Manganese in PDB 6naj: Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin.

The structure of Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin., PDB code: 6naj 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)	49.62 / 3.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.713, 129.713, 308.198, 90.00, 90.00, 120.00
R / Rfree (%)	24.3 / 27.3

The binding sites of Manganese atom in the Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin. (pdb code 6naj). 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 HR10 Variant of the 10TH Domain of Fibronectin., PDB code: 6naj:
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 HR10 Variant of the 10TH Domain of Fibronectin.


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 HR10 Variant of the 10TH Domain of Fibronectin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1018 b:58.6 occ:1.00 OD2 A:ASP234 2.2 85.8 1.0 OD1 A:ASP230 2.2 67.7 1.0 OD1 A:ASP234 2.2 87.6 1.0 OD1 A:ASP238 2.2 73.8 1.0 OD2 A:ASP238 2.2 80.0 1.0 OD1 A:ASN232 2.2 71.9 1.0 O A:ILE236 2.4 38.5 1.0 CG A:ASP238 2.4 58.9 1.0 CG A:ASP234 2.5 76.6 1.0 CG A:ASN232 3.2 46.6 1.0 CG A:ASP230 3.4 57.0 1.0 C A:ILE236 3.5 50.2 1.0 ND2 A:ASN232 3.7 33.8 1.0 CB A:ASP238 3.8 43.4 1.0 CB A:ASP234 4.0 48.1 1.0 N A:ASP238 4.0 38.9 1.0 CA A:ASP230 4.0 45.6 1.0 N A:PHE231 4.1 27.7 1.0 N A:ILE236 4.1 68.1 1.0 N A:ASN232 4.1 55.1 1.0 CB A:ASP230 4.2 58.9 1.0 OD2 A:ASP230 4.2 57.0 1.0 CA A:ILE236 4.3 60.5 1.0 CA A:ASP238 4.3 22.4 1.0 C A:ASP237 4.4 35.6 1.0 C A:ASP230 4.5 33.0 1.0 CB A:ASN232 4.5 45.1 1.0 N A:ASP237 4.6 53.5 1.0 CB A:ILE236 4.6 57.9 1.0 O A:ASN232 4.7 70.1 1.0 N A:GLY235 4.7 41.4 1.0 OD1 A:ASP257 4.7 60.5 1.0 N A:ASP234 4.7 70.7 1.0 CA A:ASP237 4.7 36.5 1.0 CA A:ASN232 4.7 58.2 1.0 CA A:ASP234 4.8 49.8 1.0 O A:GLY229 4.8 45.1 1.0 C A:ASN232 4.9 71.2 1.0 O A:ASP237 4.9 57.2 1.0 C A:GLY235 5.0 55.7 1.0

Manganese binding site 2 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin.


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 HR10 Variant of the 10TH Domain of Fibronectin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1019 b:59.0 occ:1.00 O A:TYR290 2.1 0.5 1.0 OD1 A:ASP288 2.2 96.9 1.0 OD1 A:ASP292 2.2 80.7 1.0 OD2 A:ASP288 2.2 90.5 1.0 OD2 A:ASP292 2.2 79.2 1.0 OD1 A:ASN286 2.2 81.8 1.0 CG A:ASP288 2.5 88.8 1.0 CG A:ASP292 2.5 66.5 1.0 CG A:ASN286 3.1 57.9 1.0 C A:TYR290 3.3 62.0 1.0 ND2 A:ASN286 3.4 57.0 1.0 OD2 A:ASP284 3.8 72.7 1.0 CG A:ASP284 3.9 66.8 1.0 CB A:ASP288 4.0 77.9 1.0 CB A:ASP292 4.0 41.1 1.0 CA A:ASP284 4.0 36.6 1.0 CA A:TYR290 4.0 49.8 1.0 CB A:TYR290 4.0 43.4 1.0 N A:TYR290 4.1 46.2 1.0 N A:ILE285 4.2 39.5 1.0 OD1 A:ASP284 4.2 70.4 1.0 C A:ALA291 4.3 44.1 1.0 N A:ASP292 4.3 38.7 1.0 N A:ASN286 4.3 40.1 1.0 N A:ALA291 4.3 38.8 1.0 CB A:ASP284 4.4 45.6 1.0 C A:ASP284 4.5 46.5 1.0 CB A:ASN286 4.5 32.6 1.0 CA A:ALA291 4.5 39.0 1.0 N A:ASP288 4.6 63.9 1.0 O A:GLN320 4.6 55.3 1.0 O A:ALA291 4.6 46.7 1.0 CA A:ASP292 4.6 33.7 1.0 CA A:ASP288 4.8 73.0 1.0 O A:THR283 4.8 52.7 1.0 N A:GLN320 4.8 49.6 1.0 CA A:ASN286 4.9 36.3 1.0

Manganese binding site 3 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin.


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 HR10 Variant of the 10TH Domain of Fibronectin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1020 b:48.1 occ:1.00 OD1 A:ASP351 2.2 77.9 1.0 OD1 A:ASP353 2.2 84.5 1.0 OD1 A:ASP357 2.2 75.9 1.0 OD2 A:ASP357 2.2 78.2 1.0 O A:PHE355 2.3 70.7 1.0 CG A:ASP357 2.4 67.1 1.0 OD1 A:ASP349 2.5 55.9 1.0 CG A:ASP353 3.2 75.4 1.0 CG A:ASP351 3.3 64.7 1.0 C A:PHE355 3.5 55.3 1.0 OD2 A:ASP353 3.6 82.3 1.0 OD2 A:ASP351 3.7 65.0 1.0 CG A:ASP349 3.7 43.1 1.0 CB A:ASP357 3.9 43.7 1.0 C A:ASN356 4.1 45.0 1.0 N A:ASP351 4.1 47.4 1.0 N A:LEU350 4.2 44.4 1.0 O A:ASN356 4.2 55.0 1.0 N A:ASP357 4.3 44.1 1.0 N A:PHE355 4.4 61.2 1.0 CA A:PHE355 4.4 60.2 1.0 N A:ASP353 4.4 56.4 1.0 CB A:ASP353 4.4 62.8 1.0 N A:ASN356 4.4 52.5 1.0 OD2 A:ASP349 4.4 48.0 1.0 N A:GLY378 4.5 46.6 1.0 CA A:ASP349 4.5 38.5 1.0 CA A:ASN356 4.5 46.8 1.0 CB A:ASP351 4.5 59.8 1.0 C A:ASP349 4.5 39.2 1.0 O A:GLY378 4.6 60.8 1.0 CA A:ASP357 4.6 41.9 1.0 ND2 A:ASN377 4.6 60.1 1.0 CB A:PHE355 4.6 57.4 1.0 N A:GLN352 4.6 46.7 1.0 CB A:ASP349 4.7 39.5 1.0 CA A:ASP351 4.8 48.4 1.0 CB A:ASN377 4.9 32.6 1.0 CA A:ASP353 4.9 54.5 1.0 C A:ASP351 5.0 48.5 1.0

Manganese binding site 4 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin.


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 HR10 Variant of the 10TH Domain of Fibronectin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1021 b:83.7 occ:1.00 O A:TYR419 2.1 83.5 1.0 OD1 A:ASP421 2.2 0.9 1.0 OD1 A:ASP415 2.2 0.7 1.0 OD2 A:ASP421 2.2 0.8 1.0 OD1 A:ASN417 2.2 95.5 1.0 OD1 A:ASP413 2.4 60.5 1.0 CG A:ASP421 2.5 93.7 1.0 ND2 A:ASN417 2.7 60.1 1.0 CG A:ASN417 2.8 74.1 1.0 CG A:ASP415 3.2 83.1 1.0 C A:TYR419 3.3 53.8 1.0 CG A:ASP413 3.4 57.3 1.0 OD2 A:ASP415 3.6 81.8 1.0 CB A:ASP421 4.0 52.2 1.0 N A:TYR419 4.1 50.0 1.0 CA A:TYR419 4.1 45.7 1.0 OD2 A:ASP413 4.1 54.0 1.0 C A:PRO420 4.2 44.0 1.0 N A:ASP421 4.2 41.8 1.0 CA A:ASP413 4.2 46.4 1.0 CB A:ASN417 4.3 69.3 1.0 N A:PRO420 4.3 43.5 1.0 N A:ASP415 4.3 65.2 1.0 CB A:ASP413 4.4 50.3 1.0 CB A:TYR419 4.4 52.3 1.0 CA A:PRO420 4.4 42.6 1.0 N A:ILE414 4.4 47.1 1.0 N A:ALA437 4.5 45.4 1.0 O A:PRO420 4.5 49.2 1.0 O A:ALA437 4.5 84.8 1.0 CB A:ASP415 4.6 51.7 1.0 CA A:ASP421 4.6 42.0 1.0 C A:ASP413 4.6 47.7 1.0 O A:ASP415 4.6 76.3 1.0 N A:ASN417 4.8 52.9 1.0 CA A:ASP415 4.8 59.5 1.0 C A:ASP415 4.8 68.5 1.0 CB A:ALA437 4.9 42.3 1.0 CA A:ASN417 5.0 72.4 1.0

Manganese binding site 5 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin.


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 HR10 Variant of the 10TH Domain of Fibronectin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1022 b:52.8 occ:1.00 OD1 A:ASP599 2.1 0.4 1.0 OE2 A:GLU636 2.2 92.7 1.0 OE1 A:GLU636 2.2 94.7 1.0 OD2 A:ASP599 2.2 96.8 1.0 O A:VAL601 2.4 58.6 1.0 CD A:GLU636 2.4 81.4 1.0 CG A:ASP599 2.4 88.5 1.0 O A:CYS596 2.6 77.3 1.0 C A:CYS596 3.5 85.2 1.0 C A:VAL601 3.6 66.1 1.0 CG A:GLU636 3.9 65.7 1.0 CB A:ASP599 4.0 73.1 1.0 CA A:GLY597 4.0 83.8 1.0 N A:GLY597 4.2 73.8 1.0 N A:LYS603 4.2 65.6 1.0 CE A:LYS603 4.4 76.8 1.0 N A:VAL601 4.4 71.4 1.0 CA A:CYS602 4.5 54.6 1.0 N A:CYS602 4.5 68.9 1.0 CG2 A:VAL601 4.5 62.5 1.0 CA A:CYS596 4.5 81.2 1.0 N A:ASP599 4.6 80.6 1.0 C A:GLY597 4.6 91.5 1.0 CA A:VAL601 4.6 62.6 1.0 CB A:GLU636 4.7 65.0 1.0 CA A:ASP599 4.7 82.9 1.0 CB A:LYS603 4.8 80.1 1.0 CG A:LYS603 4.8 80.8 1.0 C A:CYS602 4.8 57.6 1.0 CB A:CYS596 4.9 75.5 1.0

Manganese binding site 6 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin.


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 HR10 Variant of the 10TH Domain of Fibronectin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn708 b:37.2 occ:1.00 OD1 C:ASP1495 2.1 79.4 1.0 O C:HOH1701 2.2 50.8 1.0 OE1 B:GLU220 2.2 75.1 1.0 OG B:SER121 2.3 50.2 1.0 CD B:GLU220 2.7 62.0 1.0 CG B:GLU220 2.8 48.6 1.0 CB B:SER121 2.9 42.4 1.0 CG C:ASP1495 3.3 64.6 1.0 OD2 B:ASP119 3.7 46.0 1.0 OE2 B:GLU220 3.9 67.4 1.0 CB C:ASP1495 4.1 63.4 1.0 CB B:ALA252 4.2 64.2 1.0 OD2 C:ASP1495 4.2 65.3 1.0 CB B:GLU220 4.2 37.1 1.0 O B:ALA218 4.3 65.2 1.0 CA B:SER121 4.4 44.0 1.0 CA C:ASP1495 4.4 63.7 1.0 CG B:ASP119 4.6 44.3 1.0 OD1 B:ASP119 4.7 52.9 1.0 OD1 B:ASP251 4.7 50.8 1.0 O C:ASP1495 4.8 63.9 1.0 C B:SER121 4.9 61.3 1.0 CB B:SER123 5.0 63.7 1.0

Manganese binding site 7 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin.


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 HR10 Variant of the 10TH Domain of Fibronectin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn709 b:59.0 occ:1.00 OD1 B:ASP126 2.1 0.4 1.0 OD1 B:ASP127 2.1 86.6 1.0 OD2 B:ASP126 2.2 0.8 1.0 O B:SER123 2.2 95.8 1.0 CG B:ASP126 2.4 82.7 1.0 O B:MET335 2.7 52.7 1.0 CG B:ASP127 3.3 72.4 1.0 C B:SER123 3.4 76.0 1.0 CE B:MET124 3.5 74.3 1.0 OD2 B:ASP127 3.8 75.7 1.0 CA B:MET124 3.9 66.8 1.0 C B:MET335 3.9 66.7 1.0 CB B:ASP126 4.0 61.6 1.0 OH C:TYR1446 4.0 91.8 1.0 N B:MET124 4.1 64.3 1.0 OG B:SER123 4.2 83.6 1.0 N B:ASP127 4.2 79.8 1.0 C B:MET124 4.5 74.5 1.0 CB B:ASP127 4.5 69.7 1.0 N B:ASP126 4.5 64.5 1.0 CZ C:TYR1446 4.5 85.4 1.0 CA B:SER123 4.6 64.8 1.0 CA B:ASP126 4.7 63.1 1.0 CA B:MET335 4.7 76.2 1.0 C B:ASP126 4.8 73.8 1.0 N B:LYS125 4.8 83.0 1.0 N B:ASP336 4.9 77.0 1.0 CB B:SER123 4.9 63.7 1.0 OD2 B:ASP251 5.0 66.0 1.0 CA B:ASP127 5.0 78.0 1.0 CA B:ASP336 5.0 73.1 1.0

Manganese binding site 8 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin.


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 HR10 Variant of the 10TH Domain of Fibronectin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn710 b:32.6 occ:1.00 OE2 B:GLU220 2.2 67.4 1.0 OD1 B:ASP217 2.2 78.3 1.0 OD2 B:ASP158 2.2 63.0 1.0 OD1 B:ASN215 2.2 45.0 1.0 O B:ASP217 2.2 42.8 1.0 O B:PRO219 2.2 59.6 1.0 C B:PRO219 3.1 43.1 1.0 CG B:ASP217 3.1 33.8 1.0 C B:ASP217 3.3 36.2 1.0 CG B:ASP158 3.4 39.8 1.0 CD B:GLU220 3.4 62.0 1.0 CG B:ASN215 3.4 55.6 1.0 CA B:GLU220 3.7 45.2 1.0 OD2 B:ASP217 3.7 38.4 1.0 N B:GLU220 3.7 33.8 1.0 C B:ALA218 4.0 35.3 1.0 CB B:ASP158 4.0 35.4 1.0 N B:PRO219 4.0 33.8 1.0 CA B:ASP217 4.0 36.2 1.0 N B:ASP217 4.1 39.5 1.0 O B:ALA218 4.1 65.2 1.0 CG B:GLU220 4.1 48.6 1.0 CB B:ASP217 4.1 34.6 1.0 CA B:PRO219 4.1 32.9 1.0 NE2 B:HIS255 4.2 30.7 1.0 N B:ALA218 4.3 45.1 1.0 ND2 B:ASN215 4.3 66.6 1.0 OE1 B:GLU220 4.3 75.1 1.0 CB B:ASN215 4.3 52.0 1.0 CB B:GLU220 4.4 37.1 1.0 OD1 B:ASP158 4.4 32.8 1.0 CD2 B:HIS255 4.5 30.5 1.0 CA B:ALA218 4.6 36.4 1.0 CD B:PRO219 4.7 51.1 1.0 C B:GLU220 4.9 54.6 1.0 CB B:PRO219 4.9 31.5 1.0

J.F.Van Agthoven, M.A.Armaout. Integrin ALPHAVBETA3 Ectodomain Bound to HR10 Variant of the 10TH Domain of Fibronectin. To Be Published.