Manganese in PDB 7ucy: Integrin ALAPHIIBBETA3 Complex with Gantofiban

The structure of Integrin ALAPHIIBBETA3 Complex with Gantofiban, PDB code: 7ucy was solved by F.-Y.Lin, J.Zhu, J.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.98 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	258.55, 144.46, 105.1, 90, 90, 90
R / Rfree (%)	22.1 / 23.1

The structure of Integrin ALAPHIIBBETA3 Complex with Gantofiban also contains other interesting chemical elements:

Calcium	(Ca)	8 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Manganese atom in the Integrin ALAPHIIBBETA3 Complex with Gantofiban (pdb code 7ucy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Integrin ALAPHIIBBETA3 Complex with Gantofiban, PDB code: 7ucy:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:33.5 occ:1.00 OE2 B:GLU220 2.1 36.6 1.0 O B:HOH2188 2.1 31.8 1.0 O B:HOH2102 2.1 41.4 1.0 O3 B:MV82005 2.1 42.8 1.0 O B:HOH2153 2.2 34.2 1.0 OG B:SER121 2.2 38.6 1.0 CB B:SER121 3.0 36.9 1.0 CD B:GLU220 3.2 36.8 1.0 C11 B:MV82005 3.3 42.8 1.0 CG B:GLU220 3.7 36.0 1.0 O4 B:MV82005 3.9 42.8 1.0 O B:HOH2179 4.1 44.0 1.0 OG B:SER123 4.1 46.4 1.0 O B:HOH2373 4.2 45.7 1.0 O B:ALA218 4.3 34.9 1.0 OE1 B:GLU220 4.3 35.9 1.0 ND2 B:ASN215 4.3 39.2 1.0 CA B:SER121 4.4 37.4 1.0 C8 B:MV82005 4.4 42.8 1.0 OD1 B:ASP119 4.4 38.0 1.0 OD2 B:ASP119 4.5 36.7 1.0 CB B:ALA252 4.6 40.4 1.0 N2 B:MV82005 4.6 42.8 1.0 OD1 B:ASP251 4.6 44.5 1.0 C B:SER121 4.7 38.6 1.0 N B:TYR122 4.8 42.7 1.0 CG B:ASP119 4.9 36.2 1.0 C5 B:MV82005 4.9 42.8 1.0

Manganese binding site 2 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:71.0 occ:1.00 OD1 B:ASP127 2.2 55.0 1.0 OD1 B:ASP126 2.2 51.7 0.5 O B:SER123 2.2 48.0 1.0 O B:HOH2213 2.4 47.5 1.0 O B:HOH2158 2.5 54.0 1.0 O B:MET335 2.8 52.2 1.0 CG B:ASP126 3.0 52.0 0.5 OD2 B:ASP126 3.2 53.1 0.5 CG B:ASP127 3.4 51.5 1.0 C B:SER123 3.4 44.5 1.0 O B:HOH2250 3.8 47.3 1.0 CA B:MET124 3.9 46.3 1.0 C B:MET335 4.0 52.4 1.0 OD2 B:ASP127 4.0 50.9 1.0 O B:HOH2132 4.0 47.0 1.0 N B:MET124 4.1 44.9 1.0 N B:ASP127 4.3 49.7 1.0 CB B:ASP126 4.5 52.4 0.5 CB B:ASP127 4.5 48.8 1.0 C B:MET124 4.5 45.5 1.0 CA B:SER123 4.5 44.1 1.0 CB B:ASP126 4.5 52.5 0.5 CA B:ASP336 4.6 51.0 1.0 OD2 B:ASP251 4.6 47.0 1.0 O B:HOH2375 4.6 55.0 1.0 N B:ASP126 4.7 50.5 0.5 N B:ASP126 4.7 50.5 0.5 SD B:MET124 4.7 45.6 1.0 N B:ASP336 4.7 52.6 1.0 CB B:SER123 4.8 44.4 1.0 N B:LYS125 4.8 47.8 1.0 CA B:ASP127 4.9 49.7 1.0 C B:ASP126 4.9 50.5 0.5 C B:ASP126 4.9 50.5 0.5 CA B:MET335 4.9 52.2 1.0 CA B:ASP126 4.9 51.1 0.5 CA B:ASP126 5.0 51.1 0.5

Manganese binding site 3 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2003 b:37.9 occ:1.00 O B:PRO219 2.1 33.3 1.0 OD1 B:ASP217 2.1 35.3 1.0 OE1 B:GLU220 2.2 35.9 1.0 OD1 B:ASN215 2.2 36.6 1.0 OD2 B:ASP158 2.2 36.8 1.0 O B:ASP217 2.2 35.7 1.0 CG B:ASP217 3.2 35.9 1.0 CG B:ASN215 3.2 38.1 1.0 C B:PRO219 3.2 33.2 1.0 CD B:GLU220 3.3 36.8 1.0 CG B:ASP158 3.3 37.0 1.0 C B:ASP217 3.3 35.9 1.0 ND2 B:ASN215 3.6 39.2 1.0 CB B:ASP158 3.8 36.5 1.0 OD2 B:ASP217 3.8 36.3 1.0 CA B:GLU220 3.8 34.8 1.0 N B:GLU220 4.0 34.7 1.0 OE2 B:GLU220 4.0 36.6 1.0 CA B:ASP217 4.0 40.3 1.0 N B:ASP217 4.0 39.0 1.0 C B:ALA218 4.2 34.4 1.0 CB B:ASP217 4.2 38.9 1.0 N B:PRO219 4.2 34.6 1.0 NE2 B:HIS255 4.2 33.6 1.0 O B:ALA218 4.3 34.9 1.0 CA B:PRO219 4.3 33.7 1.0 CG B:GLU220 4.3 36.0 1.0 N B:ALA218 4.4 35.6 1.0 OD1 B:ASP158 4.4 35.8 1.0 CB B:ASN215 4.5 36.8 1.0 CB B:GLU220 4.6 34.9 1.0 CD2 B:HIS255 4.6 32.4 1.0 CA B:ALA218 4.7 35.5 1.0 CD B:PRO219 4.8 36.5 1.0 C B:GLU220 5.0 32.9 1.0

Manganese binding site 4 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2001 b:46.2 occ:1.00 OE2 D:GLU220 2.2 48.8 1.0 O D:HOH2107 2.2 50.0 1.0 O D:HOH2110 2.2 45.5 1.0 O3 D:MV82006 2.2 52.6 1.0 O D:HOH2192 2.2 43.2 1.0 OG D:SER121 2.3 44.4 1.0 CB D:SER121 2.9 44.6 1.0 O D:HOH2209 3.2 52.2 1.0 CD D:GLU220 3.3 47.0 1.0 C11 D:MV82006 3.3 52.6 1.0 CG D:GLU220 3.8 46.2 1.0 O4 D:MV82006 4.0 52.6 1.0 O D:HOH2177 4.0 48.1 1.0 OG D:SER123 4.0 54.2 1.0 O D:ALA218 4.3 42.8 1.0 OE1 D:GLU220 4.3 48.3 1.0 CA D:SER121 4.3 45.5 1.0 OD2 D:ASP119 4.4 46.2 1.0 ND2 D:ASN215 4.4 50.4 1.0 C8 D:MV82006 4.5 52.6 1.0 OD1 D:ASP251 4.5 50.4 1.0 OD1 D:ASP119 4.6 46.5 1.0 CB D:ALA252 4.6 46.4 1.0 N D:TYR122 4.6 52.2 1.0 C D:SER121 4.6 47.1 1.0 O D:HOH2278 4.6 50.7 1.0 N2 D:MV82006 4.6 52.6 1.0 CG D:ASP119 4.9 45.8 1.0 N D:SER123 4.9 53.5 1.0

Manganese binding site 5 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2002 b:58.1 occ:1.00 OD1 D:ASP126 2.2 65.1 1.0 O D:SER123 2.2 53.9 1.0 OD1 D:ASP127 2.2 58.6 1.0 O D:HOH2231 2.4 46.6 1.0 O D:HOH2102 2.5 54.2 1.0 O D:MET335 2.6 55.5 1.0 CG D:ASP126 3.1 62.9 1.0 C D:SER123 3.4 52.9 1.0 CG D:ASP127 3.4 58.4 1.0 OD2 D:ASP126 3.4 61.5 1.0 C D:MET335 3.8 57.6 1.0 CA D:MET124 3.8 56.2 1.0 O D:HOH2211 3.9 55.1 1.0 OD2 D:ASP127 4.0 56.8 1.0 O D:HOH2118 4.0 50.3 1.0 N D:MET124 4.0 55.0 1.0 N D:ASP127 4.2 58.8 1.0 O D:HOH2276 4.3 58.8 1.0 OD2 D:ASP251 4.4 52.9 1.0 C D:MET124 4.4 57.2 1.0 CB D:ASP126 4.5 61.5 1.0 N D:ASP126 4.5 61.3 1.0 CA D:SER123 4.5 53.0 1.0 CB D:ASP127 4.5 58.9 1.0 CA D:ASP336 4.6 57.2 1.0 N D:ASP336 4.6 58.8 1.0 N D:LYS125 4.6 57.9 1.0 SD D:MET124 4.7 54.2 1.0 CA D:MET335 4.7 60.1 1.0 CB D:SER123 4.8 54.3 1.0 C D:ASP126 4.8 60.3 1.0 CA D:ASP126 4.8 60.9 1.0 CA D:ASP127 4.9 60.1 1.0

Manganese binding site 6 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2003 b:47.3 occ:1.00 OD1 D:ASP217 2.2 47.4 1.0 OE1 D:GLU220 2.2 48.3 1.0 OD1 D:ASN215 2.2 53.0 1.0 O D:ASP217 2.2 46.5 1.0 OD2 D:ASP158 2.2 52.4 1.0 O D:PRO219 2.2 42.6 1.0 CG D:ASP217 3.1 48.4 1.0 CG D:ASN215 3.2 50.1 1.0 C D:PRO219 3.3 43.0 1.0 C D:ASP217 3.3 45.7 1.0 CD D:GLU220 3.3 47.0 1.0 CG D:ASP158 3.3 49.0 1.0 ND2 D:ASN215 3.6 50.4 1.0 OD2 D:ASP217 3.7 46.5 1.0 CA D:GLU220 3.8 43.4 1.0 CB D:ASP158 3.8 46.4 1.0 N D:GLU220 3.9 42.9 1.0 O D:ALA218 4.0 42.8 1.0 CA D:ASP217 4.0 46.3 1.0 C D:ALA218 4.0 43.0 1.0 N D:ASP217 4.0 44.9 1.0 OE2 D:GLU220 4.1 48.8 1.0 CB D:ASP217 4.1 49.8 1.0 N D:PRO219 4.2 44.4 1.0 NE2 D:HIS255 4.2 47.1 1.0 CG D:GLU220 4.3 46.2 1.0 N D:ALA218 4.3 44.2 1.0 CA D:PRO219 4.4 44.6 1.0 OD1 D:ASP158 4.4 45.7 1.0 CB D:GLU220 4.5 43.7 1.0 CB D:ASN215 4.5 49.8 1.0 CA D:ALA218 4.6 44.3 1.0 CD2 D:HIS255 4.6 45.4 1.0 CD D:PRO219 4.8 45.1 1.0 C D:GLU220 4.8 47.0 1.0

J.Zhu, A.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with Bms Compound 4 in MN2+. To Be Published.