Manganese in PDB 6mk0: Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161

The structure of Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161, PDB code: 6mk0 was solved by J.F.Van Agthoven, M.A.Armaout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.09 / 3.01
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.406, 129.406, 305.535, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 25.3

The binding sites of Manganese atom in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 (pdb code 6mk0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161, PDB code: 6mk0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1018 b:99.9 occ:1.00 OD1 A:ASP238 2.2 66.8 1.0 OD1 A:ASP230 2.2 66.1 1.0 OD1 A:ASN232 2.2 74.9 1.0 OD1 A:ASP234 2.2 89.0 1.0 OD2 A:ASP234 2.3 70.6 1.0 O A:ILE236 2.5 33.9 1.0 CG A:ASP234 2.6 71.8 1.0 OD2 A:ASP238 2.6 57.9 1.0 CG A:ASP238 2.7 44.1 1.0 CG A:ASN232 3.3 47.2 1.0 CG A:ASP230 3.4 53.2 1.0 C A:ILE236 3.7 39.7 1.0 ND2 A:ASN232 3.9 39.4 1.0 CB A:ASP234 4.1 36.3 1.0 CB A:ASP238 4.1 28.4 1.0 N A:ASN232 4.1 59.5 1.0 N A:PHE231 4.1 30.8 1.0 OD2 A:ASP230 4.2 55.2 1.0 CA A:ASP230 4.2 37.7 1.0 N A:ILE236 4.2 44.0 1.0 N A:ASP238 4.3 21.6 1.0 CB A:ASP230 4.3 55.9 1.0 O A:ASN232 4.4 64.0 1.0 CA A:ILE236 4.4 40.6 1.0 C A:ASP237 4.5 33.2 1.0 CB A:ASN232 4.6 44.7 1.0 CA A:ASP238 4.6 29.5 1.0 N A:ASP234 4.7 51.8 1.0 CB A:ILE236 4.7 33.3 1.0 CA A:ASN232 4.7 58.6 1.0 C A:ASN232 4.7 48.5 1.0 C A:ASP230 4.7 32.3 1.0 OD1 A:ASP257 4.7 68.8 1.0 N A:ASP237 4.7 45.5 1.0 N A:GLY235 4.8 36.5 1.0 CA A:ASP234 4.8 33.4 1.0 N A:GLY258 4.9 30.9 1.0 CA A:ASP237 4.9 42.9 1.0 O A:ASP237 5.0 37.7 1.0

Manganese binding site 2 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1019 b:1.0 occ:1.00 O A:TYR290 2.1 0.8 1.0 OD1 A:ASN286 2.1 0.3 1.0 OD1 A:ASP292 2.2 0.8 1.0 OD2 A:ASP292 2.2 0.8 1.0 OD1 A:ASP284 2.2 0.2 1.0 OD1 A:ASP288 2.2 0.1 1.0 CG A:ASP292 2.5 0.8 1.0 CG A:ASN286 2.8 82.1 1.0 ND2 A:ASN286 2.8 79.6 1.0 CG A:ASP288 3.2 91.8 1.0 C A:TYR290 3.2 76.3 1.0 CG A:ASP284 3.4 79.5 1.0 OD2 A:ASP288 3.5 93.5 1.0 CA A:TYR290 3.9 50.7 1.0 CB A:TYR290 3.9 45.2 1.0 N A:TYR290 3.9 52.5 1.0 CB A:ASP292 4.0 55.8 1.0 CA A:ASP284 4.0 25.2 1.0 CB A:ASP284 4.1 25.6 1.0 CB A:ASN286 4.3 27.1 1.0 N A:ALA291 4.3 35.5 1.0 C A:ALA291 4.3 44.0 1.0 N A:ASP292 4.3 35.2 1.0 OD2 A:ASP284 4.3 87.4 1.0 N A:ILE285 4.4 36.6 1.0 N A:ASN286 4.4 46.9 1.0 C A:ASP284 4.5 34.8 1.0 CB A:ASP288 4.5 65.1 1.0 CA A:ALA291 4.6 24.1 1.0 O A:GLN320 4.6 62.5 1.0 CA A:ASP292 4.6 40.6 1.0 O A:ALA291 4.6 41.3 1.0 N A:GLN320 4.8 38.6 1.0 N A:ASP288 4.8 44.1 1.0 CA A:ASN286 4.9 39.3 1.0 O A:THR283 4.9 52.7 1.0

Manganese binding site 3 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1020 b:76.4 occ:1.00 OD1 A:ASP351 2.2 57.5 1.0 OD1 A:ASP353 2.2 77.9 1.0 OD1 A:ASP357 2.2 74.3 1.0 OD1 A:ASP349 2.2 61.3 1.0 OD2 A:ASP357 2.2 77.0 1.0 O A:PHE355 2.3 58.7 1.0 CG A:ASP357 2.5 57.0 1.0 CG A:ASP351 3.2 43.0 1.0 CG A:ASP353 3.3 63.5 1.0 CG A:ASP349 3.4 41.1 1.0 C A:PHE355 3.5 56.2 1.0 OD2 A:ASP351 3.6 63.0 1.0 OD2 A:ASP353 3.9 79.7 1.0 CB A:ASP357 4.0 35.7 1.0 N A:ASP351 4.1 62.8 1.0 OD2 A:ASP349 4.1 31.9 1.0 N A:LEU350 4.2 49.3 1.0 C A:ASN356 4.2 40.4 1.0 CA A:ASP349 4.2 36.1 1.0 N A:ASP357 4.3 51.3 1.0 N A:PHE355 4.3 53.0 1.0 CA A:PHE355 4.3 55.1 1.0 CB A:ASP349 4.4 37.5 1.0 N A:ASN356 4.4 50.8 1.0 N A:ASP353 4.4 50.5 1.0 C A:ASP349 4.4 37.2 1.0 O A:ASN356 4.4 57.9 1.0 N A:GLY378 4.4 42.0 1.0 CB A:ASP353 4.5 44.1 1.0 CA A:ASN356 4.5 39.3 1.0 CB A:ASP351 4.5 29.8 1.0 CB A:PHE355 4.6 53.0 1.0 N A:GLN352 4.6 37.4 1.0 CA A:ASP357 4.6 51.3 1.0 CA A:ASP351 4.7 51.2 1.0 O A:GLY378 4.8 51.3 1.0 ND2 A:ASN377 4.8 32.8 1.0 CB A:ASN377 4.9 28.0 1.0 C A:ASP351 4.9 45.2 1.0 CA A:ASP353 4.9 51.2 1.0

Manganese binding site 4 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1021 b:0.0 occ:1.00 O A:TYR419 2.1 41.1 1.0 OD1 A:ASP421 2.2 85.1 1.0 OD1 A:ASP415 2.2 74.1 1.0 OD2 A:ASP421 2.2 78.9 1.0 OD1 A:ASN417 2.2 71.0 1.0 OD1 A:ASP413 2.4 60.2 1.0 CG A:ASP421 2.5 64.3 1.0 ND2 A:ASN417 2.7 33.2 1.0 CG A:ASN417 2.8 58.6 1.0 CG A:ASP415 3.2 61.2 1.0 C A:TYR419 3.3 28.4 1.0 OD2 A:ASP415 3.5 56.5 1.0 CG A:ASP413 3.6 48.2 1.0 CB A:ASP421 4.0 26.6 1.0 C A:PRO420 4.0 34.6 1.0 CA A:ASP413 4.1 28.0 1.0 N A:TYR419 4.2 44.6 1.0 CA A:TYR419 4.2 45.9 1.0 O A:PRO420 4.2 50.9 1.0 N A:ASP421 4.2 26.5 1.0 CB A:ASN417 4.3 40.2 1.0 N A:PRO420 4.3 36.8 1.0 CA A:PRO420 4.3 37.1 1.0 CB A:ASP413 4.4 30.8 1.0 N A:ALA437 4.4 40.1 1.0 N A:ASP415 4.4 50.0 1.0 CB A:TYR419 4.4 59.0 1.0 OD2 A:ASP413 4.4 36.8 1.0 N A:ILE414 4.5 26.8 1.0 O A:ALA437 4.5 60.3 1.0 O A:ASP415 4.5 86.2 1.0 CA A:ASP421 4.6 30.1 1.0 C A:ASP413 4.6 33.1 1.0 CB A:ASP415 4.6 44.4 1.0 CB A:ALA437 4.8 30.0 1.0 N A:ASN417 4.8 44.5 1.0 C A:ASP415 4.8 58.5 1.0 CA A:ASP415 4.8 48.8 1.0 CA A:ASN417 5.0 32.7 1.0

Manganese binding site 5 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1022 b:83.8 occ:1.00 OD1 A:ASP599 2.1 96.5 1.0 OE2 A:GLU636 2.2 80.3 1.0 OE1 A:GLU636 2.2 0.3 1.0 OD2 A:ASP599 2.2 85.2 1.0 O A:CYS596 2.3 47.9 1.0 O A:VAL601 2.4 47.9 1.0 CG A:ASP599 2.4 78.8 1.0 CD A:GLU636 2.5 75.4 1.0 C A:CYS596 3.4 59.4 1.0 C A:VAL601 3.6 47.7 1.0 CA A:GLY597 3.9 62.8 1.0 CB A:ASP599 4.0 51.5 1.0 CG A:GLU636 4.0 47.6 1.0 N A:GLY597 4.1 56.7 1.0 N A:LYS603 4.3 47.5 1.0 N A:VAL601 4.4 48.6 1.0 CA A:CYS596 4.4 63.9 1.0 CA A:CYS602 4.4 47.1 1.0 N A:CYS602 4.5 47.3 1.0 C A:GLY597 4.5 70.0 1.0 N A:ASP599 4.6 59.4 1.0 CA A:VAL601 4.6 48.3 1.0 CG2 A:VAL601 4.6 48.8 1.0 CE A:LYS603 4.6 79.1 1.0 CA A:ASP599 4.7 56.4 1.0 CB A:CYS596 4.8 58.6 1.0 CB A:GLU636 4.8 56.6 1.0 N A:ASN600 4.9 66.2 1.0 C A:CYS602 4.9 47.2 1.0 O A:GLY597 5.0 62.0 1.0 C A:ASP599 5.0 62.7 1.0

Manganese binding site 6 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn708 b:80.7 occ:1.00 O03 B:JUY712 2.1 45.1 1.0 OG B:SER121 2.2 61.0 1.0 OE1 B:GLU220 2.2 60.0 1.0 O B:HOH802 2.2 31.2 1.0 O B:HOH801 2.2 18.6 1.0 O B:HOH804 2.3 3.2 1.0 CB B:SER121 2.6 30.4 1.0 CD B:GLU220 3.1 41.9 1.0 C02 B:JUY712 3.1 31.0 1.0 CG B:GLU220 3.5 33.4 1.0 C04 B:JUY712 3.7 26.9 1.0 OE2 B:GLU220 4.1 64.8 1.0 CA B:SER121 4.1 31.6 1.0 O01 B:JUY712 4.1 24.2 1.0 OD2 B:ASP119 4.1 37.9 1.0 OG B:SER123 4.2 36.4 1.0 C05 B:JUY712 4.3 27.0 1.0 O B:ALA218 4.4 31.1 1.0 CB B:ALA252 4.6 27.8 1.0 C B:SER121 4.7 33.1 1.0 C06 B:JUY712 4.7 26.3 1.0 OD1 B:ASP251 4.7 46.0 1.0 OD1 B:ASP119 4.8 63.2 1.0 N B:SER121 4.8 45.3 1.0 CG B:ASP119 4.9 41.1 1.0 N B:TYR122 4.9 41.9 1.0 CB B:GLU220 5.0 25.7 1.0 N24 B:JUY712 5.0 40.4 1.0

Manganese binding site 7 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn709 b:0.4 occ:1.00 OD1 B:ASP126 2.3 79.4 1.0 O B:MET335 2.3 67.7 1.0 OD2 B:ASP126 2.4 84.8 1.0 O B:HOH803 2.4 97.9 1.0 OD1 B:ASP127 2.4 74.0 1.0 CG B:ASP126 2.6 75.1 1.0 O B:SER123 2.7 77.0 1.0 CG B:ASP127 3.4 71.7 1.0 C B:MET335 3.5 57.6 1.0 OD2 B:ASP127 3.8 70.0 1.0 CE B:MET124 3.8 56.5 1.0 C B:SER123 3.9 47.5 1.0 CB B:ASP126 4.1 43.3 1.0 CA B:MET335 4.4 58.5 1.0 CA B:MET124 4.4 47.0 1.0 N B:ASP336 4.4 68.6 1.0 N B:ASP127 4.4 67.5 1.0 CA B:ASP336 4.5 66.4 1.0 CB B:MET335 4.6 81.1 1.0 N B:MET124 4.6 38.5 1.0 N B:ASP126 4.7 51.7 1.0 CB B:ASP127 4.7 46.2 1.0 OD2 B:ASP251 4.8 61.0 1.0 CA B:ASP126 4.8 43.2 1.0 C B:MET124 4.9 50.2 1.0 C B:ASP126 5.0 54.9 1.0 CA B:SER123 5.0 35.4 1.0

Manganese binding site 8 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn710 b:46.5 occ:1.00 OD1 B:ASN215 2.0 47.1 1.0 O B:PRO219 2.1 27.0 1.0 OD2 B:ASP158 2.1 31.2 1.0 OD1 B:ASP217 2.2 45.0 1.0 OE2 B:GLU220 2.2 64.8 1.0 O B:ASP217 2.5 25.8 1.0 CG B:ASP217 3.1 25.9 1.0 C B:PRO219 3.2 24.2 1.0 CG B:ASN215 3.3 45.8 1.0 CG B:ASP158 3.3 24.1 1.0 CD B:GLU220 3.4 41.9 1.0 C B:ASP217 3.5 31.8 1.0 OD2 B:ASP217 3.7 30.3 1.0 CA B:GLU220 3.9 24.7 1.0 CB B:ASP158 3.9 25.0 1.0 N B:GLU220 3.9 24.5 1.0 O B:ALA218 4.1 31.1 1.0 N B:ASP217 4.1 25.8 1.0 CA B:ASP217 4.1 36.3 1.0 C B:ALA218 4.2 31.3 1.0 CB B:ASN215 4.2 27.9 1.0 ND2 B:ASN215 4.2 67.7 1.0 CB B:ASP217 4.2 24.2 1.0 OE1 B:GLU220 4.2 60.0 1.0 N B:PRO219 4.2 25.7 1.0 CA B:PRO219 4.3 24.2 1.0 OD1 B:ASP158 4.3 23.4 1.0 CG B:GLU220 4.4 33.4 1.0 NE2 B:HIS255 4.5 22.1 1.0 N B:ALA218 4.5 25.8 1.0 CB B:GLU220 4.5 25.7 1.0 CD2 B:HIS255 4.6 22.2 1.0 CA B:ALA218 4.8 26.1 1.0 CD B:PRO219 5.0 26.3 1.0

J.F.Van Agthoven, M.A.Armaout. Integrin ALPHAVBETA3 Ectodomain Bound to Antagonist Tdi-4161 To Be Published.