Magnesium in PDB 6tpl: D0-D1 Domain of Intimin

The structure of D0-D1 Domain of Intimin, PDB code: 6tpl was solved by J.Weikum, J.C.Leo, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.77 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.737, 45.325, 67.561, 97.08, 97.55, 99.9
R / Rfree (%)	18.7 / 23.1

The structure of D0-D1 Domain of Intimin also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the D0-D1 Domain of Intimin (pdb code 6tpl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the D0-D1 Domain of Intimin, PDB code: 6tpl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the D0-D1 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of D0-D1 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:24.1 occ:1.00 O A:HOH1264 1.9 24.3 1.0 O A:HOH1142 2.0 22.0 1.0 O A:HOH964 2.0 19.1 1.0 O B:HOH1108 2.1 27.2 1.0 O A:HOH1189 2.1 22.7 1.0 O A:HOH1192 2.3 19.9 1.0 H A:ALA677 3.5 14.6 1.0 HB3 A:ALA677 4.0 18.6 1.0 O A:HOH1202 4.1 34.1 1.0 O A:HOH1169 4.2 23.9 1.0 O A:ALA677 4.2 11.4 1.0 O B:HOH946 4.3 9.3 1.0 O A:HOH944 4.3 9.7 1.0 N A:ALA677 4.4 12.1 1.0 OD2 A:ASP676 4.4 11.9 1.0 HA A:ASP676 4.4 14.4 1.0 O A:HOH1246 4.5 28.1 1.0 HZ1 A:LYS667 4.5 13.9 1.0 O A:HOH1148 4.6 8.5 1.0 HZ3 A:LYS667 4.6 13.9 1.0 CB A:ALA677 4.9 15.5 1.0 CA A:ALA677 5.0 14.1 1.0

Magnesium binding site 2 out of 4 in the D0-D1 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of D0-D1 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:29.8 occ:1.00 O A:HOH1216 2.2 32.3 1.0 O A:HOH914 2.2 24.6 1.0 O A:HOH1038 2.5 33.5 1.0 HH A:TYR717 3.7 19.0 1.0 HZ2 A:LYS683 3.8 24.4 1.0 O A:HOH913 3.9 34.4 1.0 OE2 A:GLU662 4.2 18.8 1.0 OH A:TYR717 4.2 15.9 1.0 O A:HOH1172 4.3 33.7 1.0 O A:HOH1162 4.3 35.4 1.0 HZ3 A:LYS683 4.4 24.4 1.0 HZ1 A:LYS664 4.4 33.3 1.0 NZ A:LYS683 4.5 20.3 1.0 O A:HOH903 4.6 19.9 1.0 HZ2 A:LYS664 4.6 33.3 1.0 O A:HOH926 4.8 36.5 1.0 HD2 A:LYS683 4.9 16.8 1.0 HZ1 A:LYS683 4.9 24.4 1.0 OE1 A:GLU662 4.9 12.5 1.0 CD A:GLU662 4.9 17.3 1.0 NZ A:LYS664 5.0 27.7 1.0

Magnesium binding site 3 out of 4 in the D0-D1 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of D0-D1 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:49.4 occ:1.00 OE1 A:GLU576 2.0 50.1 1.0 O A:HOH956 2.4 53.4 1.0 O A:HOH905 2.4 41.3 1.0 O A:HOH1218 2.6 60.9 1.0 O A:HOH965 2.8 63.0 1.0 HE2 A:LYS567 3.1 26.6 1.0 CD A:GLU576 3.2 58.5 1.0 HZ3 A:LYS567 3.2 30.5 1.0 HD3 A:LYS567 3.6 27.3 1.0 OE2 A:GLU576 3.7 72.1 1.0 CE A:LYS567 3.8 22.2 1.0 NZ A:LYS567 3.8 25.4 1.0 HZ1 A:LYS567 4.0 30.5 1.0 HA A:ALA570 4.0 23.6 1.0 CD A:LYS567 4.1 22.8 1.0 O A:SER569 4.3 17.9 1.0 HZ3 A:LYS571 4.3 131.7 1.0 CG A:GLU576 4.3 54.5 1.0 HG3 A:GLU576 4.4 65.4 1.0 HG2 A:LYS567 4.4 30.4 1.0 OD2 A:ASP688 4.5 33.7 1.0 HG2 A:GLU576 4.5 65.4 1.0 HZ2 A:LYS567 4.6 30.5 1.0 HE3 A:LYS567 4.6 26.6 1.0 O A:HOH960 4.7 24.0 1.0 HZ1 A:LYS571 4.7 131.7 1.0 CG A:LYS567 4.8 25.3 1.0 HB3 A:LYS567 4.9 28.9 1.0 O A:HOH1143 4.9 50.9 1.0 OD1 A:ASP688 4.9 36.4 1.0 HD2 A:LYS567 4.9 27.3 1.0 NZ A:LYS571 5.0 109.8 1.0 HB2 A:ALA570 5.0 23.8 1.0 CA A:ALA570 5.0 19.7 1.0

Magnesium binding site 4 out of 4 in the D0-D1 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of D0-D1 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:31.1 occ:1.00 O B:HOH1023 2.0 31.3 1.0 O B:HOH1095 2.0 29.5 1.0 O B:HOH925 2.1 28.6 1.0 O B:HOH1085 2.2 41.5 1.0 O B:HOH966 3.5 52.9 1.0 O B:ALA572 4.3 23.8 1.0 HB3 B:ASP627 4.3 44.9 1.0 HA B:ASP573 4.3 37.6 1.0 OD1 B:ASP627 4.3 27.7 1.0 O B:ASP627 4.3 44.3 1.0 O B:HOH1094 4.6 49.0 1.0 O B:HOH1124 4.6 46.7 1.0 HA B:ASP627 4.9 45.4 1.0 CB B:ASP627 5.0 37.4 1.0

J.Weikum, A.V.Kulakova, G.Tesei, L.V.Jaegerum, M.Skepoe, P.Harris, J.C.Leo, J.P.Morth. Structural Similarly Between the Intimin Stalk Modules D0 and D00 with E-Cadherin Suggest Functional Equivalence. To Be Published.