Magnesium in PDB 9iwt: Crystal Structure of Human Nampt Complexed with Amp

All present enzymatic activity of Crystal Structure of Human Nampt Complexed with Amp:
2.4.2.12;

The structure of Crystal Structure of Human Nampt Complexed with Amp, PDB code: 9iwt was solved by G.Wang, C.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.51 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.17, 93.374, 241.942, 90, 90, 90
R / Rfree (%)	18.5 / 22.7

The binding sites of Magnesium atom in the Crystal Structure of Human Nampt Complexed with Amp (pdb code 9iwt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Nampt Complexed with Amp, PDB code: 9iwt:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Nampt Complexed with Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Nampt Complexed with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:57.9 occ:1.00 O3' A:AMP501 2.5 60.0 1.0 OD1 A:ASP354 2.6 45.4 1.0 O B:HOH709 2.6 43.2 1.0 O A:HOH691 3.1 47.6 1.0 C3' A:AMP501 3.5 52.1 1.0 C4' A:AMP501 3.5 52.7 1.0 OD1 A:ASP313 3.6 43.0 1.0 CG A:ASP354 3.6 41.6 1.0 O1P A:AMP501 3.7 50.6 1.0 O2' A:AMP501 3.8 53.1 1.0 NZ B:LYS423 3.9 52.9 1.0 OD2 A:ASP313 4.0 44.0 1.0 O3 B:PO4502 4.0 58.1 1.0 CB A:ASP354 4.0 41.3 1.0 C5' A:AMP501 4.0 54.6 1.0 CG A:ASP313 4.2 46.3 1.0 CA A:ASP354 4.2 42.9 1.0 C2' A:AMP501 4.3 56.5 1.0 O A:GLY353 4.3 43.0 1.0 O2 B:PO4502 4.3 53.1 1.0 P B:PO4502 4.6 69.2 1.0 OD2 A:ASP354 4.7 42.6 1.0 P A:AMP501 4.7 53.2 1.0 O5' A:AMP501 4.8 56.4 1.0 O4 B:PO4502 4.8 59.8 1.0 O A:ASP313 4.8 41.4 1.0 O4' A:AMP501 4.8 60.4 1.0 O A:HOH677 4.9 48.2 1.0 CE B:LYS423 5.0 47.2 1.0 O2P A:AMP501 5.0 46.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Nampt Complexed with Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Nampt Complexed with Amp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg504 b:54.8 occ:1.00 OD1 C:ASP354 2.6 38.6 1.0 O D:HOH708 2.6 42.2 1.0 O3' C:AMP501 2.8 49.9 1.0 O C:HOH692 3.1 41.8 1.0 CG C:ASP354 3.6 34.9 1.0 OD1 C:ASP313 3.7 35.8 1.0 NZ D:LYS423 3.8 40.0 1.0 C3' C:AMP501 3.8 52.3 1.0 C4' C:AMP501 3.8 52.1 1.0 O2' C:AMP501 3.9 52.0 1.0 O1P C:AMP501 3.9 53.5 1.0 CB C:ASP354 4.0 33.0 1.0 OD2 C:ASP313 4.1 35.4 1.0 CA C:ASP354 4.3 32.2 1.0 CG C:ASP313 4.3 32.2 1.0 O1 D:PO4502 4.3 52.2 1.0 O3 D:PO4502 4.3 52.5 1.0 C2' C:AMP501 4.5 48.3 1.0 C5' C:AMP501 4.5 44.4 1.0 O C:GLY353 4.5 35.8 1.0 O C:ASP313 4.7 33.1 1.0 O2P C:AMP501 4.7 46.0 1.0 P D:PO4502 4.7 53.1 1.0 OD2 C:ASP354 4.7 38.3 1.0 P C:AMP501 4.8 48.6 1.0 O4 D:PO4502 4.8 49.9 1.0 O5' C:AMP501 4.8 54.8 1.0 CE D:LYS423 4.9 38.0 1.0 N C:GLY355 5.0 34.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Nampt Complexed with Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Nampt Complexed with Amp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg504 b:57.0 occ:1.00 OD1 D:ASP354 2.7 39.8 1.0 O D:HOH679 3.0 42.8 1.0 O1P D:AMP501 3.3 50.7 1.0 O3' D:AMP501 3.3 53.9 1.0 C4' D:AMP501 3.5 58.5 1.0 O D:HOH605 3.5 41.9 1.0 O1 C:PO4502 3.7 52.3 1.0 O C:HOH849 3.8 48.9 1.0 CG D:ASP354 3.9 38.7 1.0 C3' D:AMP501 3.9 52.9 1.0 C5' D:AMP501 4.0 48.4 1.0 O2' D:AMP501 4.1 50.9 1.0 O4 C:PO4502 4.1 48.0 1.0 NZ C:LYS423 4.2 36.1 1.0 O5' D:AMP501 4.3 54.2 1.0 P D:AMP501 4.3 54.6 1.0 OD1 D:ASP313 4.4 36.5 1.0 CB D:ASP354 4.4 32.1 1.0 CA D:ASP354 4.5 31.0 1.0 P C:PO4502 4.5 52.5 1.0 O4' D:AMP501 4.5 51.1 1.0 O2P D:AMP501 4.6 48.4 1.0 OD2 D:ASP313 4.6 31.8 1.0 C2' D:AMP501 4.6 49.1 1.0 NH2 C:ARG392 4.8 31.1 1.0 O D:GLY353 4.8 40.5 1.0 CG D:ASP313 4.9 36.5 1.0 OD2 D:ASP354 4.9 34.8 1.0 N D:GLY355 4.9 32.9 1.0

G.Wang, C.Wu. Crystal Structure of Human Nampt Complexed with Amp To Be Published.