Manganese in PDB 4ekk: AKT1 with Amp-Pnp

All present enzymatic activity of AKT1 with Amp-Pnp:
2.7.11.1; 2.7.11.26;

The structure of AKT1 with Amp-Pnp, PDB code: 4ekk was solved by W.-I.Wu, G.P.A.Vigers, T.H.Morales, B.J.Brandhuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.69 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.637, 55.853, 91.402, 90.00, 103.43, 90.00
R / Rfree (%)	21.7 / 28

The binding sites of Manganese atom in the AKT1 with Amp-Pnp (pdb code 4ekk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the AKT1 with Amp-Pnp, PDB code: 4ekk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the AKT1 with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of AKT1 with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:71.1 occ:1.00 O2A A:ANP501 2.1 77.0 1.0 OD2 A:ASP292 2.3 48.0 1.0 O1G A:ANP501 2.3 81.0 1.0 OD1 A:ASN279 2.4 37.3 1.0 N3B A:ANP501 2.9 80.2 1.0 PG A:ANP501 3.0 80.6 1.0 CG A:ASP292 3.3 46.3 1.0 O3G A:ANP501 3.4 80.5 1.0 CG A:ASN279 3.5 37.7 1.0 PA A:ANP501 3.5 77.5 1.0 CB A:ASP292 3.7 45.2 1.0 O3A A:ANP501 3.8 78.8 1.0 PB A:ANP501 3.8 80.1 1.0 ND2 A:ASN279 4.0 38.0 1.0 O2B A:ANP501 4.1 79.9 1.0 CE A:LYS276 4.3 35.9 1.0 OD1 A:ASP292 4.3 47.6 1.0 MN A:MN503 4.4 73.8 1.0 O1A A:ANP501 4.4 77.6 1.0 O2G A:ANP501 4.5 80.6 1.0 NZ A:LYS276 4.5 35.4 1.0 O5' A:ANP501 4.6 76.0 1.0 O3' A:ANP501 4.6 70.9 1.0 CB A:ASN279 4.7 37.7 1.0 C5' A:ANP501 4.8 73.2 1.0 CA A:ASN279 4.8 37.9 1.0 C3' A:ANP501 4.9 70.7 1.0

Manganese binding site 2 out of 4 in the AKT1 with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of AKT1 with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:73.8 occ:1.00 O2B A:ANP501 2.1 79.9 1.0 O3G A:ANP501 2.2 80.5 1.0 OD1 A:ASP292 2.5 47.6 1.0 OD2 A:ASP292 2.6 48.0 1.0 CG A:ASP292 2.9 46.3 1.0 PB A:ANP501 3.6 80.1 1.0 PG A:ANP501 3.6 80.6 1.0 OG C:SER7 3.8 55.3 1.0 N3B A:ANP501 3.9 80.2 1.0 OD2 A:ASP274 4.3 37.5 1.0 CB A:ASP292 4.4 45.2 1.0 MN A:MN502 4.4 71.1 1.0 O1B A:ANP501 4.5 80.4 1.0 O1G A:ANP501 4.5 81.0 1.0 O3A A:ANP501 4.6 78.8 1.0 N A:GLY294 4.6 42.9 1.0 O2G A:ANP501 4.7 80.6 1.0 CA A:GLY294 4.7 42.7 1.0 CG A:LEU295 4.7 41.7 1.0 O A:HOH646 4.7 36.6 1.0 CB C:SER7 4.8 55.1 1.0 CD1 A:LEU295 4.9 41.2 1.0 NZ A:LYS179 4.9 59.5 1.0

Manganese binding site 3 out of 4 in the AKT1 with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of AKT1 with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:64.7 occ:1.00 OD1 B:ASN279 2.4 40.4 1.0 O2A B:ANP501 2.4 74.4 1.0 N3B B:ANP501 2.5 76.4 1.0 O1G B:ANP501 2.9 76.6 1.0 OD2 B:ASP292 2.9 46.1 1.0 PG B:ANP501 3.2 76.9 1.0 CG B:ASN279 3.5 39.2 1.0 O2G B:ANP501 3.7 76.2 1.0 CG B:ASP292 3.8 43.5 1.0 PA B:ANP501 3.8 73.7 1.0 CB B:ASP292 3.9 42.0 1.0 PB B:ANP501 3.9 76.2 1.0 CE B:LYS276 4.0 38.0 1.0 ND2 B:ASN279 4.0 38.4 1.0 O3A B:ANP501 4.0 74.8 1.0 NZ B:LYS276 4.3 37.8 1.0 O3' B:ANP501 4.6 70.7 1.0 OD2 B:ASP274 4.6 38.5 1.0 O3G B:ANP501 4.6 76.6 1.0 C5' B:ANP501 4.7 70.7 1.0 O2B B:ANP501 4.7 76.7 1.0 CB B:ASN279 4.7 38.4 1.0 O5' B:ANP501 4.8 72.7 1.0 O1A B:ANP501 4.8 73.5 1.0 O B:GLU278 4.8 38.5 1.0 CA B:ASN279 4.8 38.5 1.0 CB B:GLU278 4.9 38.9 1.0 MN B:MN503 4.9 78.5 1.0 C B:GLU278 4.9 38.4 1.0 N B:ASN279 4.9 38.3 1.0 O1B B:ANP501 5.0 76.5 1.0 OD1 B:ASP292 5.0 44.5 1.0

Manganese binding site 4 out of 4 in the AKT1 with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of AKT1 with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:78.5 occ:1.00 O2B B:ANP501 2.5 76.7 1.0 OD2 B:ASP292 2.5 46.1 1.0 OD1 B:ASP292 2.9 44.5 1.0 CG B:ASP292 3.1 43.5 1.0 OG D:SER7 3.5 68.8 1.0 N3B B:ANP501 3.5 76.4 1.0 PB B:ANP501 3.6 76.2 1.0 O3G B:ANP501 4.0 76.6 1.0 PG B:ANP501 4.2 76.9 1.0 CA B:GLY294 4.2 41.2 1.0 O1G B:ANP501 4.4 76.6 1.0 OD2 B:ASP274 4.4 38.5 1.0 N B:GLY294 4.5 41.2 1.0 O1B B:ANP501 4.6 76.5 1.0 CB B:ASP292 4.6 42.0 1.0 CB D:SER7 4.7 68.8 1.0 O3A B:ANP501 4.7 74.8 1.0 CG B:LEU295 4.7 41.3 1.0 N B:LEU295 4.8 41.5 1.0 C B:GLY294 4.8 41.4 1.0 MN B:MN502 4.9 64.7 1.0 CE1 B:PHE161 4.9 81.0 1.0

K.Lin, J.Lin, W.I.Wu, J.Ballard, B.B.Lee, S.L.Gloor, G.P.Vigers, T.H.Morales, L.S.Friedman, N.Skelton, B.J.Brandhuber. An Atp-Site on-Off Switch That Restricts Phosphatase Accessibility of Akt. Sci.Signal. V. 5 RA37 2012.
ISSN: ESSN 1937-9145
PubMed: 22569334
DOI: 10.1126/SCISIGNAL.2002618