Manganese in PDB 7u9v: Integrin ALAPHIIBBETA3 Complex with BMS4-1

The structure of Integrin ALAPHIIBBETA3 Complex with BMS4-1, PDB code: 7u9v was solved by J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.95 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	257.796, 143.887, 104.678, 90, 90, 90
R / Rfree (%)	20.3 / 22.6

The structure of Integrin ALAPHIIBBETA3 Complex with BMS4-1 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 BMS4-1 (pdb code 7u9v). 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 BMS4-1, PDB code: 7u9v:
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 BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:34.6 occ:1.00 OE2 B:GLU220 2.1 37.1 1.0 O B:HOH2103 2.1 39.6 1.0 O B:HOH2134 2.2 23.0 1.0 O25 B:M6K2005 2.2 47.5 1.0 O B:HOH2166 2.2 37.2 1.0 OG B:SER121 2.3 45.4 1.0 CB B:SER121 2.9 35.7 1.0 CD B:GLU220 3.2 33.9 1.0 C23 B:M6K2005 3.4 47.5 1.0 CG B:GLU220 3.7 31.6 1.0 O24 B:M6K2005 3.8 47.5 1.0 O B:HOH2149 4.0 41.6 1.0 OG B:SER123 4.2 46.1 1.0 OE1 B:GLU220 4.3 37.0 1.0 ND2 B:ASN215 4.3 39.9 1.0 O B:ALA218 4.3 37.6 1.0 CA B:SER121 4.3 39.9 1.0 OD2 B:ASP119 4.4 33.9 1.0 OD1 B:ASP119 4.5 36.4 1.0 CB B:ALA252 4.5 38.4 1.0 C22 B:M6K2005 4.5 47.5 1.0 OD1 B:ASP251 4.6 47.3 1.0 N19 B:M6K2005 4.7 47.5 1.0 N B:TYR122 4.7 42.6 1.0 C B:SER121 4.7 35.7 1.0 C18 B:M6K2005 4.8 47.5 1.0 O B:HOH2327 4.8 52.6 1.0 CG B:ASP119 4.9 32.3 1.0

Manganese binding site 2 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:78.8 occ:1.00 OD1 B:ASP126 2.1 58.6 0.5 OD1 B:ASP127 2.2 53.1 1.0 OD2 B:ASP126 2.2 59.8 0.5 O B:SER123 2.2 46.3 1.0 O B:HOH2183 2.3 47.1 1.0 O B:HOH2216 2.3 53.4 1.0 CG B:ASP126 2.5 57.7 0.5 O B:MET335 2.7 48.5 1.0 CG B:ASP127 3.4 42.0 1.0 C B:SER123 3.4 44.9 1.0 O B:HOH2101 3.8 50.2 1.0 CA B:MET124 3.8 47.5 1.0 CB B:ASP126 3.9 58.4 0.5 C B:MET335 4.0 53.9 1.0 OD2 B:ASP127 4.0 47.5 1.0 N B:MET124 4.1 47.7 1.0 CB B:ASP126 4.1 57.5 0.5 N B:ASP127 4.1 47.9 1.0 O B:HOH2121 4.2 43.4 1.0 C B:MET124 4.4 43.9 1.0 N B:ASP126 4.4 49.5 0.5 N B:ASP126 4.4 49.5 0.5 CB B:ASP127 4.5 43.3 1.0 CA B:ASP336 4.5 49.5 1.0 CA B:SER123 4.6 41.3 1.0 CA B:ASP126 4.6 52.3 0.5 CA B:ASP126 4.7 51.9 0.5 N B:LYS125 4.7 45.1 1.0 OD2 B:ASP251 4.7 40.1 1.0 N B:ASP336 4.7 47.3 1.0 SD B:MET124 4.8 49.8 1.0 C B:ASP126 4.8 47.6 0.5 C B:ASP126 4.8 47.6 0.5 OD2 B:ASP126 4.8 62.2 0.5 CB B:SER123 4.8 41.4 1.0 CA B:ASP127 4.9 47.2 1.0 CG B:ASP126 4.9 59.4 0.5 O B:MET124 5.0 43.8 1.0 CA B:MET335 5.0 52.8 1.0

Manganese binding site 3 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2003 b:35.7 occ:1.00 O B:PRO219 2.0 34.9 1.0 OD1 B:ASP217 2.1 38.3 1.0 OD1 B:ASN215 2.2 35.0 1.0 OE1 B:GLU220 2.2 37.0 1.0 OD2 B:ASP158 2.2 37.1 1.0 O B:ASP217 2.2 38.4 1.0 CG B:ASP217 3.0 37.4 1.0 C B:PRO219 3.2 33.9 1.0 CG B:ASN215 3.2 37.1 1.0 CD B:GLU220 3.3 33.9 1.0 C B:ASP217 3.3 36.5 1.0 CG B:ASP158 3.3 32.0 1.0 OD2 B:ASP217 3.5 39.1 1.0 ND2 B:ASN215 3.7 39.9 1.0 CB B:ASP158 3.7 32.2 1.0 CA B:GLU220 3.8 36.6 1.0 CA B:ASP217 3.9 41.6 1.0 N B:GLU220 3.9 32.3 1.0 OE2 B:GLU220 4.0 37.1 1.0 N B:ASP217 4.0 37.2 1.0 CB B:ASP217 4.0 36.2 1.0 NE2 B:HIS255 4.1 29.6 1.0 C B:ALA218 4.2 36.0 1.0 N B:PRO219 4.2 37.9 1.0 CG B:GLU220 4.3 31.6 1.0 CA B:PRO219 4.3 34.9 1.0 N B:ALA218 4.3 39.8 1.0 O B:ALA218 4.3 37.6 1.0 OD1 B:ASP158 4.4 33.7 1.0 CD2 B:HIS255 4.4 33.3 1.0 CB B:GLU220 4.5 36.0 1.0 CB B:ASN215 4.5 34.0 1.0 CA B:ALA218 4.7 36.1 1.0 CD B:PRO219 4.9 35.5 1.0 C B:GLU220 4.9 35.1 1.0 CD1 B:TYR164 4.9 35.9 1.0

Manganese binding site 4 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2001 b:47.8 occ:1.00 OE2 D:GLU220 2.1 58.8 1.0 O D:HOH2106 2.2 57.2 1.0 O D:HOH2125 2.2 39.9 1.0 O25 D:M6K2006 2.2 57.4 1.0 O D:HOH2168 2.2 42.1 1.0 OG D:SER121 2.3 46.6 1.0 CB D:SER121 3.0 46.6 1.0 CD D:GLU220 3.1 46.0 1.0 C23 D:M6K2006 3.4 57.4 1.0 CG D:GLU220 3.7 47.5 1.0 O24 D:M6K2006 3.8 57.4 1.0 OE1 D:GLU220 4.1 55.5 1.0 O D:HOH2190 4.1 59.0 1.0 OG D:SER123 4.2 63.0 1.0 OD2 D:ASP119 4.2 50.7 1.0 O D:ALA218 4.3 52.0 1.0 ND2 D:ASN215 4.3 49.4 1.0 CA D:SER121 4.4 54.6 1.0 OD1 D:ASP251 4.5 49.5 1.0 CB D:ALA252 4.5 45.1 1.0 OD1 D:ASP119 4.5 51.4 1.0 C22 D:M6K2006 4.6 57.4 1.0 C D:SER121 4.7 59.6 1.0 N19 D:M6K2006 4.7 57.4 1.0 N D:TYR122 4.7 60.7 1.0 CG D:ASP119 4.8 49.3 1.0 O D:HOH2243 4.8 56.6 1.0 C18 D:M6K2006 5.0 57.4 1.0

Manganese binding site 5 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2002 b:66.3 occ:1.00 OD1 D:ASP126 2.2 74.7 1.0 OD1 D:ASP127 2.2 58.2 1.0 O D:SER123 2.2 59.7 1.0 O D:HOH2228 2.3 50.9 1.0 O D:HOH2102 2.3 62.5 1.0 O D:MET335 2.5 62.9 1.0 CG D:ASP126 3.1 67.9 1.0 OD2 D:ASP126 3.3 63.2 1.0 CG D:ASP127 3.3 61.7 1.0 C D:SER123 3.4 54.3 1.0 C D:MET335 3.8 63.7 1.0 O D:HOH2192 3.8 57.5 1.0 CA D:MET124 3.8 60.7 1.0 OD2 D:ASP127 3.9 59.0 1.0 O D:HOH2113 4.0 49.9 1.0 N D:MET124 4.0 59.1 1.0 N D:ASP127 4.2 63.9 1.0 OD2 D:ASP251 4.3 58.9 1.0 C D:MET124 4.4 59.8 1.0 CB D:ASP126 4.5 66.8 1.0 CA D:SER123 4.5 53.5 1.0 CB D:ASP127 4.5 63.5 1.0 N D:ASP126 4.6 63.4 1.0 CA D:MET335 4.6 68.9 1.0 N D:ASP336 4.7 60.9 1.0 CA D:ASP336 4.7 61.1 1.0 SD D:MET124 4.7 52.7 1.0 N D:LYS125 4.7 55.1 1.0 CB D:SER123 4.7 56.5 1.0 CA D:ASP126 4.9 62.3 1.0 C D:ASP126 4.9 65.4 1.0 CB D:MET335 4.9 77.3 1.0 CA D:ASP127 4.9 66.0 1.0 OG D:SER123 5.0 63.0 1.0 CE D:MET335 5.0 66.5 1.0

Manganese binding site 6 out of 6 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2003 b:48.2 occ:1.00 O D:PRO219 2.1 47.8 1.0 OD1 D:ASP217 2.1 46.5 1.0 OE1 D:GLU220 2.2 55.5 1.0 OD1 D:ASN215 2.2 56.0 1.0 OD2 D:ASP158 2.2 54.5 1.0 O D:ASP217 2.2 51.5 1.0 CG D:ASP217 3.0 51.5 1.0 CG D:ASN215 3.2 52.7 1.0 C D:PRO219 3.2 43.4 1.0 C D:ASP217 3.3 46.8 1.0 CG D:ASP158 3.3 49.9 1.0 CD D:GLU220 3.4 46.0 1.0 OD2 D:ASP217 3.6 48.9 1.0 ND2 D:ASN215 3.7 49.4 1.0 CB D:ASP158 3.8 51.3 1.0 CA D:GLU220 3.8 46.6 1.0 N D:GLU220 4.0 41.9 1.0 CA D:ASP217 4.0 51.9 1.0 N D:ASP217 4.0 47.1 1.0 NE2 D:HIS255 4.1 44.7 1.0 CB D:ASP217 4.1 51.9 1.0 C D:ALA218 4.1 48.4 1.0 OE2 D:GLU220 4.2 58.8 1.0 N D:PRO219 4.2 47.5 1.0 O D:ALA218 4.2 52.0 1.0 N D:ALA218 4.3 44.5 1.0 CA D:PRO219 4.3 48.1 1.0 OD1 D:ASP158 4.4 42.7 1.0 CG D:GLU220 4.4 47.5 1.0 CD2 D:HIS255 4.4 44.6 1.0 CB D:ASN215 4.5 51.6 1.0 CB D:GLU220 4.5 48.8 1.0 CA D:ALA218 4.6 50.6 1.0 CD D:PRO219 4.9 47.7 1.0 C D:GLU220 4.9 50.1 1.0

J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with BMS4-1 To Be Published.