Magnesium in PDB 4phh: Crystal Structure of YPT7 Covalently Modified with Gnp

The structure of Crystal Structure of YPT7 Covalently Modified with Gnp, PDB code: 4phh was solved by D.Wiegandt, S.Vieweg, F.Hofmann, D.Koch, Y.Wu, A.Itzen, M.P.Mueller, R.S.Goody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.18 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.570, 72.230, 82.340, 90.00, 91.49, 90.00
R / Rfree (%)	20 / 26.3

The structure of Crystal Structure of YPT7 Covalently Modified with Gnp also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of YPT7 Covalently Modified with Gnp (pdb code 4phh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of YPT7 Covalently Modified with Gnp, PDB code: 4phh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of YPT7 Covalently Modified with Gnp


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 YPT7 Covalently Modified with Gnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:58.2 occ:1.00 OG1 A:THR40 1.9 58.1 1.0 OG1 A:THR22 1.9 55.6 1.0 O A:HOH304 1.9 53.5 1.0 O2B A:2UK201 2.0 54.8 1.0 O1G A:2UK201 2.0 56.5 1.0 O A:HOH303 2.1 62.8 1.0 CB A:THR40 3.0 57.8 1.0 PB A:2UK201 3.1 52.2 1.0 CB A:THR22 3.1 56.6 1.0 PG A:2UK201 3.2 56.0 1.0 N3B A:2UK201 3.3 53.6 1.0 N A:THR40 3.7 63.0 1.0 OD2 A:ASP64 3.8 67.4 1.0 O2G A:2UK201 3.9 57.3 1.0 N A:THR22 3.9 51.5 1.0 CA A:THR40 4.0 63.0 1.0 O2A A:2UK201 4.0 55.9 1.0 CA A:THR22 4.1 50.8 1.0 CG2 A:THR22 4.1 55.3 1.0 CG2 A:THR40 4.1 53.9 1.0 O3A A:2UK201 4.1 52.2 1.0 OD1 A:ASP64 4.2 59.8 1.0 O1B A:2UK201 4.2 52.9 1.0 PA A:2UK201 4.3 57.8 1.0 CG A:ASP64 4.4 65.0 1.0 O3G A:2UK201 4.4 59.2 1.0 O A:THR65 4.5 54.4 1.0 O A:LYS38 4.6 61.9 1.0 O1A A:2UK201 4.6 52.7 1.0 C A:ALA39 4.8 66.4 1.0 CB A:LYS21 4.9 48.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of YPT7 Covalently Modified with Gnp


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 YPT7 Covalently Modified with Gnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:68.6 occ:1.00 O B:HOH302 1.8 56.2 1.0 OG1 B:THR22 2.0 63.6 1.0 O2B B:2UK201 2.2 67.1 1.0 O1G B:2UK201 2.3 69.0 1.0 O B:HOH301 2.4 57.9 1.0 OG1 B:THR40 2.4 77.6 1.0 CB B:THR40 2.9 77.8 1.0 CB B:THR22 3.1 64.3 1.0 PB B:2UK201 3.4 64.6 1.0 PG B:2UK201 3.4 69.8 1.0 OD2 B:ASP64 3.6 74.5 1.0 OD1 B:ASP64 3.7 73.3 1.0 N B:THR22 3.8 59.4 1.0 N3B B:2UK201 3.8 66.2 1.0 O2G B:2UK201 3.8 59.6 1.0 CG2 B:THR40 3.9 76.7 1.0 CA B:THR22 4.0 61.1 1.0 N B:THR40 4.0 83.3 1.0 CG B:ASP64 4.0 73.9 1.0 CA B:THR40 4.1 83.6 1.0 O B:THR65 4.2 79.9 1.0 CG2 B:THR22 4.2 67.6 1.0 O1B B:2UK201 4.2 63.2 1.0 O3A B:2UK201 4.6 61.7 1.0 O2A B:2UK201 4.6 64.7 1.0 O3G B:2UK201 4.7 69.8 1.0 CB B:LYS21 4.8 48.6 1.0 C B:LYS21 4.8 54.3 1.0 NZ B:LYS21 4.8 50.4 1.0 PA B:2UK201 4.9 64.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of YPT7 Covalently Modified with Gnp


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 YPT7 Covalently Modified with Gnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:66.6 occ:1.00 OG1 C:THR40 1.7 82.5 1.0 O C:HOH303 1.8 68.4 1.0 O1G C:2UK201 1.9 73.1 1.0 O2B C:2UK201 2.0 64.4 1.0 O C:HOH302 2.0 63.6 1.0 OG1 C:THR22 2.2 63.6 1.0 CB C:THR40 3.0 79.3 1.0 PG C:2UK201 3.0 73.5 1.0 PB C:2UK201 3.1 65.8 1.0 CB C:THR22 3.3 65.2 1.0 N3B C:2UK201 3.4 66.6 1.0 O2G C:2UK201 3.6 71.0 1.0 N C:THR40 3.7 81.6 1.0 OD1 C:ASP64 3.8 75.8 1.0 CA C:THR40 3.9 83.0 1.0 N C:THR22 3.9 61.1 1.0 CG2 C:THR40 4.0 78.3 1.0 OD2 C:ASP64 4.0 77.5 1.0 O2A C:2UK201 4.2 70.8 1.0 O3A C:2UK201 4.2 66.2 1.0 CA C:THR22 4.2 62.5 1.0 O1B C:2UK201 4.2 62.0 1.0 O C:THR65 4.3 78.1 1.0 CG C:ASP64 4.3 78.2 1.0 O3G C:2UK201 4.3 75.2 1.0 CG2 C:THR22 4.3 63.4 1.0 PA C:2UK201 4.5 70.7 1.0 O C:LYS38 4.6 84.2 1.0 O1A C:2UK201 4.6 71.3 1.0 NZ C:LYS21 4.7 56.3 1.0 C C:ALA39 4.8 81.2 1.0 CB C:LYS21 4.8 58.6 1.0 CE C:LYS21 4.9 61.6 1.0 C C:LYS21 5.0 59.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of YPT7 Covalently Modified with Gnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of YPT7 Covalently Modified with Gnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:82.5 occ:1.00 O2B D:2UK201 1.8 59.8 1.0 O D:HOH301 2.0 55.3 1.0 OG1 D:THR40 2.0 80.5 1.0 O D:HOH302 2.0 55.5 1.0 O1G D:2UK201 2.1 74.3 1.0 OG1 D:THR22 2.5 67.5 1.0 PB D:2UK201 3.0 59.7 1.0 CB D:THR40 3.0 77.6 1.0 PG D:2UK201 3.1 67.4 1.0 O2G D:2UK201 3.3 60.4 1.0 CB D:THR22 3.4 67.1 1.0 N3B D:2UK201 3.4 65.4 1.0 N D:THR40 3.8 88.1 1.0 O1B D:2UK201 3.9 58.5 1.0 OD2 D:ASP64 3.9 75.0 1.0 O2A D:2UK201 4.0 70.1 1.0 CA D:THR40 4.0 83.3 1.0 N D:THR22 4.0 56.7 1.0 OD1 D:ASP64 4.1 63.4 1.0 CG2 D:THR40 4.1 75.2 1.0 O3A D:2UK201 4.2 63.1 1.0 CA D:THR22 4.3 58.4 1.0 O D:THR65 4.3 58.0 1.0 CG D:ASP64 4.4 69.0 1.0 O3G D:2UK201 4.4 68.2 1.0 CG2 D:THR22 4.5 68.4 1.0 PA D:2UK201 4.6 69.1 1.0 C D:ALA39 4.7 96.0 1.0 NZ D:LYS21 4.8 47.3 1.0 CB D:LYS21 4.8 46.7 1.0 O1A D:2UK201 4.8 66.6 1.0 CE D:LYS21 4.9 45.3 1.0

D.Wiegandt, S.Vieweg, F.Hofmann, D.Koch, Y.Wu, A.Itzen, M.P.Mueller, R.S.Goody. Crystal Structure of YPT7 Covalently Modified with Gnp To Be Published.