Manganese in PDB 6msl: Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D

The structure of Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D, PDB code: 6msl was solved by J.F.Van Agthoven, M.A.Arnaout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.21 / 3.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.764, 129.764, 305.896, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 26.6

The binding sites of Manganese atom in the Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D (pdb code 6msl). 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 Eeti-II 2.5D, PDB code: 6msl:
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 Eeti-II 2.5D


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 Eeti-II 2.5D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1025 b:0.7 occ:1.00 O A:ILE236 1.9 66.6 1.0 OD1 A:ASN232 2.1 73.0 1.0 OD1 A:ASP238 2.1 71.5 1.0 OD1 A:ASP234 2.1 80.9 1.0 OD1 A:ASP230 2.2 69.2 1.0 OD2 A:ASP238 2.3 69.6 1.0 CG A:ASP238 2.4 66.1 1.0 ND2 A:ASN232 2.7 49.5 1.0 CG A:ASN232 2.7 62.0 1.0 C A:ILE236 3.1 65.9 1.0 CG A:ASP234 3.3 72.6 1.0 CG A:ASP230 3.5 60.8 1.0 OD2 A:ASP234 3.7 83.7 1.0 CB A:ASP238 3.8 44.9 1.0 N A:ASP238 3.9 49.3 1.0 C A:ASP237 3.9 50.6 1.0 CA A:ILE236 4.0 65.8 1.0 N A:ASP237 4.1 65.9 1.0 N A:ILE236 4.1 62.3 1.0 CB A:ASP230 4.1 64.1 1.0 CA A:ASP230 4.1 48.1 1.0 CB A:ILE236 4.2 64.8 1.0 CB A:ASN232 4.2 39.3 1.0 CA A:ASP237 4.2 58.4 1.0 O A:ASP237 4.3 46.5 1.0 CA A:ASP238 4.3 36.4 1.0 O A:ASP234 4.4 65.9 1.0 N A:PHE231 4.4 44.4 1.0 OD2 A:ASP230 4.4 49.4 1.0 N A:ASN232 4.5 63.8 1.0 CB A:ASP234 4.6 58.8 1.0 C A:ASP234 4.7 56.9 1.0 N A:GLY258 4.7 60.9 1.0 CG2 A:ILE236 4.7 61.4 1.0 C A:ASP230 4.8 48.3 1.0 C A:GLY235 4.9 64.1 1.0 CA A:ASN232 4.9 61.3 1.0 OD1 A:ASP257 5.0 77.1 1.0

Manganese binding site 2 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D


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 Eeti-II 2.5D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1026 b:69.1 occ:1.00 OD1 A:ASN286 2.2 54.8 1.0 OD1 A:ASP288 2.2 75.4 1.0 O A:TYR290 2.3 70.3 1.0 OD1 A:ASP292 2.4 67.9 1.0 OD2 A:ASP292 2.6 56.5 1.0 OD2 A:ASP284 2.8 62.5 1.0 CG A:ASP292 2.9 56.4 1.0 CG A:ASP288 3.2 74.0 1.0 CG A:ASN286 3.3 47.2 1.0 C A:TYR290 3.4 62.9 1.0 OD2 A:ASP288 3.4 71.0 1.0 CG A:ASP284 3.7 54.9 1.0 ND2 A:ASN286 3.8 62.5 1.0 CB A:TYR290 3.9 57.9 1.0 CA A:TYR290 4.0 56.2 1.0 N A:TYR290 4.0 69.5 1.0 N A:ILE285 4.2 51.4 1.0 CA A:ASP284 4.2 47.0 1.0 N A:ASN286 4.2 49.2 1.0 CB A:ASP292 4.3 32.9 1.0 CB A:ASP284 4.4 49.9 1.0 OD1 A:ASP284 4.4 57.3 1.0 N A:ALA291 4.5 55.7 1.0 CB A:ASN286 4.5 47.6 1.0 O A:GLN320 4.5 69.2 1.0 C A:ALA291 4.5 51.5 1.0 C A:ASP284 4.5 53.4 1.0 N A:ASP292 4.6 43.3 1.0 CB A:ASP288 4.6 52.9 1.0 N A:ASP288 4.6 65.0 1.0 CA A:ASN286 4.8 44.8 1.0 CA A:ALA291 4.8 49.5 1.0 O A:ALA291 4.8 56.3 1.0 N A:GLN320 4.8 48.8 1.0 CA A:ASP292 4.9 35.2 1.0 CA A:ASP288 5.0 51.3 1.0 C A:ASN286 5.0 58.2 1.0

Manganese binding site 3 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D


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 Eeti-II 2.5D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1027 b:74.7 occ:1.00 OD1 A:ASP357 2.2 54.5 1.0 OD1 A:ASP351 2.3 55.1 1.0 OD1 A:ASP353 2.3 66.7 1.0 O A:PHE355 2.4 56.3 1.0 OD1 A:ASP349 2.5 50.8 1.0 OD2 A:ASP357 2.5 52.5 1.0 CG A:ASP357 2.7 50.7 1.0 OD2 A:ASP353 2.7 61.0 1.0 CG A:ASP353 2.8 59.9 1.0 CG A:ASP351 3.1 53.9 1.0 OD2 A:ASP351 3.2 60.0 1.0 C A:PHE355 3.5 50.1 1.0 CG A:ASP349 3.7 47.9 1.0 CB A:ASP357 4.2 42.1 1.0 CB A:ASP353 4.2 53.5 1.0 O A:GLY378 4.2 48.5 1.0 C A:ASN356 4.3 34.8 1.0 CA A:PHE355 4.3 49.1 1.0 N A:PHE355 4.3 48.6 1.0 O A:ASN356 4.4 49.6 1.0 OD2 A:ASP349 4.4 44.6 1.0 N A:GLY378 4.4 37.4 1.0 CB A:PHE355 4.5 41.1 1.0 N A:ASP351 4.5 56.3 1.0 N A:ASN356 4.5 38.9 1.0 N A:ASP357 4.5 31.2 1.0 CA A:ASP349 4.5 53.6 1.0 N A:ASP353 4.5 44.2 1.0 CB A:ASP351 4.5 46.0 1.0 CB A:ASN377 4.6 29.3 1.0 N A:LEU350 4.6 49.6 1.0 ND2 A:ASN377 4.6 52.1 1.0 CA A:ASN356 4.6 44.8 1.0 CB A:ASP349 4.7 41.9 1.0 CA A:ASP357 4.8 39.8 1.0 C A:ASP349 4.8 51.5 1.0 CA A:ASN377 4.8 30.9 1.0 CA A:ASP353 4.9 57.3 1.0 N A:GLN352 5.0 58.3 1.0 CA A:ASP351 5.0 49.5 1.0

Manganese binding site 4 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D


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 Eeti-II 2.5D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1028 b:64.8 occ:1.00 O A:TYR419 2.1 35.1 1.0 OD1 A:ASP421 2.2 65.1 1.0 OD1 A:ASP415 2.4 63.6 1.0 OD2 A:ASP421 2.4 56.5 1.0 OD1 A:ASN417 2.4 64.7 1.0 OD1 A:ASP413 2.5 54.9 1.0 CG A:ASP421 2.6 54.8 1.0 OD2 A:ASP415 2.9 46.5 1.0 CG A:ASP415 3.0 67.1 1.0 C A:TYR419 3.3 40.1 1.0 CG A:ASN417 3.4 60.7 1.0 O A:PRO420 3.7 52.4 1.0 C A:PRO420 3.7 26.6 1.0 CG A:ASP413 3.7 51.8 1.0 ND2 A:ASN417 3.7 58.3 1.0 N A:ALA437 3.9 38.0 1.0 N A:ASP421 3.9 22.9 1.0 CB A:ASP421 3.9 34.4 1.0 CB A:ALA437 4.1 27.1 1.0 N A:PRO420 4.2 30.3 1.0 CA A:TYR419 4.2 44.6 1.0 CA A:PRO420 4.2 21.9 1.0 CA A:ASP413 4.3 33.5 1.0 N A:TYR419 4.3 46.2 1.0 O A:ALA437 4.3 64.7 1.0 CA A:ASP421 4.3 25.5 1.0 CB A:TYR419 4.4 49.7 1.0 CB A:ASP413 4.4 40.8 1.0 CB A:ASP415 4.4 57.9 1.0 CA A:ALA437 4.5 35.6 1.0 N A:ASP415 4.5 66.9 1.0 OD2 A:ASP413 4.6 42.7 1.0 N A:ILE414 4.6 33.5 1.0 C A:ASP413 4.7 36.9 1.0 CB A:ASN417 4.7 59.0 1.0 C A:ALA437 4.9 51.0 1.0 N A:ASN417 4.9 61.9 1.0 C A:ARG436 4.9 44.7 1.0 CA A:ARG436 4.9 50.4 1.0 CA A:ASP415 5.0 53.5 1.0

Manganese binding site 5 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D


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 Eeti-II 2.5D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1029 b:0.1 occ:1.00 OE2 A:GLU636 2.1 94.9 1.0 O A:VAL601 2.1 63.5 1.0 OD1 A:ASP599 2.2 91.7 1.0 OE1 A:GLU636 2.2 71.8 1.0 O A:CYS596 2.2 75.5 1.0 OD2 A:ASP599 2.3 83.5 1.0 CD A:GLU636 2.4 83.5 1.0 CG A:ASP599 2.6 94.0 1.0 C A:VAL601 3.3 65.8 1.0 C A:CYS596 3.4 70.4 1.0 CG A:GLU636 3.9 72.8 1.0 CA A:GLY597 4.0 82.6 1.0 N A:LYS603 4.1 43.0 1.0 CB A:ASP599 4.1 74.9 1.0 CA A:CYS602 4.1 57.2 1.0 N A:CYS602 4.1 50.0 1.0 N A:GLY597 4.1 67.2 1.0 N A:VAL601 4.3 70.3 1.0 CA A:VAL601 4.4 67.4 1.0 CA A:CYS596 4.4 68.9 1.0 C A:CYS602 4.5 49.5 1.0 CG1 A:VAL601 4.5 61.4 1.0 CB A:GLU636 4.6 63.1 1.0 CE A:LYS603 4.6 72.5 1.0 C A:GLY597 4.6 85.8 1.0 N A:ASP599 4.8 83.5 1.0 CB A:LYS603 4.8 67.2 1.0 CB A:CYS596 4.8 75.6 1.0 CG A:LYS603 4.9 63.4 1.0 CA A:ASP599 4.9 79.0 1.0

Manganese binding site 6 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D


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 Eeti-II 2.5D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn708 b:56.2 occ:1.00 O B:HOH801 2.2 38.4 1.0 OE1 B:GLU220 2.2 52.6 1.0 OG B:SER123 2.2 50.2 1.0 OD1 C:ASP8 2.3 58.5 1.0 OG B:SER121 2.3 40.0 1.0 O B:HOH802 2.4 41.7 1.0 CD B:GLU220 2.8 58.1 1.0 CG C:ASP8 3.3 51.6 1.0 CG B:GLU220 3.3 43.7 1.0 CB B:SER121 3.3 40.7 1.0 CB B:SER123 3.4 56.6 1.0 OE2 B:GLU220 3.8 63.6 1.0 OD2 C:ASP8 3.9 35.1 1.0 O B:ALA218 4.0 50.4 1.0 N B:SER123 4.0 36.8 1.0 CA C:ASP8 4.2 36.0 1.0 CB C:ASP8 4.2 50.0 1.0 CA B:SER123 4.3 48.7 1.0 OD2 B:ASP119 4.5 30.0 1.0 CA B:SER121 4.5 29.5 1.0 N B:TYR122 4.6 39.9 1.0 OD1 B:ASP119 4.6 39.4 1.0 C B:SER121 4.6 46.3 1.0 CB B:GLU220 4.7 23.7 1.0 OD1 B:ASN215 4.9 73.2 1.0 C B:ALA218 4.9 40.7 1.0 CB B:ASP251 4.9 45.6 1.0

Manganese binding site 7 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D


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 Eeti-II 2.5D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn709 b:86.2 occ:1.00 OD1 B:ASP251 2.3 0.6 1.0 O B:SER123 2.3 48.8 1.0 OD1 B:ASP126 2.4 69.5 1.0 OD1 B:ASP127 2.5 72.5 1.0 OD2 B:ASP251 2.6 97.1 1.0 CG B:ASP251 2.7 83.7 1.0 OD2 B:ASP126 3.0 74.6 1.0 CG B:ASP126 3.0 69.1 1.0 O B:HOH803 3.3 53.8 1.0 C B:SER123 3.4 56.5 1.0 CG B:ASP127 3.6 70.9 1.0 CA B:SER123 4.1 48.7 1.0 CB B:SER123 4.1 56.6 1.0 CB B:ASP251 4.1 45.6 1.0 OD2 B:ASP127 4.2 66.7 1.0 N B:MET124 4.3 37.0 1.0 O C:TRP9 4.5 61.1 1.0 CB B:ASP126 4.5 46.5 1.0 CA B:MET124 4.5 57.0 1.0 CB B:ASP127 4.8 55.6 1.0 N B:ASP126 5.0 49.7 1.0

Manganese binding site 8 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to Eeti-II 2.5D


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 Eeti-II 2.5D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn710 b:0.5 occ:1.00 OD1 B:ASP217 2.2 55.7 1.0 O B:PRO219 2.2 41.2 1.0 OD2 B:ASP158 2.3 45.0 1.0 O B:ASP217 2.3 43.2 1.0 OE2 B:GLU220 2.4 63.6 1.0 ND2 B:ASN215 2.7 69.3 1.0 CG B:ASN215 3.1 61.7 1.0 OD1 B:ASN215 3.3 73.2 1.0 CG B:ASP158 3.3 54.2 1.0 CG B:ASP217 3.4 48.8 1.0 C B:PRO219 3.4 39.5 1.0 C B:ASP217 3.5 52.3 1.0 CD B:GLU220 3.6 58.1 1.0 CB B:ASP158 3.7 31.3 1.0 CA B:GLU220 4.0 39.4 1.0 N B:ASP217 4.1 41.9 1.0 CB B:ASN215 4.1 44.1 1.0 CA B:ASP217 4.2 37.4 1.0 N B:GLU220 4.2 21.8 1.0 OD2 B:ASP217 4.2 45.5 1.0 CB B:ASP217 4.4 30.8 1.0 OE1 B:GLU220 4.4 52.6 1.0 C B:ALA218 4.5 40.7 1.0 OD1 B:ASP158 4.5 21.8 1.0 N B:PRO219 4.5 28.3 1.0 CA B:PRO219 4.5 25.0 1.0 N B:ALA218 4.6 42.0 1.0 CG B:GLU220 4.6 43.7 1.0 NE2 B:HIS255 4.6 39.5 1.0 O B:ALA218 4.7 50.4 1.0 CB B:GLU220 4.8 23.7 1.0 CB B:TYR164 4.8 29.6 1.0 CD2 B:HIS255 4.9 27.2 1.0 CA B:ALA218 4.9 28.8 1.0 N B:ARG216 4.9 21.8 1.0 CD1 B:TYR164 4.9 21.8 1.0 O B:VAL157 5.0 28.6 1.0 C B:ARG216 5.0 35.7 1.0

J.F.Van Agthoven, M.A.Arnaout. Integrin ALPHAVBETA3 Ectodomain Bound Eeti-II 2.5D To Be Published.