Manganese in PDB 1m1x: Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+

The structure of Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+, PDB code: 1m1x 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 / 3.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.400, 130.400, 310.300, 90.00, 90.00, 120.00
R / Rfree (%)	24.4 / 32.3

The binding sites of Manganese atom in the Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+ (pdb code 1m1x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+, PDB code: 1m1x:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+


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 Alpha VBETA3 Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn4002 b:56.2 occ:1.00 OD1 B:ASP127 1.9 82.9 1.0 O B:SER123 2.5 78.9 1.0 CG B:ASP127 2.7 83.2 1.0 OD2 B:ASP126 2.8 68.2 1.0 O B:MET335 2.9 86.2 1.0 OD2 B:ASP127 3.0 89.4 1.0 OD1 B:ASP126 3.0 74.5 1.0 CG B:ASP126 3.2 69.0 1.0 C B:SER123 3.5 73.6 1.0 CA B:MET124 3.6 74.4 1.0 N B:MET124 4.0 80.7 1.0 CB B:ASP127 4.0 70.4 1.0 N B:ASP127 4.2 86.5 1.0 C B:MET335 4.2 0.0 1.0 CG B:MET124 4.2 41.7 1.0 CB B:MET124 4.4 42.9 1.0 N B:LYS125 4.4 50.9 1.0 C B:MET124 4.5 71.0 1.0 CB B:ASP126 4.6 66.5 1.0 N B:ASP126 4.6 68.1 1.0 CA B:ASP127 4.7 80.0 1.0 CA B:SER123 4.7 71.3 1.0 C B:ASP126 4.8 77.2 1.0 CE B:MET124 4.9 31.4 1.0 CA B:ASP336 4.9 99.0 1.0 CB B:SER123 4.9 79.1 1.0 CA B:ASP126 4.9 69.6 1.0 OD1 B:ASP251 4.9 49.3 1.0 N B:ASP336 5.0 0.0 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+


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 Alpha VBETA3 Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4004 b:40.5 occ:1.00 OD1 A:ASP238 2.4 13.6 1.0 O A:ILE236 2.4 20.9 1.0 OD2 A:ASP230 2.7 52.2 1.0 O A:ASN232 2.9 87.6 1.0 CG A:ASP238 3.4 16.8 1.0 O A:ASP234 3.5 60.8 1.0 C A:ILE236 3.5 55.7 1.0 CG A:ASP230 3.6 60.5 1.0 OD1 A:ASN232 3.7 72.2 1.0 OD2 A:ASP238 3.7 19.0 1.0 N A:ILE236 3.7 60.5 1.0 C A:ASN232 4.0 80.2 1.0 C A:ASP234 4.1 90.0 1.0 CA A:ILE236 4.1 58.9 1.0 CB A:ASP230 4.3 44.6 1.0 OD1 A:ASP230 4.3 59.3 1.0 CD1 A:ILE236 4.3 12.5 1.0 CA A:ASP230 4.4 17.3 1.0 C A:GLY235 4.4 39.0 1.0 CG A:ASN232 4.5 85.2 1.0 CB A:ASN232 4.5 88.6 1.0 N A:ASN232 4.5 76.8 1.0 N A:PHE231 4.6 54.5 1.0 CA A:ASN232 4.6 78.9 1.0 N A:ASP237 4.6 48.3 1.0 N A:GLY235 4.7 31.0 1.0 CA A:GLY235 4.7 38.0 1.0 CB A:ASP238 4.8 2.7 1.0 N A:ASP234 4.8 0.0 1.0 C A:ASP237 4.8 33.0 1.0 N A:ASP238 4.8 27.5 1.0 CA A:ASP234 4.9 0.0 1.0 C A:ASP230 4.9 27.9 1.0 C A:GLY233 4.9 87.2 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+


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 Alpha VBETA3 Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4005 b:59.7 occ:1.00 OD2 A:ASP284 2.3 18.0 1.0 O A:TYR290 2.4 79.2 1.0 ND2 A:ASN286 2.5 30.8 1.0 OD2 A:ASP288 2.6 45.0 1.0 OD2 A:ASP292 2.8 26.5 1.0 OD1 A:ASP292 2.8 6.2 1.0 CB A:TYR290 3.1 76.1 1.0 CG A:ASP292 3.2 19.9 1.0 C A:TYR290 3.2 51.3 1.0 CG A:ASP288 3.3 39.2 1.0 OD1 A:ASP288 3.4 26.4 1.0 CG A:ASP284 3.5 30.0 1.0 CA A:TYR290 3.5 50.0 1.0 CG A:ASN286 3.6 34.4 1.0 N A:TYR290 3.7 53.1 1.0 OD1 A:ASN286 3.8 45.2 1.0 CA A:ASP284 4.2 24.9 1.0 CB A:ASP284 4.3 31.8 1.0 CG A:TYR290 4.4 76.0 1.0 OD1 A:ASP284 4.5 41.0 1.0 N A:ALA291 4.5 45.1 1.0 CB A:ASP292 4.6 13.5 1.0 O A:GLN320 4.6 49.4 1.0 N A:ASN286 4.7 55.3 1.0 N A:ILE285 4.7 55.6 1.0 C A:ALA291 4.7 37.1 1.0 CD1 A:TYR290 4.7 81.1 1.0 N A:ASP292 4.7 32.3 1.0 C A:ASP284 4.8 27.0 1.0 CB A:ASP288 4.8 38.7 1.0 C A:ASP289 4.8 48.2 1.0 O A:ALA291 4.9 39.5 1.0 CB A:ASN286 4.9 34.1 1.0 C A:ASP288 4.9 35.5 1.0 N A:ASP288 5.0 26.4 1.0 CA A:ALA291 5.0 40.7 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+


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 Alpha VBETA3 Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4006 b:62.6 occ:1.00 O A:PHE355 2.4 42.5 1.0 OD2 A:ASP353 2.7 75.6 1.0 OD2 A:ASP351 2.7 28.2 1.0 OD1 A:ASP357 2.8 92.2 1.0 OD1 A:ASP349 3.1 34.0 1.0 CG A:ASP357 3.3 85.1 1.0 C A:PHE355 3.3 50.7 1.0 OD2 A:ASP357 3.4 84.1 1.0 OD1 A:ASP351 3.4 37.3 1.0 CG A:ASP351 3.5 37.4 1.0 CG A:ASP353 3.6 76.1 1.0 CB A:PHE355 3.8 38.3 1.0 OD1 A:ASP353 3.9 82.5 1.0 O A:ASN356 3.9 36.7 1.0 C A:ASN356 4.0 66.6 1.0 CA A:PHE355 4.1 50.9 1.0 N A:GLY378 4.1 6.5 1.0 CG A:ASP349 4.1 25.2 1.0 N A:ASN356 4.2 70.0 1.0 OD1 A:ASN377 4.3 31.0 1.0 N A:ASP357 4.4 25.7 1.0 N A:PHE355 4.4 56.5 1.0 CA A:ASN356 4.4 69.9 1.0 CB A:ASN377 4.4 22.6 1.0 O A:GLY378 4.4 89.2 1.0 CB A:ASP357 4.6 75.2 1.0 CG A:ASN377 4.6 32.4 1.0 CA A:ASP349 4.7 24.4 1.0 CA A:ASP357 4.7 31.0 1.0 OD2 A:ASP349 4.7 27.8 1.0 CA A:ASN377 4.8 33.1 1.0 CA A:GLY378 4.9 11.9 1.0 CB A:ASP351 4.9 39.3 1.0 C A:ASP349 5.0 22.8 1.0 C A:ASN377 5.0 39.8 1.0 CB A:ASP353 5.0 65.7 1.0 N A:ASP353 5.0 35.3 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+


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 Alpha VBETA3 Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4007 b:24.0 occ:1.00 O A:TYR419 2.4 7.0 1.0 OD2 A:ASP415 2.6 32.4 1.0 OD1 A:ASP421 2.8 34.0 1.0 OD1 A:ASP413 2.8 33.8 1.0 O A:PRO420 3.0 2.0 1.0 OD1 A:ASN417 3.0 52.3 1.0 CG A:ASP415 3.1 31.9 1.0 ND2 A:ASN417 3.1 52.7 1.0 OD2 A:ASP421 3.1 36.2 1.0 OD1 A:ASP415 3.2 25.2 1.0 CG A:ASN417 3.3 54.8 1.0 CG A:ASP421 3.3 23.9 1.0 C A:TYR419 3.5 32.2 1.0 O A:ASN417 3.6 70.2 1.0 CG A:ASP413 3.8 28.8 1.0 C A:PRO420 4.0 2.0 1.0 O A:ALA437 4.1 33.0 1.0 N A:ASP415 4.2 27.7 1.0 CB A:ASP415 4.3 24.6 1.0 N A:TYR419 4.3 49.1 1.0 CA A:ASP413 4.4 15.8 1.0 N A:ALA437 4.4 7.3 1.0 CA A:TYR419 4.4 39.8 1.0 C A:ASN417 4.5 55.0 1.0 N A:PRO420 4.5 2.0 1.0 CA A:ASP415 4.5 34.6 1.0 CB A:ASN417 4.5 58.7 1.0 C A:ASP413 4.6 13.2 1.0 O A:ASP415 4.6 19.9 1.0 OD2 A:ASP413 4.6 39.1 1.0 CB A:ASP413 4.6 18.1 1.0 CA A:PRO420 4.6 3.2 1.0 C A:ASP415 4.7 41.5 1.0 CB A:ASP421 4.7 7.1 1.0 CB A:ALA437 4.7 18.0 1.0 N A:ILE414 4.8 2.0 1.0 CA A:ASN417 4.8 55.1 1.0 CB A:TYR419 4.8 28.2 1.0 N A:ASN417 4.9 56.3 1.0 O A:ASP413 4.9 3.8 1.0 CA A:ALA437 4.9 2.8 1.0 N A:ASP421 4.9 20.6 1.0 C A:ALA437 4.9 12.1 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3 Bound to MN2+


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 Alpha VBETA3 Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn4008 b:44.4 occ:1.00 O A:VAL601 2.3 32.8 1.0 OD2 A:ASP599 2.5 67.8 1.0 OE2 A:GLU636 2.6 70.7 1.0 OE1 A:GLU636 2.7 72.7 1.0 OD1 A:ASP599 2.7 58.9 1.0 CG A:ASP599 2.9 69.9 1.0 CD A:GLU636 2.9 78.4 1.0 O A:GLY597 3.2 67.8 1.0 C A:VAL601 3.5 67.2 1.0 O A:CYS596 3.7 74.2 1.0 C A:CYS596 3.8 88.2 1.0 C A:GLY597 4.1 96.0 1.0 N A:GLY597 4.1 97.3 1.0 N A:VAL601 4.3 72.8 1.0 CG A:GLU636 4.3 75.3 1.0 CA A:CYS596 4.3 82.7 1.0 CB A:ASP599 4.3 73.8 1.0 N A:ASP599 4.4 64.7 1.0 CA A:GLY597 4.4 97.6 1.0 CA A:VAL601 4.4 68.4 1.0 N A:CYS602 4.4 20.1 1.0 CG A:LYS603 4.5 76.2 1.0 N A:LYS603 4.5 2.4 1.0 CA A:CYS602 4.5 11.1 1.0 N A:ASN600 4.7 85.7 1.0 CE A:LYS603 4.7 81.7 1.0 CB A:CYS596 4.7 68.3 1.0 CA A:ASP599 4.8 53.0 1.0 CB A:VAL601 5.0 42.1 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