Manganese in PDB 1l5g: Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand

The structure of Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand, PDB code: 1l5g was solved by J.-P.Xiong, T.Stehle, R.Zhang, A.Joachimiak, M.Frech, S.L.Goodman, M.A.Arnaout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.790, 129.790, 308.780, 90.00, 90.00, 120.00
R / Rfree (%)	24.8 / 32.8

The binding sites of Manganese atom in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand (pdb code 1l5g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand, PDB code: 1l5g:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn4001 b:17.0 occ:1.00 OG B:SER121 2.5 10.6 1.0 OD1 C:ASP5003 2.7 17.0 1.0 OE1 B:GLU220 2.7 46.4 1.0 OG B:SER123 2.7 27.2 1.0 CD B:GLU220 3.1 40.1 1.0 OE2 B:GLU220 3.6 47.6 1.0 CB B:SER121 3.7 13.1 1.0 CG B:GLU220 3.7 32.6 1.0 CG C:ASP5003 3.7 20.4 1.0 OD1 B:ASP119 3.9 17.2 1.0 CB B:SER123 3.9 28.4 1.0 O B:ALA218 4.2 21.3 1.0 CB B:GLU220 4.5 26.7 1.0 OD2 B:ASP119 4.5 35.5 1.0 CB C:ASP5003 4.5 15.9 1.0 CA C:ASP5003 4.6 20.3 1.0 OD2 C:ASP5003 4.6 18.6 1.0 CG B:ASP119 4.6 29.8 1.0 CB B:ASP251 4.7 29.6 1.0 CA B:SER121 4.8 18.7 1.0 C B:SER121 4.8 23.5 1.0 O B:SER121 4.9 17.5 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn4002 b:30.8 occ:1.00 O B:SER123 2.4 21.4 1.0 OD1 B:ASP251 2.7 35.1 1.0 OD2 B:ASP251 2.7 42.4 1.0 OD1 B:ASP126 2.9 63.2 1.0 CG B:ASP251 3.0 37.4 1.0 OD2 B:ASP126 3.1 61.6 1.0 CG B:ASP126 3.4 61.7 1.0 OD1 B:ASP127 3.6 50.0 1.0 C B:SER123 3.6 29.9 1.0 OD2 B:ASP127 4.2 50.0 1.0 CG B:ASP127 4.3 50.0 1.0 CA B:SER123 4.5 29.6 1.0 CB B:ASP251 4.5 29.6 1.0 N B:MET124 4.5 34.3 1.0 CA B:MET124 4.6 38.3 1.0 CB B:SER123 4.7 28.4 1.0 CB B:ASP126 4.9 59.2 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn4003 b:28.3 occ:1.00 ND2 B:ASN215 2.4 27.2 1.0 OD2 B:ASP158 2.6 9.6 1.0 O B:PRO219 2.6 10.4 1.0 OE2 B:GLU220 2.7 47.6 1.0 O B:ASP217 2.8 34.4 1.0 CB B:ASP217 3.0 19.9 1.0 CG B:ASN215 3.1 27.5 1.0 OD1 B:ASN215 3.2 27.5 1.0 CD B:GLU220 3.3 40.1 1.0 C B:ASP217 3.4 25.5 1.0 CA B:ASP217 3.5 18.3 1.0 N B:ASP217 3.6 21.2 1.0 CG B:ASP158 3.6 9.8 1.0 OE1 B:GLU220 3.7 46.4 1.0 C B:PRO219 3.8 18.7 1.0 CB B:ASP158 3.9 2.4 1.0 CA B:GLU220 4.0 29.1 1.0 CG B:GLU220 4.1 32.6 1.0 NE2 B:HIS255 4.2 12.1 1.0 CG B:ASP217 4.3 27.4 1.0 CB B:ASN215 4.3 16.7 1.0 N B:GLU220 4.4 21.9 1.0 N B:ALA218 4.6 24.6 1.0 CB B:GLU220 4.6 26.7 1.0 C B:ALA218 4.7 16.1 1.0 O B:ALA218 4.7 21.3 1.0 OD1 B:ASP158 4.7 2.0 1.0 C B:ARG216 4.8 19.9 1.0 OD1 B:ASP217 4.8 29.7 1.0 N B:PRO219 4.8 14.5 1.0 CD2 B:HIS255 4.8 6.8 1.0 N B:ARG216 4.8 14.4 1.0 C B:GLU220 4.9 33.3 1.0 CB B:TYR164 4.9 10.1 1.0 CA B:PRO219 5.0 15.8 1.0 O B:VAL157 5.0 2.0 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4004 b:39.1 occ:1.00 OD1 A:ASN232 2.5 27.1 1.0 OD1 A:ASP238 2.5 28.6 1.0 OD2 A:ASP230 2.8 25.4 1.0 O A:ILE236 2.8 39.5 1.0 C A:ILE236 3.2 40.8 1.0 CG A:ASN232 3.2 31.9 1.0 CG A:ASP230 3.3 34.6 1.0 ND2 A:ASN232 3.3 29.3 1.0 CG A:ASP238 3.3 28.3 1.0 O A:ASP234 3.5 40.8 1.0 N A:ILE236 3.6 47.8 1.0 OD2 A:ASP238 3.7 36.7 1.0 OD1 A:ASP230 3.7 38.5 1.0 N A:ASP237 3.8 34.1 1.0 C A:ASP237 3.9 26.5 1.0 C A:GLY235 3.9 44.7 1.0 CA A:ILE236 3.9 47.3 1.0 CA A:ASP230 3.9 24.9 1.0 O A:ASP237 4.0 24.6 1.0 C A:ASP234 4.0 45.0 1.0 CB A:ASP230 4.0 29.0 1.0 CA A:ASP237 4.1 25.6 1.0 N A:ASP238 4.2 23.7 1.0 CA A:GLY235 4.3 43.1 1.0 O A:GLY235 4.3 43.3 1.0 N A:GLY235 4.4 38.1 1.0 CB A:ASP238 4.4 17.8 1.0 N A:PHE231 4.5 28.0 1.0 CG1 A:ILE236 4.6 41.8 1.0 C A:ASP230 4.7 30.6 1.0 CB A:ASN232 4.7 36.6 1.0 CA A:ASP238 4.7 22.1 1.0 N A:ASN232 4.8 42.2 1.0 CB A:ILE236 4.9 50.7 1.0 CD1 A:ILE236 4.9 29.2 1.0 O A:GLY229 4.9 21.9 1.0 CA A:ASP234 4.9 54.6 1.0 N A:ASP230 5.0 21.5 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4005 b:46.9 occ:1.00 OD1 A:ASN286 2.6 15.6 1.0 OD2 A:ASP288 2.7 36.5 1.0 O A:TYR290 2.7 28.9 1.0 OD2 A:ASP292 2.7 18.9 1.0 OD1 A:ASP292 2.9 2.2 1.0 OD2 A:ASP284 3.0 28.5 1.0 CG A:ASP292 3.2 12.0 1.0 OD1 A:ASP288 3.3 36.1 1.0 CG A:ASP288 3.3 39.5 1.0 CB A:TYR290 3.4 36.0 1.0 C A:TYR290 3.5 31.2 1.0 CG A:ASN286 3.6 13.3 1.0 O A:GLN320 3.8 46.4 1.0 ND2 A:ASN286 3.9 11.5 1.0 CA A:TYR290 3.9 35.7 1.0 N A:TYR290 4.1 43.4 1.0 CG A:ASP284 4.1 38.7 1.0 N A:GLN320 4.3 39.6 1.0 O A:ALA291 4.5 2.5 1.0 C A:ALA291 4.6 16.4 1.0 CB A:ASP292 4.6 17.1 1.0 N A:ALA291 4.6 23.0 1.0 CG A:TYR290 4.7 44.9 1.0 CB A:GLN320 4.7 43.2 1.0 C A:GLN320 4.7 44.8 1.0 CB A:ASP288 4.7 42.1 1.0 CA A:GLN320 4.8 39.6 1.0 N A:ASP292 4.8 17.0 1.0 N A:ASN286 4.9 28.0 1.0 OD1 A:ASP284 4.9 43.5 1.0 CA A:ASP284 4.9 29.7 1.0 CB A:ASN286 4.9 17.4 1.0 CB A:ASP284 5.0 36.0 1.0 CD1 A:TYR290 5.0 56.3 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4006 b:55.2 occ:1.00 O A:PHE355 2.5 30.0 1.0 OD2 A:ASP351 2.8 33.5 1.0 OD1 A:ASP353 2.8 35.6 1.0 OD2 A:ASP357 2.9 39.0 1.0 OD1 A:ASP349 3.0 48.8 1.0 OD1 A:ASP357 3.1 47.2 1.0 CG A:ASP353 3.2 38.3 1.0 OD2 A:ASP353 3.2 39.6 1.0 C A:PHE355 3.3 26.4 1.0 CG A:ASP357 3.3 45.0 1.0 CG A:ASP349 3.8 42.5 1.0 CG A:ASP351 3.9 41.6 1.0 CA A:PHE355 3.9 24.7 1.0 N A:PHE355 3.9 26.4 1.0 CB A:PHE355 4.0 17.5 1.0 O A:ASN356 4.1 34.6 1.0 N A:ASN356 4.2 29.5 1.0 C A:ASN356 4.2 34.1 1.0 CA A:ASP349 4.2 35.8 1.0 OD1 A:ASP351 4.3 47.4 1.0 OD1 A:ASN377 4.4 29.0 1.0 O A:GLY378 4.4 38.5 1.0 N A:GLY378 4.4 25.9 1.0 CB A:ASP353 4.4 34.0 1.0 CA A:ASN356 4.4 34.8 1.0 OD2 A:ASP349 4.4 40.9 1.0 N A:ASP353 4.5 32.7 1.0 C A:ASP349 4.5 38.2 1.0 CB A:ASP349 4.6 36.1 1.0 N A:ASP357 4.7 34.1 1.0 N A:LEU350 4.7 33.2 1.0 CB A:ASP357 4.7 40.4 1.0 N A:ASP351 4.8 38.2 1.0 CA A:ASP353 4.9 34.5 1.0 N A:GLY354 4.9 34.3 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4007 b:38.1 occ:1.00 O A:TYR419 2.3 2.0 1.0 OD2 A:ASP415 2.5 29.5 1.0 OD1 A:ASP413 2.5 24.8 1.0 OD1 A:ASP421 2.6 26.5 1.0 OD1 A:ASN417 2.7 38.7 1.0 OD2 A:ASP421 3.1 34.1 1.0 CG A:ASP421 3.2 24.1 1.0 ND2 A:ASN417 3.2 26.6 1.0 CG A:ASN417 3.2 32.3 1.0 O A:ASN417 3.3 24.9 1.0 CG A:ASP413 3.4 26.9 1.0 C A:TYR419 3.5 10.6 1.0 CG A:ASP415 3.7 31.2 1.0 CB A:ASP413 3.9 18.6 1.0 CA A:ASP413 3.9 10.8 1.0 N A:TYR419 4.2 24.2 1.0 OD1 A:ASP415 4.2 32.0 1.0 CA A:TYR419 4.2 18.1 1.0 OD2 A:ASP413 4.3 24.3 1.0 C A:ASP413 4.3 4.4 1.0 O A:ALA437 4.3 26.6 1.0 N A:ASP415 4.3 16.6 1.0 N A:ILE414 4.4 3.4 1.0 CB A:TYR419 4.4 28.2 1.0 N A:ALA437 4.4 8.2 1.0 C A:ASN417 4.4 19.4 1.0 C A:PRO420 4.5 10.8 1.0 CB A:ASP421 4.5 8.6 1.0 N A:PRO420 4.5 7.1 1.0 CB A:ASN417 4.6 29.6 1.0 N A:ASP421 4.6 12.9 1.0 CB A:ALA437 4.7 3.2 1.0 O A:PRO420 4.7 18.8 1.0 CA A:PRO420 4.8 4.9 1.0 CB A:ASP415 4.8 20.4 1.0 CA A:ASP415 4.9 21.3 1.0 CA A:ASN417 4.9 25.9 1.0 C A:ASP415 4.9 26.7 1.0 O A:ASP415 4.9 14.8 1.0 O A:ASP413 5.0 6.9 1.0 CA A:ALA437 5.0 11.6 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the Extracellular Segment of Integrin AVB3 in Complex with An Arg-Gly-Asp Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4008 b:37.7 occ:1.00 O A:VAL601 2.4 30.8 1.0 OE1 A:GLU636 2.6 67.4 1.0 O A:CYS596 2.8 69.7 1.0 CG A:ASP599 2.9 71.5 1.0 OE2 A:GLU636 2.9 69.0 1.0 OD1 A:ASP599 2.9 69.1 1.0 CB A:ASP599 2.9 64.6 1.0 C A:VAL601 3.0 32.4 1.0 CD A:GLU636 3.0 62.4 1.0 N A:VAL601 3.1 33.4 1.0 N A:ASN600 3.5 48.2 1.0 C A:ASP599 3.5 48.2 1.0 OD2 A:ASP599 3.5 76.5 1.0 CA A:VAL601 3.6 28.5 1.0 CA A:ASP599 3.7 58.3 1.0 C A:CYS596 3.8 69.5 1.0 N A:CYS602 3.9 31.3 1.0 C A:ASN600 3.9 43.7 1.0 O A:ASP599 4.2 36.2 1.0 CA A:ASN600 4.2 47.8 1.0 N A:ASP599 4.2 71.8 1.0 CA A:CYS596 4.2 63.6 1.0 CA A:CYS602 4.2 30.9 1.0 CB A:CYS596 4.5 57.8 1.0 CG A:GLU636 4.5 54.9 1.0 CG2 A:VAL601 4.5 21.4 1.0 N A:LYS603 4.6 28.4 1.0 CB A:VAL601 4.7 29.0 1.0 O A:ASN600 4.9 40.5 1.0 N A:GLY597 4.9 76.8 1.0 C A:CYS602 4.9 30.3 1.0

J.P.Xiong, T.Stehle, R.Zhang, A.Joachimiak, M.Frech, S.L.Goodman, M.A.Arnaout. Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 in Complex with An Arg-Gly-Asp Ligand. Science V. 296 151 2002.
ISSN: ISSN 0036-8075
PubMed: 11884718
DOI: 10.1126/SCIENCE.1069040