Magnesium in PDB 3tcx: Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation

The structure of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation, PDB code: 3tcx was solved by S.Kang, C.U.Kim, X.Gu, R.M.Owens, S.J.Van Rijn, V.Boonyaleepun, Y.Mao, T.A.Springer, M.M.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.54 / 3.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.041, 166.334, 299.372, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 23.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation (pdb code 3tcx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation, PDB code: 3tcx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:51.4 occ:1.00 OG B:SER141 1.9 77.1 1.0 OG1 B:THR206 2.2 69.3 1.0 OG B:SER139 2.5 74.1 1.0 OE2 A:GLU34 3.0 82.6 1.0 CB B:SER141 3.0 80.0 1.0 CB B:THR206 3.2 69.5 1.0 OD1 B:ASP239 3.2 83.7 1.0 O B:GLU241 3.2 81.1 1.0 CG2 B:THR206 3.3 70.4 1.0 OE1 A:GLU34 3.4 78.0 1.0 CD A:GLU34 3.5 78.8 1.0 CB B:SER139 3.7 73.4 1.0 OE2 B:GLU241 3.7 89.5 1.0 OD2 B:ASP239 3.8 88.7 1.0 OD1 B:ASP137 3.8 79.4 1.0 CG B:ASP239 3.9 87.2 1.0 CB B:GLU241 4.1 87.2 1.0 CA B:SER141 4.2 82.0 1.0 C B:GLU241 4.3 82.8 1.0 OD2 B:ASP137 4.3 78.4 1.0 N B:SER141 4.4 80.1 1.0 CA B:THR206 4.5 68.4 1.0 CG B:ASP137 4.5 78.8 1.0 CD B:GLU241 4.6 91.4 1.0 CA B:GLU241 4.7 86.3 1.0 CG B:GLU241 4.8 89.1 1.0 C B:SER141 4.9 85.0 1.0 N B:GLU241 4.9 86.6 1.0 CG A:GLU34 5.0 75.8 1.0 N B:THR206 5.0 68.8 1.0

Magnesium binding site 2 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:62.0 occ:1.00 OG D:SER141 1.9 85.5 1.0 OG1 D:THR206 2.2 79.2 1.0 OG D:SER139 2.6 82.6 1.0 OE2 C:GLU34 3.0 91.9 1.0 CB D:SER141 3.0 87.3 1.0 OD1 D:ASP239 3.2 96.2 1.0 CB D:THR206 3.2 80.8 1.0 O D:GLU241 3.2 94.3 1.0 CG2 D:THR206 3.3 83.1 1.0 OE1 C:GLU34 3.5 87.1 1.0 CD C:GLU34 3.6 87.6 1.0 OE2 D:GLU241 3.6 98.5 1.0 OD2 D:ASP239 3.7 99.7 1.0 OD1 D:ASP137 3.7 91.0 1.0 CB D:SER139 3.8 81.6 1.0 CG D:ASP239 3.8 99.5 1.0 CB D:GLU241 4.0 0.1 1.0 CA D:SER141 4.2 88.1 1.0 C D:GLU241 4.3 97.3 1.0 OD2 D:ASP137 4.4 88.4 1.0 N D:SER141 4.4 85.4 1.0 CD D:GLU241 4.5 0.5 1.0 CG D:ASP137 4.5 89.9 1.0 CA D:THR206 4.5 79.5 1.0 CA D:GLU241 4.7 0.9 1.0 CG D:GLU241 4.7 0.1 1.0 N D:GLU241 4.8 0.1 1.0 C D:SER141 4.9 91.4 1.0 N D:THR206 4.9 78.5 1.0 CG C:GLU34 5.0 83.8 1.0

Magnesium binding site 3 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:0.3 occ:1.00 OG F:SER141 2.0 0.8 1.0 OG1 F:THR206 2.1 0.8 1.0 OG F:SER139 2.6 0.7 1.0 CB F:THR206 3.1 0.4 1.0 CB F:SER141 3.1 1.0 1.0 OE2 E:GLU34 3.2 0.4 1.0 CG2 F:THR206 3.2 0.9 1.0 OD1 F:ASP239 3.2 0.9 1.0 O F:GLU241 3.2 0.3 1.0 OE1 E:GLU34 3.6 0.2 1.0 CB F:SER139 3.7 0.7 1.0 OD1 F:ASP137 3.7 0.0 1.0 OE2 F:GLU241 3.7 0.8 1.0 CD E:GLU34 3.8 0.6 1.0 OD2 F:ASP239 3.9 0.5 1.0 CG F:ASP239 3.9 0.7 1.0 CB F:GLU241 4.1 0.6 1.0 C F:GLU241 4.2 1.0 1.0 OD2 F:ASP137 4.3 0.9 1.0 CA F:SER141 4.4 0.7 1.0 CA F:THR206 4.4 0.3 1.0 CG F:ASP137 4.5 0.2 1.0 N F:SER141 4.5 0.9 1.0 CD F:GLU241 4.6 0.8 1.0 CA F:GLU241 4.6 0.9 1.0 CG F:GLU241 4.8 0.1 1.0 N F:THR206 4.8 0.6 1.0 N F:GLU241 4.9 0.2 1.0 C F:SER141 5.0 0.3 1.0

Magnesium binding site 4 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg901 b:88.6 occ:1.00 OG H:SER141 1.9 0.6 1.0 OG1 H:THR206 2.1 0.6 1.0 OG H:SER139 2.5 0.9 1.0 CB H:SER141 3.1 0.2 1.0 CB H:THR206 3.1 0.6 1.0 OE2 G:GLU34 3.1 0.0 1.0 OD1 H:ASP239 3.1 0.5 1.0 CG2 H:THR206 3.2 0.3 1.0 O H:GLU241 3.3 0.1 1.0 CB H:SER139 3.7 0.8 1.0 OE1 G:GLU34 3.7 0.1 1.0 OD1 H:ASP137 3.7 0.5 1.0 OE2 H:GLU241 3.7 0.9 1.0 CD G:GLU34 3.7 0.4 1.0 OD2 H:ASP239 3.8 0.1 1.0 CG H:ASP239 3.9 0.9 1.0 CB H:GLU241 4.1 0.9 1.0 CA H:SER141 4.3 0.2 1.0 OD2 H:ASP137 4.3 0.9 1.0 C H:GLU241 4.3 0.3 1.0 N H:SER141 4.4 0.2 1.0 CG H:ASP137 4.5 0.8 1.0 CA H:THR206 4.5 0.2 1.0 CD H:GLU241 4.6 0.7 1.0 CA H:GLU241 4.7 0.1 1.0 CG H:GLU241 4.8 0.1 1.0 C H:SER141 4.9 0.1 1.0 N H:GLU241 4.9 0.8 1.0 N H:THR206 4.9 0.6 1.0 CA H:SER139 5.0 0.0 1.0

Magnesium binding site 5 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg901 b:88.5 occ:1.00 OG J:SER141 1.8 0.7 1.0 OG1 J:THR206 2.1 0.3 1.0 OG J:SER139 2.5 0.6 1.0 OE2 I:GLU34 2.9 0.5 1.0 CB J:SER141 3.0 0.2 1.0 CB J:THR206 3.1 0.8 1.0 O J:GLU241 3.3 0.4 1.0 CG2 J:THR206 3.3 0.5 1.0 OD1 J:ASP239 3.4 1.0 1.0 OE1 I:GLU34 3.4 0.0 1.0 CD I:GLU34 3.5 0.1 1.0 OE2 J:GLU241 3.6 0.3 1.0 CB J:SER139 3.6 0.1 1.0 OD2 J:ASP239 3.9 0.8 1.0 OD1 J:ASP137 3.9 0.8 1.0 CG J:ASP239 4.1 1.0 1.0 CB J:GLU241 4.1 0.2 1.0 CA J:SER141 4.2 0.6 1.0 N J:SER141 4.3 0.4 1.0 C J:GLU241 4.3 0.0 1.0 CA J:THR206 4.4 0.9 1.0 OD2 J:ASP137 4.4 0.3 1.0 CD J:GLU241 4.5 0.0 1.0 CG J:ASP137 4.7 0.9 1.0 CG J:GLU241 4.7 0.9 1.0 CA J:GLU241 4.8 0.5 1.0 N J:THR206 4.8 99.6 1.0 CG I:GLU34 4.9 0.7 1.0 C J:SER141 4.9 1.0 1.0 CA J:SER139 4.9 0.7 1.0

Magnesium binding site 6 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg901 b:52.7 occ:1.00 OG L:SER141 1.8 78.2 1.0 OG1 L:THR206 2.2 71.6 1.0 OG L:SER139 2.5 76.0 1.0 OE2 K:GLU34 2.6 86.3 1.0 CB L:SER141 3.0 81.1 1.0 CB L:THR206 3.1 71.8 1.0 OD1 L:ASP239 3.2 82.2 1.0 CG2 L:THR206 3.3 71.7 1.0 O L:GLU241 3.4 82.8 1.0 CD K:GLU34 3.4 83.3 1.0 OE1 K:GLU34 3.5 82.8 1.0 CB L:SER139 3.6 75.7 1.0 OE2 L:GLU241 3.7 91.3 1.0 OD1 L:ASP137 3.8 78.4 1.0 OD2 L:ASP239 3.8 87.5 1.0 CG L:ASP239 3.9 85.5 1.0 CB L:GLU241 4.2 87.5 1.0 CA L:SER141 4.2 82.7 1.0 N L:SER141 4.3 81.2 1.0 C L:GLU241 4.4 83.6 1.0 OD2 L:ASP137 4.4 78.7 1.0 CA L:THR206 4.5 71.5 1.0 CG L:ASP137 4.5 78.2 1.0 CD L:GLU241 4.6 93.0 1.0 CA L:GLU241 4.8 86.2 1.0 CG K:GLU34 4.8 81.2 1.0 CG L:GLU241 4.8 90.3 1.0 C L:SER141 4.8 84.5 1.0 N L:THR206 4.8 72.8 1.0 CA L:SER139 4.9 77.0 1.0 N L:GLU241 4.9 85.5 1.0

Magnesium binding site 7 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg901 b:94.3 occ:1.00 OG N:SER141 1.8 0.5 1.0 OG1 N:THR206 2.0 0.4 1.0 OG N:SER139 2.4 0.9 1.0 OE2 M:GLU34 2.8 0.5 1.0 CB N:THR206 3.0 0.1 1.0 CB N:SER141 3.0 0.6 1.0 CG2 N:THR206 3.2 0.1 1.0 O N:GLU241 3.4 0.5 1.0 OD1 N:ASP239 3.4 0.9 1.0 OE1 M:GLU34 3.5 0.1 1.0 CD M:GLU34 3.5 0.5 1.0 CB N:SER139 3.5 0.2 1.0 OE2 N:GLU241 3.7 0.0 1.0 OD1 N:ASP137 3.9 0.4 1.0 OD2 N:ASP239 4.0 0.6 1.0 CG N:ASP239 4.1 0.1 1.0 CA N:SER141 4.2 0.6 1.0 CB N:GLU241 4.2 0.4 1.0 N N:SER141 4.3 0.2 1.0 OD2 N:ASP137 4.3 0.7 1.0 CA N:THR206 4.3 0.7 1.0 C N:GLU241 4.4 0.7 1.0 CG N:ASP137 4.6 0.8 1.0 CD N:GLU241 4.6 0.4 1.0 N N:THR206 4.7 1.0 1.0 CA N:GLU241 4.8 0.3 1.0 CG N:GLU241 4.9 0.1 1.0 CG M:GLU34 4.9 0.8 1.0 CA N:SER139 4.9 0.1 1.0 C N:SER141 4.9 0.8 1.0

Magnesium binding site 8 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg901 b:97.7 occ:1.00 OG P:SER141 1.9 0.4 1.0 OG1 P:THR206 2.0 0.2 1.0 OG P:SER139 2.5 0.3 1.0 OE2 O:GLU34 2.9 0.9 1.0 CB P:THR206 3.0 0.8 1.0 CB P:SER141 3.1 0.3 1.0 CG2 P:THR206 3.2 0.8 1.0 OD1 P:ASP239 3.2 0.4 1.0 O P:GLU241 3.3 0.9 1.0 OE1 O:GLU34 3.5 0.4 1.0 CD O:GLU34 3.6 0.8 1.0 CB P:SER139 3.6 0.6 1.0 OE2 P:GLU241 3.7 1.0 1.0 OD1 P:ASP137 3.8 0.4 1.0 OD2 P:ASP239 3.9 0.1 1.0 CG P:ASP239 4.0 0.3 1.0 CB P:GLU241 4.1 0.6 1.0 C P:GLU241 4.3 0.4 1.0 CA P:SER141 4.3 0.4 1.0 OD2 P:ASP137 4.4 0.1 1.0 CA P:THR206 4.4 0.5 1.0 N P:SER141 4.4 0.0 1.0 CG P:ASP137 4.5 0.1 1.0 CD P:GLU241 4.6 0.7 1.0 CA P:GLU241 4.7 0.6 1.0 N P:THR206 4.8 0.8 1.0 CG P:GLU241 4.8 0.0 1.0 C P:SER141 4.9 0.2 1.0 N P:GLU241 4.9 0.2 1.0 CA P:SER139 5.0 0.0 1.0 CG O:GLU34 5.0 0.4 1.0

Magnesium binding site 9 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg901 b:88.1 occ:1.00 OG R:SER141 1.9 0.1 1.0 OG1 R:THR206 2.1 0.2 1.0 OG R:SER139 2.5 0.8 1.0 OE2 Q:GLU34 2.8 0.6 1.0 CB R:THR206 3.1 0.2 1.0 OD1 R:ASP239 3.1 0.5 1.0 CB R:SER141 3.1 0.7 1.0 CG2 R:THR206 3.2 0.4 1.0 O R:GLU241 3.4 0.4 1.0 CD Q:GLU34 3.5 0.1 1.0 CB R:SER139 3.6 0.3 1.0 OE1 Q:GLU34 3.6 0.5 1.0 OD1 R:ASP137 3.6 0.7 1.0 OD2 R:ASP239 3.8 0.5 1.0 CG R:ASP239 3.9 0.8 1.0 OE2 R:GLU241 3.9 0.0 1.0 OD2 R:ASP137 4.2 0.1 1.0 CB R:GLU241 4.2 0.9 1.0 CA R:SER141 4.3 0.2 1.0 CG R:ASP137 4.4 0.6 1.0 C R:GLU241 4.4 0.2 1.0 N R:SER141 4.4 0.8 1.0 CA R:THR206 4.4 0.9 1.0 CD R:GLU241 4.7 0.1 1.0 CA R:GLU241 4.8 0.3 1.0 C R:SER141 4.9 0.1 1.0 N R:THR206 4.9 0.7 1.0 CG Q:GLU34 4.9 0.3 1.0 CA R:SER139 4.9 0.7 1.0 CG R:GLU241 4.9 0.9 1.0 N R:GLU241 4.9 0.3 1.0

Magnesium binding site 10 out of 14 in the Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Engineered Single Domain Icam-1 D1 with High-Affinity Al Integrin I Domain of Native C-Terminal Helix Conformation within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg901 b:84.9 occ:1.00 OG T:SER141 1.9 0.7 1.0 OG1 T:THR206 2.2 0.1 1.0 OG T:SER139 2.5 0.6 1.0 OE2 S:GLU34 3.0 0.7 1.0 OD1 T:ASP239 3.1 0.4 1.0 CB T:SER141 3.1 0.3 1.0 CB T:THR206 3.1 0.9 1.0 CG2 T:THR206 3.2 0.8 1.0 O T:GLU241 3.4 0.7 1.0 OD1 T:ASP137 3.6 0.5 1.0 CD S:GLU34 3.6 0.4 1.0 OE1 S:GLU34 3.6 0.6 1.0 CB T:SER139 3.7 0.3 1.0 OD2 T:ASP239 3.8 0.3 1.0 CG T:ASP239 3.8 0.1 1.0 OE2 T:GLU241 3.9 0.8 1.0 CB T:GLU241 4.2 0.3 1.0 OD2 T:ASP137 4.3 0.8 1.0 CA T:SER141 4.3 0.7 1.0 C T:GLU241 4.3 0.4 1.0 CG T:ASP137 4.4 0.8 1.0 N T:SER141 4.4 0.1 1.0 CA T:THR206 4.5 99.6 1.0 CD T:GLU241 4.7 0.3 1.0 CA T:GLU241 4.7 0.5 1.0 CG T:GLU241 4.9 0.3 1.0 N T:GLU241 4.9 0.7 1.0 C T:SER141 4.9 0.9 1.0 N T:THR206 5.0 98.0 1.0 CA T:SER139 5.0 0.5 1.0

S.Kang, C.U.Kim, X.Gu, R.M.Owens, S.J.Van Rijn, V.Boonyaleepun, Y.Mao, T.A.Springer, M.M.Jin. Structure of Engineered Single Domain Icam-1 D1 with High-Affinity L Integrin I Domain of Native C-Terminal Helix Conformation To Be Published.