Manganese in PDB 4mmy: Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif

The structure of Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif, PDB code: 4mmy was solved by J.Van Agthoven, J.Xiong, M.A.Arnaout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.02 / 3.18
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.018, 130.018, 308.203, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 25.2

The binding sites of Manganese atom in the Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif (pdb code 4mmy). 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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif, PDB code: 4mmy:
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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif


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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1027 b:0.5 occ:1.00 OD2 A:ASP230 2.1 0.8 1.0 OD1 A:ASP238 2.2 0.5 1.0 OD1 A:ASP234 2.2 0.3 1.0 OD2 A:ASP238 2.2 0.7 1.0 OD1 A:ASN232 2.3 0.4 1.0 O A:ILE236 2.4 86.8 1.0 CG A:ASP238 2.4 0.8 1.0 CG A:ASP234 3.1 0.0 1.0 CG A:ASN232 3.2 0.8 1.0 CG A:ASP230 3.3 0.3 1.0 OD2 A:ASP234 3.3 0.1 1.0 ND2 A:ASN232 3.5 1.0 1.0 C A:ILE236 3.5 0.2 1.0 CB A:ASP238 3.8 86.4 1.0 CB A:ASP230 4.0 99.2 1.0 N A:ASP238 4.1 80.4 1.0 CA A:ASP230 4.1 90.3 1.0 N A:ILE236 4.3 0.3 1.0 C A:ASP237 4.3 78.8 1.0 OD1 A:ASP230 4.3 0.5 1.0 CA A:ILE236 4.3 1.0 1.0 CA A:ASP238 4.4 81.0 1.0 N A:ASN232 4.4 0.9 1.0 N A:PHE231 4.4 98.0 1.0 CB A:ASP234 4.5 0.1 1.0 N A:GLY258 4.5 95.2 1.0 CB A:ILE236 4.5 0.7 1.0 OD1 A:ASP257 4.6 0.9 1.0 N A:ASP237 4.6 0.1 1.0 CB A:ASN232 4.6 0.4 1.0 C A:ASP230 4.7 95.7 1.0 O A:ASP237 4.7 80.5 1.0 CA A:ASP237 4.7 91.6 1.0 O A:ASP234 4.8 0.9 1.0 C A:ASP234 4.9 0.2 1.0 O A:ASN232 4.9 0.9 1.0 CA A:ASN232 4.9 0.4 1.0 CA A:GLY258 5.0 93.0 1.0

Manganese binding site 2 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif


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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1028 b:0.5 occ:1.00 O A:TYR290 2.1 0.6 1.0 OD2 A:ASP284 2.2 99.7 1.0 OD2 A:ASP292 2.2 0.1 1.0 OD1 A:ASP288 2.2 0.6 1.0 OD1 A:ASP292 2.2 96.4 1.0 OD1 A:ASN286 2.2 0.9 1.0 CG A:ASP292 2.5 98.3 1.0 CG A:ASP288 3.1 0.0 1.0 CG A:ASN286 3.2 0.9 1.0 C A:TYR290 3.3 0.3 1.0 OD2 A:ASP288 3.3 0.9 1.0 CG A:ASP284 3.4 96.7 1.0 ND2 A:ASN286 3.5 0.9 1.0 CB A:ASP292 4.0 92.2 1.0 CA A:TYR290 4.1 0.0 1.0 CA A:ASP284 4.1 95.0 1.0 CB A:TYR290 4.1 0.8 1.0 CB A:ASP284 4.2 90.3 1.0 N A:TYR290 4.2 1.0 1.0 N A:ASP292 4.2 91.4 1.0 C A:ALA291 4.2 93.8 1.0 OD1 A:ASP284 4.2 0.8 1.0 N A:ILE285 4.3 0.3 1.0 N A:ALA291 4.3 97.8 1.0 N A:ASN286 4.3 96.9 1.0 CB A:ASP288 4.4 0.1 1.0 O A:GLN320 4.5 0.9 1.0 CA A:ALA291 4.5 92.2 1.0 CB A:ASN286 4.5 0.6 1.0 C A:ASP284 4.5 0.3 1.0 O A:ALA291 4.6 98.9 1.0 CA A:ASP292 4.6 91.2 1.0 N A:ASP288 4.7 0.0 1.0 N A:GLN320 4.8 0.9 1.0 CA A:ASN286 4.9 0.9 1.0 CD2 A:LEU319 5.0 98.7 1.0 CA A:ASP288 5.0 0.0 1.0

Manganese binding site 3 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif


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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1029 b:0.6 occ:1.00 OD2 A:ASP353 2.2 0.2 1.0 OD1 A:ASP353 2.2 0.5 1.0 OD1 A:ASP357 2.2 0.1 1.0 OD2 A:ASP351 2.2 1.0 1.0 OD2 A:ASP357 2.2 0.1 1.0 OD1 A:ASP349 2.4 0.3 1.0 CG A:ASP353 2.4 0.1 1.0 O A:PHE355 2.4 0.2 1.0 CG A:ASP357 2.4 0.8 1.0 CG A:ASP351 3.3 0.9 1.0 CG A:ASP349 3.6 0.7 1.0 C A:PHE355 3.6 91.0 1.0 OD1 A:ASP351 3.7 0.8 1.0 CB A:ASP353 3.8 98.8 1.0 CB A:ASP357 3.9 81.2 1.0 N A:ASP351 4.1 87.6 1.0 N A:ASP353 4.1 1.0 1.0 OD2 A:ASP349 4.1 0.2 1.0 ND2 A:ASN377 4.2 82.2 1.0 N A:ASP357 4.3 83.1 1.0 C A:ASN356 4.3 90.8 1.0 N A:LEU350 4.4 0.5 1.0 N A:PHE355 4.5 94.2 1.0 CA A:ASP353 4.5 0.0 1.0 CA A:PHE355 4.5 93.6 1.0 O A:ASN356 4.5 98.8 1.0 CB A:ASP351 4.6 1.0 1.0 N A:ASN356 4.6 86.9 1.0 N A:GLN352 4.6 0.8 1.0 N A:GLY378 4.6 86.5 1.0 CA A:ASN356 4.6 87.4 1.0 CA A:ASP357 4.6 76.8 1.0 CA A:ASP349 4.6 94.8 1.0 CB A:ASP349 4.7 92.4 1.0 CA A:ASP351 4.7 0.7 1.0 C A:ASP349 4.8 0.4 1.0 O A:GLY378 4.8 94.5 1.0 CB A:PHE355 4.9 95.3 1.0 CB A:ASN377 4.9 83.1 1.0 C A:ASP351 4.9 0.4 1.0 C A:LEU350 4.9 84.8 1.0 CG A:ASN377 4.9 86.8 1.0 CA A:LEU350 5.0 81.2 1.0

Manganese binding site 4 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif


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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1030 b:0.8 occ:1.00 O A:TYR419 2.1 90.0 1.0 OD1 A:ASP413 2.1 0.7 1.0 OD2 A:ASP421 2.2 0.7 1.0 OD1 A:ASP421 2.2 0.3 1.0 OD1 A:ASN417 2.2 0.6 1.0 OD1 A:ASP415 2.2 0.2 1.0 OD2 A:ASP415 2.4 0.4 1.0 CG A:ASP421 2.5 1.0 1.0 CG A:ASP415 2.6 0.5 1.0 CG A:ASN417 3.2 0.4 1.0 C A:TYR419 3.2 89.0 1.0 CG A:ASP413 3.3 0.6 1.0 ND2 A:ASN417 3.6 0.6 1.0 CB A:ASP421 4.0 82.4 1.0 C A:PRO420 4.0 85.7 1.0 CB A:ASP415 4.1 0.3 1.0 OD2 A:ASP413 4.1 96.9 1.0 N A:PRO420 4.2 85.5 1.0 CA A:TYR419 4.2 92.0 1.0 O A:PRO420 4.2 0.1 1.0 CB A:ASP413 4.2 90.2 1.0 CA A:ASP413 4.2 87.3 1.0 CA A:PRO420 4.3 82.6 1.0 N A:TYR419 4.3 95.8 1.0 N A:ASP421 4.3 88.3 1.0 N A:ALA437 4.3 90.5 1.0 N A:ASP415 4.3 0.4 1.0 CB A:TYR419 4.4 0.2 1.0 CB A:ASN417 4.4 0.8 1.0 N A:ILE414 4.5 95.7 1.0 O A:ALA437 4.5 0.4 1.0 CB A:ALA437 4.6 86.0 1.0 CA A:ASP421 4.6 83.2 1.0 N A:ASN417 4.7 0.4 1.0 C A:ASP413 4.7 1.0 1.0 CA A:ASP415 4.8 0.3 1.0 CA A:ALA437 4.9 89.6 1.0

Manganese binding site 5 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif


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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1031 b:0.1 occ:1.00 OE2 A:GLU636 2.1 0.6 1.0 OD1 A:ASP599 2.2 0.5 1.0 OD2 A:ASP599 2.2 0.4 1.0 OE1 A:GLU636 2.2 0.1 1.0 O A:CYS596 2.2 0.9 1.0 O A:VAL601 2.3 0.7 1.0 CD A:GLU636 2.5 0.2 1.0 CG A:ASP599 2.5 0.3 1.0 C A:CYS596 3.3 0.7 1.0 C A:VAL601 3.5 0.9 1.0 CG A:GLU636 4.0 0.0 1.0 CB A:ASP599 4.0 0.9 1.0 CA A:GLY597 4.0 0.1 1.0 N A:GLY597 4.1 0.6 1.0 CA A:CYS602 4.3 0.1 1.0 N A:VAL601 4.3 0.8 1.0 CA A:CYS596 4.3 0.5 1.0 N A:LYS603 4.3 0.9 1.0 N A:CYS602 4.3 0.8 1.0 CA A:VAL601 4.5 0.0 1.0 N A:ASP599 4.6 0.3 1.0 C A:GLY597 4.6 0.9 1.0 CG1 A:VAL601 4.6 0.9 1.0 C A:CYS602 4.7 0.5 1.0 CA A:ASP599 4.8 0.1 1.0 CB A:CYS596 4.8 0.6 1.0 CB A:GLU636 4.8 0.2 1.0 N A:GLU598 5.0 0.5 1.0 CB A:LYS603 5.0 0.7 1.0 N A:ASN600 5.0 0.4 1.0

Manganese binding site 6 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif


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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn708 b:65.1 occ:1.00 OE1 B:GLU220 2.1 95.8 1.0 OG B:SER123 2.2 90.4 1.0 OG B:SER121 2.2 91.3 1.0 O B:HOH802 2.2 0.7 1.0 O B:HOH801 2.2 60.1 1.0 CB B:SER121 2.9 93.3 1.0 OD1 C:ASP1495 2.9 0.7 1.0 CD B:GLU220 3.0 86.3 1.0 CB B:SER123 3.2 92.7 1.0 CG C:ASP1495 3.4 91.0 1.0 CG B:GLU220 3.5 74.1 1.0 N B:SER123 3.8 94.9 1.0 OD1 B:ASP119 3.9 98.0 1.0 OD2 C:ASP1495 3.9 90.3 1.0 CB C:ASP1495 4.0 86.7 1.0 OE2 B:GLU220 4.0 0.4 1.0 CA B:SER121 4.1 95.8 1.0 CA B:SER123 4.1 94.9 1.0 C B:SER121 4.1 97.2 1.0 ND2 B:ASN215 4.3 81.3 1.0 N B:TYR122 4.4 98.7 1.0 O B:SER121 4.5 0.9 1.0 O B:ALA218 4.5 86.0 1.0 OD2 B:ASP119 4.6 0.0 1.0 CB B:GLU220 4.6 70.4 1.0 CA C:ASP1495 4.6 88.7 1.0 CG B:ASP119 4.6 0.6 1.0 N B:MET124 4.8 0.9 1.0 C B:SER123 4.9 0.6 1.0 N B:SER121 4.9 94.9 1.0 CB B:ASP251 4.9 95.1 1.0 C B:TYR122 4.9 98.7 1.0

Manganese binding site 7 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif


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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn709 b:0.6 occ:1.00 OD1 B:ASP251 2.1 0.5 1.0 OD1 B:ASP127 2.2 0.3 1.0 OD2 B:ASP126 2.2 0.4 1.0 OD1 B:ASP126 2.2 0.1 1.0 O B:SER123 2.2 89.0 1.0 OD2 B:ASP251 2.2 0.5 1.0 CG B:ASP251 2.3 0.8 1.0 CG B:ASP126 2.5 1.0 1.0 CG B:ASP127 3.2 0.9 1.0 C B:SER123 3.4 0.6 1.0 ND2 C:ASN1497 3.5 0.5 1.0 OD2 B:ASP127 3.6 0.8 1.0 CB B:ASP251 3.7 95.1 1.0 CB B:ASP126 4.0 0.1 1.0 CA B:MET124 4.2 0.5 1.0 N B:MET124 4.2 0.9 1.0 CA B:SER123 4.4 94.9 1.0 CB B:ASP127 4.5 0.1 1.0 N B:ASP127 4.5 0.9 1.0 CB B:SER123 4.7 92.7 1.0 N B:ASP126 4.7 0.4 1.0 CA B:ASP126 4.8 0.3 1.0 CA B:ASP251 4.8 93.4 1.0 CG C:ASN1497 4.8 0.8 1.0 C B:MET124 4.8 0.7 1.0 C B:ASP126 5.0 0.2 1.0

Manganese binding site 8 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to the Tenth Domain of Fibronectin with the Iakgdwnd Motif


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 the Tenth Domain of Fibronectin with the Iakgdwnd Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn710 b:99.5 occ:1.00 OD1 B:ASP217 2.1 0.0 1.0 OE2 B:GLU220 2.2 0.4 1.0 O B:ASP217 2.2 81.8 1.0 OD2 B:ASP158 2.2 82.0 1.0 OD1 B:ASN215 2.2 79.3 1.0 O B:PRO219 2.2 66.9 1.0 CG B:ASP217 3.1 96.7 1.0 C B:PRO219 3.2 78.5 1.0 C B:ASP217 3.2 70.8 1.0 CD B:GLU220 3.3 86.3 1.0 CG B:ASN215 3.3 77.7 1.0 CG B:ASP158 3.3 83.3 1.0 CA B:GLU220 3.5 78.5 1.0 N B:GLU220 3.8 77.7 1.0 OD2 B:ASP217 3.8 96.5 1.0 ND2 B:ASN215 3.8 81.3 1.0 CB B:ASP158 3.9 87.3 1.0 CA B:ASP217 4.0 68.8 1.0 OE1 B:GLU220 4.0 95.8 1.0 C B:ALA218 4.1 78.0 1.0 NE2 B:HIS255 4.1 80.9 1.0 N B:ASP217 4.1 72.7 1.0 CB B:ASP217 4.1 68.7 1.0 N B:PRO219 4.2 62.5 1.0 O B:ALA218 4.2 86.0 1.0 CG B:GLU220 4.2 74.1 1.0 N B:ALA218 4.2 74.3 1.0 CA B:PRO219 4.3 73.2 1.0 CD2 B:HIS255 4.3 67.5 1.0 OD1 B:ASP158 4.4 78.7 1.0 C B:GLU220 4.4 75.8 1.0 CB B:GLU220 4.5 70.4 1.0 CB B:ASN215 4.5 76.3 1.0 CA B:ALA218 4.6 83.3 1.0 O B:GLU220 4.8 91.0 1.0 CD2 B:TYR164 4.8 69.1 1.0 CD B:PRO219 4.9 79.0 1.0 O B:VAL157 5.0 90.4 1.0

J.F.Van Agthoven, J.P.Xiong, J.L.Alonso, X.Rui, B.D.Adair, S.L.Goodman, M.A.Arnaout. Structural Basis For Pure Antagonism of Integrin Alpha V Beta 3 By A High-Affinity Form of Fibronectin. Nat.Struct.Mol.Biol. V. 21 383 2014.
ISSN: ISSN 1545-9993
PubMed: 24658351
DOI: 10.1038/NSMB.2797