Manganese in PDB 7ukp: Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog

The structure of Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog, PDB code: 7ukp 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)	48.25 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	259.322, 144.495, 104.848, 90, 90, 90
R / Rfree (%)	21.9 / 24.1

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

Calcium	(Ca)	8 atoms
Chlorine	(Cl)	1 atom

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

Manganese binding site 1 out of 4 in the Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:66.7 occ:1.00 O B:HOH2120 2.0 65.5 1.0 O4 B:NJ92004 2.1 73.5 1.0 OG B:SER123 2.1 69.8 1.0 OE2 B:GLU220 2.2 65.9 1.0 OG B:SER121 2.2 66.8 1.0 O B:HOH2109 2.2 62.6 1.0 CB B:SER121 2.7 67.4 1.0 C18 B:NJ92004 3.2 73.5 1.0 CD B:GLU220 3.3 64.5 1.0 CB B:SER123 3.4 71.4 1.0 CG B:GLU220 3.7 63.7 1.0 O3 B:NJ92004 3.9 73.5 1.0 N B:SER123 4.1 72.1 1.0 CA B:SER121 4.1 68.2 1.0 C8 B:NJ92004 4.1 73.5 1.0 OD2 B:ASP119 4.2 65.0 1.0 OD1 B:ASP251 4.2 68.9 1.0 OD1 B:ASP119 4.3 65.5 1.0 C17 B:NJ92004 4.3 73.5 1.0 O B:ALA218 4.3 63.7 1.0 CA B:SER123 4.4 72.8 1.0 C B:SER121 4.4 70.2 1.0 OE1 B:GLU220 4.4 64.1 1.0 ND2 B:ASN215 4.5 66.2 1.0 CG B:ASP119 4.6 65.2 1.0 N B:TYR122 4.7 71.2 1.0 CB B:ALA252 4.7 67.3 1.0 N B:SER121 4.8 67.4 1.0 O B:SER121 4.9 70.8 1.0

Manganese binding site 2 out of 4 in the Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:65.5 occ:1.00 O B:PRO219 2.0 62.7 1.0 OD1 B:ASP217 2.2 63.5 1.0 OD1 B:ASN215 2.2 64.8 1.0 OD2 B:ASP158 2.2 63.2 1.0 OE1 B:GLU220 2.2 64.1 1.0 O B:ASP217 2.2 64.8 1.0 CG B:ASP217 3.1 63.6 1.0 C B:PRO219 3.2 62.4 1.0 CG B:ASN215 3.2 65.7 1.0 CG B:ASP158 3.3 62.8 1.0 CD B:GLU220 3.3 64.5 1.0 C B:ASP217 3.4 65.8 1.0 OD2 B:ASP217 3.7 62.6 1.0 ND2 B:ASN215 3.7 66.2 1.0 CB B:ASP158 3.8 63.6 1.0 CA B:GLU220 3.8 61.6 1.0 N B:GLU220 3.9 62.0 1.0 CA B:ASP217 4.0 66.4 1.0 N B:ASP217 4.1 67.0 1.0 OE2 B:GLU220 4.1 65.9 1.0 CB B:ASP217 4.1 65.2 1.0 C B:ALA218 4.2 63.9 1.0 N B:PRO219 4.2 64.4 1.0 NE2 B:HIS255 4.2 60.1 1.0 O B:ALA218 4.2 63.7 1.0 CA B:PRO219 4.3 63.0 1.0 CG B:GLU220 4.3 63.7 1.0 OD1 B:ASP158 4.4 62.0 1.0 N B:ALA218 4.4 65.8 1.0 CB B:GLU220 4.5 62.3 1.0 CB B:ASN215 4.5 66.6 1.0 CD2 B:HIS255 4.5 59.3 1.0 CA B:ALA218 4.8 65.7 1.0 CD B:PRO219 4.9 64.7 1.0 C B:GLU220 4.9 60.5 1.0 CD1 B:TYR164 4.9 63.3 1.0

Manganese binding site 3 out of 4 in the Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2001 b:98.4 occ:1.00 OE2 D:GLU220 2.1 99.5 1.0 O4 D:NJ92004 2.2 100.1 1.0 O D:HOH2106 2.2 102.1 1.0 O D:HOH2113 2.2 99.4 1.0 OG D:SER121 2.2 100.0 1.0 OG D:SER123 2.4 105.1 1.0 CB D:SER121 2.8 99.2 1.0 C18 D:NJ92004 3.2 100.1 1.0 CD D:GLU220 3.3 97.5 1.0 C8 D:NJ92004 3.5 100.1 1.0 CB D:SER123 3.9 108.0 1.0 CG D:GLU220 3.9 97.2 1.0 C17 D:NJ92004 3.9 100.1 1.0 O3 D:NJ92004 4.1 100.1 1.0 CA D:SER121 4.1 100.9 1.0 N D:SER123 4.2 108.0 1.0 OE1 D:GLU220 4.2 95.8 1.0 OD2 D:ASP119 4.3 98.0 1.0 C D:SER121 4.4 103.7 1.0 ND2 D:ASN215 4.4 98.9 1.0 OD1 D:ASP251 4.4 104.8 1.0 N D:TYR122 4.5 106.3 1.0 O D:ALA218 4.5 96.7 1.0 OD1 D:ASP119 4.5 98.3 1.0 CA D:SER123 4.6 109.7 1.0 N2 D:NJ92004 4.8 100.1 1.0 CB D:ALA252 4.8 99.4 1.0 CG D:ASP119 4.8 98.5 1.0 O D:SER121 4.9 105.5 1.0 N D:SER121 5.0 100.9 1.0

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


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2002 b:98.1 occ:1.00 OD1 D:ASP217 2.1 92.6 1.0 OD2 D:ASP158 2.2 91.0 1.0 OD1 D:ASN215 2.2 95.7 1.0 O D:PRO219 2.2 92.2 1.0 OE1 D:GLU220 2.2 95.8 1.0 O D:ASP217 2.2 96.3 1.0 CG D:ASN215 3.1 97.1 1.0 CG D:ASP217 3.1 92.2 1.0 C D:PRO219 3.3 92.8 1.0 CG D:ASP158 3.3 90.2 1.0 CD D:GLU220 3.3 97.5 1.0 C D:ASP217 3.4 96.7 1.0 ND2 D:ASN215 3.5 98.9 1.0 OD2 D:ASP217 3.8 90.8 1.0 CA D:GLU220 3.8 93.2 1.0 CB D:ASP158 3.9 91.3 1.0 N D:GLU220 4.0 93.5 1.0 CA D:ASP217 4.1 95.9 1.0 N D:ASP217 4.1 96.1 1.0 OE2 D:GLU220 4.1 99.5 1.0 C D:ALA218 4.1 96.0 1.0 O D:ALA218 4.2 96.7 1.0 CB D:ASP217 4.2 93.5 1.0 N D:PRO219 4.2 94.8 1.0 CG D:GLU220 4.3 97.2 1.0 CB D:ASN215 4.3 97.0 1.0 OD1 D:ASP158 4.3 88.8 1.0 NE2 D:HIS255 4.4 87.9 1.0 CA D:PRO219 4.4 93.6 1.0 N D:ALA218 4.4 96.3 1.0 CB D:GLU220 4.5 95.2 1.0 CA D:ALA218 4.7 97.5 1.0 CD2 D:HIS255 4.7 87.7 1.0 CD D:PRO219 4.9 93.9 1.0 C D:GLU220 4.9 91.6 1.0

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