Manganese in PDB 7u60: Integrin ALAPHIIBBETA3 Complex with Crgdfv

The structure of Integrin ALAPHIIBBETA3 Complex with Crgdfv, PDB code: 7u60 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)	48.60 / 2.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	260.89, 145.77, 105.16, 90, 90, 90
R / Rfree (%)	18.8 / 22.5

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

Calcium

(Ca)

8 atoms

The binding sites of Manganese atom in the Integrin ALAPHIIBBETA3 Complex with Crgdfv (pdb code 7u60). 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 Crgdfv, PDB code: 7u60:
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 Crgdfv


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 Crgdfv within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:87.9 occ:1.00 OG B:SER121 2.1 21.2 1.0 O B:HOH2122 2.2 13.6 1.0 OG B:SER123 2.2 36.3 1.0 O B:HOH2176 2.2 22.9 1.0 OE2 B:GLU220 2.2 24.8 1.0 OD2 M:ASP3 2.4 43.6 1.0 CB B:SER121 2.9 21.0 1.0 CG M:ASP3 3.2 43.1 1.0 CD B:GLU220 3.3 28.9 1.0 CB B:SER123 3.6 33.5 1.0 CB M:ASP3 3.7 47.9 1.0 CG B:GLU220 3.7 28.9 1.0 CA M:ASP3 3.9 49.5 1.0 OD1 M:ASP3 4.1 43.1 1.0 N B:SER123 4.2 26.1 1.0 OD1 B:ASP251 4.2 34.1 1.0 CA B:SER121 4.2 22.1 1.0 O M:HOH103 4.3 39.3 1.0 OE1 B:GLU220 4.4 22.5 1.0 OD2 B:ASP119 4.4 21.4 1.0 O B:ALA218 4.4 35.1 1.0 OD1 B:ASP119 4.4 20.3 1.0 CA B:SER123 4.5 35.7 1.0 C B:SER121 4.5 31.4 1.0 CB B:ALA252 4.7 21.0 1.0 N B:TYR122 4.7 26.8 1.0 C M:ASP3 4.8 57.3 1.0 ND2 B:ASN215 4.8 20.4 1.0 CG B:ASP119 4.9 23.6 1.0

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


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 Crgdfv within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:159.8 occ:1.00 OD1 B:ASP126 2.2 46.4 0.4 OD2 B:ASP126 2.2 48.5 0.4 OD1 B:ASP127 2.2 59.8 1.0 O B:HOH2190 2.2 50.9 1.0 O B:HOH2113 2.2 62.1 1.0 CG B:ASP126 2.4 49.9 0.4 O B:MET335 2.7 70.5 1.0 CG B:ASP127 3.3 52.6 1.0 O B:SER123 3.5 47.8 1.0 OD2 B:ASP127 3.7 43.6 1.0 CB B:ASP126 3.9 51.3 0.4 C B:MET335 4.0 56.4 1.0 CB B:ASP126 4.1 51.6 0.6 O B:HOH2163 4.1 42.4 1.0 N B:ASP127 4.1 53.4 1.0 CA B:MET124 4.2 39.8 1.0 N B:ASP126 4.3 47.7 1.0 CA B:ASP336 4.4 42.3 1.0 C B:MET124 4.4 40.1 1.0 CA B:ASP126 4.5 49.7 0.4 CB B:ASP127 4.5 37.4 1.0 C B:SER123 4.5 43.7 1.0 CA B:ASP126 4.5 49.6 0.6 OD2 B:ASP126 4.5 52.5 0.6 C B:ASP126 4.6 50.5 1.0 N B:ASP336 4.6 45.2 1.0 N B:LYS125 4.7 40.4 1.0 OD2 B:ASP251 4.8 33.9 1.0 O B:MET124 4.8 33.4 1.0 CA B:ASP127 4.8 38.3 1.0 CG B:ASP126 4.8 51.7 0.6 N B:MET124 4.9 44.5 1.0

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


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 Crgdfv within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2003 b:26.3 occ:1.00 OD1 B:ASN215 2.2 22.2 1.0 OD1 B:ASP217 2.2 21.3 1.0 OE1 B:GLU220 2.2 22.5 1.0 O B:ASP217 2.2 27.5 1.0 OD2 B:ASP158 2.2 25.8 1.0 O B:PRO219 2.3 22.8 1.0 CG B:ASP217 3.2 24.8 1.0 CG B:ASN215 3.3 21.2 1.0 CD B:GLU220 3.3 28.9 1.0 C B:ASP217 3.3 24.4 1.0 CG B:ASP158 3.4 18.7 1.0 C B:PRO219 3.4 17.9 1.0 ND2 B:ASN215 3.8 20.4 1.0 OD2 B:ASP217 3.9 23.1 1.0 CB B:ASP158 3.9 21.5 1.0 CA B:GLU220 3.9 22.2 1.0 CA B:ASP217 4.0 20.8 1.0 N B:ASP217 4.0 24.9 1.0 OE2 B:GLU220 4.0 24.8 1.0 N B:GLU220 4.1 17.7 1.0 CB B:ASP217 4.2 22.3 1.0 C B:ALA218 4.3 41.3 1.0 CG B:GLU220 4.3 28.9 1.0 O B:ALA218 4.4 35.1 1.0 N B:PRO219 4.4 39.9 1.0 N B:ALA218 4.4 21.4 1.0 NE2 B:HIS255 4.4 17.2 1.0 OD1 B:ASP158 4.4 19.1 1.0 CA B:PRO219 4.5 18.4 1.0 CB B:ASN215 4.5 20.4 1.0 CB B:GLU220 4.6 24.3 1.0 CD2 B:HIS255 4.6 26.9 1.0 CA B:ALA218 4.7 20.9 1.0

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


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 Crgdfv within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2001 b:46.5 occ:1.00 O D:HOH2101 2.2 89.9 1.0 OG D:SER121 2.2 36.0 1.0 O D:HOH2104 2.2 29.7 1.0 O D:HOH2110 2.2 26.3 1.0 OE2 D:GLU220 2.3 34.6 1.0 OG D:SER123 2.4 31.3 0.4 OD1 N:ASP3 2.5 87.1 1.0 CB D:SER121 2.9 29.0 1.0 CG N:ASP3 3.1 86.6 1.0 CB N:ASP3 3.4 86.2 1.0 CD D:GLU220 3.5 37.7 1.0 CA N:ASP3 3.7 91.1 1.0 CB D:SER123 3.8 41.4 0.4 OG D:SER123 3.9 38.1 0.6 OD2 N:ASP3 4.0 86.3 1.0 CG D:GLU220 4.1 25.8 1.0 CA D:SER121 4.2 31.2 1.0 CB D:SER123 4.3 41.6 0.6 OD2 D:ASP119 4.3 28.5 1.0 OD1 D:ASP251 4.4 28.6 1.0 OD1 D:ASP119 4.4 27.3 1.0 N D:SER123 4.4 41.7 1.0 OE1 D:GLU220 4.5 26.5 1.0 C D:SER121 4.5 36.7 1.0 C N:ASP3 4.6 116.5 1.0 N D:TYR122 4.6 40.3 1.0 ND2 D:ASN215 4.7 28.9 1.0 CA D:SER123 4.8 39.1 0.4 CG D:ASP119 4.8 34.0 1.0 CB D:ALA252 4.8 27.0 1.0 O D:ALA218 4.9 29.3 1.0 N N:ASP3 4.9 86.6 1.0 N D:SER121 4.9 29.7 1.0 CA D:SER123 5.0 36.3 0.6

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


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 Crgdfv within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2002 b:94.6 occ:1.00 OD1 D:ASP126 2.2 78.7 1.0 O D:HOH2172 2.2 40.4 1.0 O D:HOH2180 2.2 43.6 1.0 OD1 D:ASP127 2.2 42.6 1.0 OD2 D:ASP126 2.3 78.6 1.0 O D:SER123 2.3 44.4 1.0 CG D:ASP126 2.5 66.5 1.0 O D:MET335 3.1 34.0 1.0 CG D:ASP127 3.4 37.8 1.0 C D:SER123 3.5 36.0 1.0 CA D:MET124 3.8 33.5 1.0 CB D:ASP126 4.0 59.6 1.0 N D:ASP127 4.0 39.8 1.0 N D:MET124 4.0 31.8 1.0 OD2 D:ASP127 4.1 43.1 1.0 O D:HOH2215 4.2 51.0 1.0 N D:ASP126 4.3 54.1 1.0 C D:MET124 4.3 45.5 1.0 C D:MET335 4.3 41.6 1.0 N D:LYS125 4.5 42.1 1.0 O D:HOH2102 4.5 25.9 1.0 OD2 D:ASP251 4.5 33.3 1.0 CA D:ASP126 4.6 57.2 1.0 CB D:ASP127 4.6 34.1 1.0 O D:HOH2278 4.6 49.6 1.0 CA D:SER123 4.7 36.3 0.6 CA D:SER123 4.7 39.1 0.4 C D:ASP126 4.8 49.7 1.0 CA D:ASP127 4.8 43.3 1.0 CA D:ASP336 4.9 38.4 1.0 SD D:MET124 4.9 41.8 1.0 CB D:MET124 5.0 30.5 1.0 O D:MET124 5.0 48.4 1.0

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


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 Crgdfv within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2003 b:43.1 occ:1.00 OD1 D:ASP217 2.1 38.8 1.0 OE1 D:GLU220 2.2 26.5 1.0 OD1 D:ASN215 2.2 31.5 1.0 OD2 D:ASP158 2.2 42.2 1.0 O D:ASP217 2.3 37.0 1.0 O D:PRO219 2.3 27.3 1.0 CG D:ASP217 3.2 33.8 1.0 CG D:ASN215 3.3 30.7 1.0 CG D:ASP158 3.3 32.1 1.0 C D:ASP217 3.3 31.6 1.0 C D:PRO219 3.4 33.4 1.0 CD D:GLU220 3.4 37.7 1.0 ND2 D:ASN215 3.7 28.9 1.0 CA D:GLU220 3.8 24.6 1.0 CB D:ASP158 3.8 27.9 1.0 OD2 D:ASP217 4.0 31.1 1.0 N D:GLU220 4.0 24.6 1.0 CA D:ASP217 4.1 29.6 1.0 N D:ASP217 4.1 29.4 1.0 C D:ALA218 4.2 34.7 1.0 O D:ALA218 4.2 29.3 1.0 OE2 D:GLU220 4.2 34.6 1.0 CB D:ASP217 4.2 28.5 1.0 CG D:GLU220 4.3 25.8 1.0 NE2 D:HIS255 4.3 24.6 1.0 N D:PRO219 4.3 27.4 1.0 N D:ALA218 4.4 36.2 1.0 CB D:GLU220 4.4 31.1 1.0 OD1 D:ASP158 4.4 24.7 1.0 CA D:PRO219 4.5 34.4 1.0 CD2 D:HIS255 4.5 24.0 1.0 CB D:ASN215 4.6 29.6 1.0 CA D:ALA218 4.7 34.4 1.0 C D:GLU220 4.9 42.1 1.0

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