THR231 4.1 15.2 1.0 ND2 A:ASN242 4.1 12.9 1.0 O A:LEU241 4.2 12.6 1.0 N A:LEU241 4.4 13.3 1.0 CB A:ASP240 4.4 13.8 1.0 O2 A:Y16503 4.4 18.1 1.0 C03 A:Y16503 4.4 14.0 1.0 O A:HOH603 4.5 15.7 1.0 CG A:GLU367 4.5 14.7 1.0 C06 A:Y16503 4.5 13.7 1.0 C A:LEU241 4.5 11.5 1.0 O A:ILE230 4.6 13.3 1.0 C A:ASP240 4.7 13.2 1.0 CB A:ASN242 4.8 12.1 1.0 CB A:GLU367 4.8 12.6 1.0 CD A:GLU336 4.8 14.5 1.0 CA A:ASP240 4.8 13.6 1.0 OE1 A:GLU336 4.8 15.1 1.0 CA A:LEU241 4.8 12.2 1.0 CA A:ASP229 4.9 11.9 1.0 N A:ILE230 5.0 12.2 1.0

W.Xu, J.P.Lu, Q.Z.Ye. Structural Analysis of Bengamide Derivatives As Inhibitors of Methionine Aminopeptidases. J.Med.Chem. V. 55 8021 2012.
ISSN: ISSN 0022-2623
PubMed: 22913487
DOI: 10.1021/JM3008695