Manganese in PDB 7udh: Integrin ALAPHIIBBETA3 Complex with BMS4-3

The structure of Integrin ALAPHIIBBETA3 Complex with BMS4-3, PDB code: 7udh 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)	48.99 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	258.33, 144.67, 105.06, 90, 90, 90
R / Rfree (%)	18.5 / 21.4

The structure of Integrin ALAPHIIBBETA3 Complex with BMS4-3 also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	8 atoms

The binding sites of Manganese atom in the Integrin ALAPHIIBBETA3 Complex with BMS4-3 (pdb code 7udh). 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 BMS4-3, PDB code: 7udh:
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 BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:36.9 occ:1.00 O B:HOH2129 2.1 28.2 1.0 O2 B:MWO2005 2.1 36.6 1.0 OE2 B:GLU220 2.2 42.5 1.0 O B:HOH2109 2.2 38.1 1.0 OG B:SER121 2.3 41.5 1.0 O B:HOH2168 2.3 34.4 1.0 CB B:SER121 3.0 34.7 1.0 CD B:GLU220 3.3 41.1 1.0 C10 B:MWO2005 3.4 44.8 1.0 CG B:GLU220 3.7 34.0 1.0 O3 B:MWO2005 3.9 40.8 1.0 O B:HOH2140 4.0 52.4 1.0 OG B:SER123 4.3 42.6 1.0 O B:ALA218 4.3 44.3 1.0 OE1 B:GLU220 4.3 40.0 1.0 ND2 B:ASN215 4.3 38.8 1.0 CA B:SER121 4.4 38.3 1.0 OD2 B:ASP119 4.5 39.9 1.0 OD1 B:ASP119 4.5 37.9 1.0 O B:HOH2409 4.5 48.7 1.0 C9 B:MWO2005 4.6 47.6 1.0 N3 B:MWO2005 4.6 55.8 1.0 CB B:ALA252 4.6 36.9 1.0 OD1 B:ASP251 4.6 48.4 1.0 C6 B:MWO2005 4.7 58.3 1.0 N B:TYR122 4.7 38.1 1.0 C B:SER121 4.7 40.8 1.0 O B:HOH2323 4.9 63.9 1.0 CG B:ASP119 5.0 38.5 1.0

Manganese binding site 2 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:74.6 occ:1.00 OD1 B:ASP127 2.2 50.9 1.0 OD1 B:ASP126 2.2 76.1 1.0 O B:HOH2177 2.2 44.7 1.0 O B:HOH2295 2.2 50.0 1.0 O B:MET335 2.4 49.2 1.0 O B:SER123 2.4 45.5 1.0 CG B:ASP126 3.2 75.5 1.0 CG B:ASP127 3.3 46.4 1.0 OD2 B:ASP126 3.5 86.8 1.0 C B:SER123 3.6 44.5 1.0 C B:MET335 3.6 50.2 1.0 OD2 B:ASP127 3.8 45.9 1.0 O B:HOH2224 3.9 56.1 1.0 O B:HOH2112 4.0 44.8 1.0 CA B:MET124 4.0 41.4 1.0 N B:MET124 4.2 44.5 1.0 N B:ASP127 4.3 42.2 1.0 CA B:ASP336 4.4 42.7 1.0 N B:ASP336 4.4 43.7 1.0 OD2 B:ASP251 4.5 52.3 1.0 C B:MET124 4.6 45.0 1.0 CB B:ASP127 4.6 41.7 1.0 CB B:ASP126 4.6 58.2 1.0 CA B:MET335 4.6 55.3 1.0 N B:ASP126 4.7 50.7 1.0 SD B:MET124 4.7 52.3 1.0 CA B:SER123 4.7 46.3 1.0 N B:LYS125 4.9 44.7 1.0 CB B:SER123 4.9 43.6 1.0 C B:ASP126 5.0 49.6 1.0 CB B:MET335 5.0 65.0 1.0 CA B:ASP127 5.0 39.8 1.0 CA B:ASP126 5.0 50.5 1.0

Manganese binding site 3 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2003 b:37.6 occ:1.00 OD1 B:ASP217 2.1 44.9 1.0 OE1 B:GLU220 2.1 40.0 1.0 OD1 B:ASN215 2.2 38.1 1.0 O B:PRO219 2.2 34.8 1.0 OD2 B:ASP158 2.2 33.5 1.0 O B:ASP217 2.3 37.7 1.0 CG B:ASP217 3.2 41.6 1.0 CG B:ASN215 3.3 40.1 1.0 CD B:GLU220 3.3 41.1 1.0 CG B:ASP158 3.3 37.2 1.0 C B:PRO219 3.3 32.9 1.0 C B:ASP217 3.4 35.2 1.0 CB B:ASP158 3.7 30.6 1.0 ND2 B:ASN215 3.7 38.8 1.0 CA B:GLU220 3.8 33.8 1.0 OD2 B:ASP217 3.8 43.3 1.0 OE2 B:GLU220 3.9 42.5 1.0 N B:GLU220 4.0 30.8 1.0 CA B:ASP217 4.0 41.4 1.0 N B:ASP217 4.1 34.8 1.0 NE2 B:HIS255 4.1 40.1 1.0 CB B:ASP217 4.2 41.3 1.0 C B:ALA218 4.3 40.1 1.0 N B:PRO219 4.3 37.0 1.0 CG B:GLU220 4.3 34.0 1.0 O B:ALA218 4.4 44.3 1.0 OD1 B:ASP158 4.4 33.2 1.0 N B:ALA218 4.4 37.4 1.0 CA B:PRO219 4.4 32.6 1.0 CD2 B:HIS255 4.4 33.8 1.0 CB B:GLU220 4.5 34.3 1.0 CB B:ASN215 4.6 37.8 1.0 CA B:ALA218 4.8 35.6 1.0 C B:GLU220 4.9 38.9 1.0 CD1 B:TYR164 4.9 36.6 1.0 CD B:PRO219 5.0 39.0 1.0 CB B:TYR164 5.0 34.3 1.0

Manganese binding site 4 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2001 b:48.6 occ:1.00 OE2 D:GLU220 2.1 67.3 1.0 O D:HOH2162 2.2 42.4 1.0 O2 D:MWO2006 2.2 54.9 1.0 O D:HOH2144 2.2 45.3 1.0 OG D:SER121 2.2 49.4 1.0 O D:HOH2114 2.2 50.3 1.0 CB D:SER121 3.1 47.2 1.0 CD D:GLU220 3.2 55.5 1.0 C10 D:MWO2006 3.4 53.8 1.0 CG D:GLU220 3.7 46.9 1.0 O3 D:MWO2006 3.9 52.3 1.0 O D:HOH2134 4.0 64.9 1.0 OE1 D:GLU220 4.3 66.1 1.0 OG D:SER123 4.3 56.4 1.0 O D:ALA218 4.3 46.7 1.0 O D:HOH2283 4.4 65.0 1.0 ND2 D:ASN215 4.4 44.9 1.0 OD2 D:ASP119 4.4 52.2 1.0 CA D:SER121 4.4 48.8 1.0 OD1 D:ASP119 4.5 44.9 1.0 OD1 D:ASP251 4.5 48.7 1.0 CB D:ALA252 4.6 45.1 1.0 C9 D:MWO2006 4.6 54.3 1.0 N3 D:MWO2006 4.6 63.3 1.0 N D:TYR122 4.7 54.5 1.0 C D:SER121 4.7 53.9 1.0 C6 D:MWO2006 4.8 63.8 1.0 CG D:ASP119 4.9 50.2 1.0

Manganese binding site 5 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2002 b:61.7 occ:1.00 OD1 D:ASP127 2.2 68.4 1.0 O D:HOH2240 2.2 48.3 1.0 OD1 D:ASP126 2.2 66.9 1.0 O D:HOH2124 2.2 47.6 1.0 O D:MET335 2.3 53.0 1.0 O D:SER123 2.3 54.6 1.0 CG D:ASP126 3.1 65.7 1.0 OD2 D:ASP126 3.2 71.5 1.0 CG D:ASP127 3.3 59.7 1.0 C D:SER123 3.5 53.5 1.0 C D:MET335 3.5 58.2 1.0 OD2 D:ASP127 3.8 62.4 1.0 O D:HOH2186 4.0 65.5 1.0 O D:HOH2107 4.0 52.8 1.0 CA D:MET124 4.1 48.3 1.0 N D:MET124 4.2 48.3 1.0 N D:ASP127 4.2 58.5 1.0 CA D:ASP336 4.4 58.5 1.0 N D:ASP336 4.4 57.1 1.0 OD2 D:ASP251 4.4 52.7 1.0 CB D:ASP126 4.5 66.5 1.0 CA D:MET335 4.5 62.9 1.0 CB D:ASP127 4.6 54.2 1.0 CA D:SER123 4.6 55.8 1.0 C D:MET124 4.6 55.8 1.0 SD D:MET124 4.7 57.7 1.0 N D:ASP126 4.7 64.2 1.0 CB D:SER123 4.8 55.1 1.0 CB D:MET335 4.8 70.5 1.0 CE D:MET335 4.8 83.1 1.0 CA D:ASP127 4.9 59.9 1.0 C D:ASP126 4.9 60.4 1.0 CA D:ASP126 5.0 63.7 1.0 N D:LYS125 5.0 55.1 1.0

Manganese binding site 6 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2003 b:50.7 occ:1.00 OD1 D:ASP217 2.1 55.6 1.0 OE1 D:GLU220 2.2 66.1 1.0 O D:PRO219 2.2 49.0 1.0 OD1 D:ASN215 2.2 44.6 1.0 OD2 D:ASP158 2.3 47.2 1.0 O D:ASP217 2.3 47.1 1.0 CG D:ASP217 3.2 53.4 1.0 CG D:ASN215 3.3 46.8 1.0 CD D:GLU220 3.3 55.5 1.0 C D:PRO219 3.3 41.1 1.0 CG D:ASP158 3.3 46.4 1.0 C D:ASP217 3.4 48.8 1.0 ND2 D:ASN215 3.6 44.9 1.0 CB D:ASP158 3.8 43.6 1.0 CA D:GLU220 3.8 43.4 1.0 OD2 D:ASP217 3.8 48.0 1.0 OE2 D:GLU220 4.0 67.3 1.0 N D:GLU220 4.0 37.4 1.0 CA D:ASP217 4.0 51.5 1.0 N D:ASP217 4.0 47.6 1.0 NE2 D:HIS255 4.2 49.1 1.0 CB D:ASP217 4.2 52.5 1.0 C D:ALA218 4.2 45.9 1.0 O D:ALA218 4.3 46.7 1.0 CG D:GLU220 4.3 46.9 1.0 N D:PRO219 4.3 49.5 1.0 N D:ALA218 4.4 44.2 1.0 CA D:PRO219 4.4 45.3 1.0 OD1 D:ASP158 4.5 44.0 1.0 CD2 D:HIS255 4.5 46.6 1.0 CB D:GLU220 4.5 45.2 1.0 CB D:ASN215 4.6 44.3 1.0 CA D:ALA218 4.8 47.9 1.0 C D:GLU220 4.8 47.8 1.0 CD D:PRO219 4.9 44.0 1.0 CB D:TYR164 5.0 45.0 1.0

F.-Y.Lin, J.Zhu, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece Complex with BMS4-3 To Be Published.