Manganese in PDB 4z7q: Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide

The structure of Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide, PDB code: 4z7q was solved by F.-Y.Lin, J.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.94 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	259.440, 144.240, 104.500, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.6

The structure of Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide also contains other interesting chemical elements:

Calcium	(Ca)	8 atoms
Chlorine	(Cl)	1 atom

The binding sites of Manganese atom in the Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide (pdb code 4z7q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide, PDB code: 4z7q:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:49.1 occ:1.00 OE2 B:GLU220 2.1 53.1 1.0 OD1 G:ASP410 2.1 45.5 1.0 OG B:SER121 2.2 43.1 1.0 O B:HOH2105 2.2 40.6 1.0 OG B:SER123 2.2 56.6 1.0 O B:HOH2147 2.2 45.8 1.0 HB2 B:SER121 3.0 63.0 1.0 CB B:SER121 3.1 52.5 1.0 CD B:GLU220 3.2 54.3 1.0 CG G:ASP410 3.2 53.4 1.0 HG3 B:GLU220 3.3 63.2 1.0 H B:SER123 3.4 60.0 1.0 HA G:ASP410 3.4 78.7 1.0 CB B:SER123 3.4 41.3 1.0 HB3 B:SER123 3.5 49.6 1.0 HB3 B:SER121 3.5 63.0 1.0 CG B:GLU220 3.7 52.7 1.0 HG2 B:GLU220 3.7 63.2 1.0 HB2 B:ALA252 3.9 74.2 1.0 HD21 B:ASN215 3.9 96.6 1.0 HB2 B:SER123 4.0 49.6 1.0 HB3 B:ALA252 4.0 74.2 1.0 CB G:ASP410 4.0 67.1 1.0 OD2 G:ASP410 4.1 61.8 1.0 HB2 G:ASP410 4.1 80.5 1.0 CA G:ASP410 4.1 65.6 1.0 OD2 B:ASP119 4.1 41.5 1.0 OD1 B:ASP251 4.1 54.0 1.0 N B:SER123 4.1 50.0 1.0 O B:ALA218 4.2 46.1 1.0 OE1 B:GLU220 4.3 42.4 1.0 CA B:SER121 4.4 49.2 1.0 CB B:ALA252 4.4 61.9 1.0 CA B:SER123 4.4 43.3 1.0 HG2 B:MET124 4.5 54.1 1.0 HA B:ALA218 4.5 46.8 1.0 C B:SER121 4.5 43.4 1.0 C G:ASP410 4.6 56.9 1.0 OD1 B:ASP119 4.6 44.4 1.0 ND2 B:ASN215 4.6 80.5 1.0 H B:TYR122 4.7 47.9 1.0 H G:VAL411 4.7 85.5 1.0 HB1 B:ALA252 4.7 74.2 1.0 N B:TYR122 4.7 39.9 1.0 HD22 B:ASN215 4.8 96.6 1.0 H B:SER121 4.8 59.6 1.0 CG B:ASP119 4.8 42.7 1.0 N G:VAL411 4.8 71.2 1.0 HB3 G:ASP410 4.9 80.5 1.0 H B:MET124 5.0 60.7 1.0 O B:SER121 5.0 40.5 1.0

Manganese binding site 2 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:0.9 occ:1.00 OD2 B:ASP251 2.2 86.7 1.0 O B:SER123 2.2 62.4 1.0 O B:HOH2102 2.2 97.0 1.0 O B:HOH2239 2.2 85.2 1.0 O B:HOH2104 2.2 70.6 1.0 C B:SER123 3.2 54.5 1.0 CG B:ASP251 3.2 65.1 1.0 HB2 B:SER123 3.3 49.6 1.0 HA B:MET124 3.4 58.4 1.0 OD1 B:ASP127 3.6 0.8 1.0 HB3 B:ASP251 3.6 58.9 1.0 HB2 B:ASP251 3.7 58.9 1.0 CB B:ASP251 3.8 49.0 1.0 OD1 B:ASP126 4.0 60.4 0.4 CB B:SER123 4.1 41.3 1.0 N B:MET124 4.1 50.6 1.0 CA B:SER123 4.1 43.3 1.0 HA B:SER123 4.2 51.9 1.0 CA B:MET124 4.2 48.6 1.0 OD1 B:ASP251 4.2 54.0 1.0 OD2 B:ASP126 4.4 62.8 0.4 O B:MET335 4.4 92.0 1.0 SD B:MET124 4.6 52.3 1.0 CG B:ASP126 4.6 68.1 0.4 HG2 B:MET124 4.6 54.1 1.0 CG B:ASP127 4.6 91.0 1.0 HB3 B:SER123 4.7 49.6 1.0 OG B:SER123 4.9 56.6 1.0 H B:MET124 4.9 60.7 1.0 OD2 B:ASP127 4.9 91.1 1.0

Manganese binding site 3 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2003 b:74.4 occ:1.00 O B:PRO219 2.1 45.6 1.0 OD1 B:ASP217 2.1 54.6 1.0 OD2 B:ASP158 2.2 57.6 1.0 OE1 B:GLU220 2.2 42.4 1.0 OD1 B:ASN215 2.2 53.0 1.0 O B:ASP217 2.2 64.2 1.0 HA B:GLU220 2.9 56.1 1.0 C B:PRO219 3.1 35.8 1.0 CG B:ASN215 3.2 56.9 1.0 CG B:ASP217 3.2 48.6 1.0 CD B:GLU220 3.3 54.3 1.0 CG B:ASP158 3.3 44.5 1.0 C B:ASP217 3.3 44.0 1.0 HB2 B:ASP158 3.4 58.1 1.0 HD21 B:ASN215 3.4 96.6 1.0 HE2 B:HIS255 3.5 56.4 1.0 CA B:GLU220 3.7 46.8 1.0 H B:ASP217 3.7 49.2 1.0 ND2 B:ASN215 3.7 80.5 1.0 N B:GLU220 3.8 39.5 1.0 CB B:ASP158 3.8 48.4 1.0 OD2 B:ASP217 3.9 46.2 1.0 OE2 B:GLU220 4.0 53.1 1.0 HD2 B:HIS255 4.1 45.5 1.0 CA B:ASP217 4.1 52.8 1.0 C B:ALA218 4.1 39.2 1.0 HB3 B:ASP158 4.1 58.1 1.0 N B:PRO219 4.1 41.9 1.0 N B:ASP217 4.2 41.0 1.0 NE2 B:HIS255 4.2 47.0 1.0 HD2 B:PRO219 4.2 65.3 1.0 O B:ALA218 4.2 46.1 1.0 CB B:ASP217 4.2 56.0 1.0 CA B:PRO219 4.2 37.9 1.0 CG B:GLU220 4.3 52.7 1.0 N B:ALA218 4.3 36.4 1.0 OD1 B:ASP158 4.3 30.8 1.0 HB2 B:ASN215 4.4 51.0 1.0 CB B:GLU220 4.4 43.2 1.0 HG2 B:GLU220 4.4 63.2 1.0 CB B:ASN215 4.4 42.5 1.0 CD2 B:HIS255 4.4 37.9 1.0 HB3 B:TYR164 4.5 58.8 1.0 HB3 B:GLU220 4.5 51.8 1.0 HD22 B:ASN215 4.5 96.6 1.0 CA B:ALA218 4.6 39.0 1.0 H B:GLU220 4.6 47.4 1.0 HB2 B:PRO219 4.7 56.9 1.0 HB2 G:ASP410 4.7 80.5 1.0 HA B:ALA218 4.7 46.8 1.0 CD B:PRO219 4.7 54.4 1.0 HB2 B:ASP217 4.7 67.2 1.0 HD1 B:TYR164 4.8 47.8 1.0 C B:GLU220 4.8 42.7 1.0 H B:GLY221 4.8 47.6 1.0 HB3 B:ASN215 4.9 51.0 1.0 HB3 B:ASP217 4.9 67.2 1.0 HA B:PRO219 4.9 45.4 1.0 HA B:ASP217 5.0 63.3 1.0

Manganese binding site 4 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:0.4 occ:1.00 OD1 D:ASP126 2.2 0.5 1.0 OD2 D:ASP126 2.2 0.9 1.0 OD1 D:ASP127 2.2 98.6 1.0 O D:HOH684 2.2 81.1 1.0 O D:HOH611 2.2 0.6 1.0 O D:MET335 2.3 94.4 1.0 CG D:ASP126 2.4 0.3 1.0 CG D:ASP127 3.3 99.0 1.0 O D:SER123 3.4 90.3 1.0 HA D:ASP336 3.5 91.8 1.0 C D:MET335 3.5 90.5 1.0 HA D:MET124 3.6 0.6 1.0 OD2 D:ASP127 3.8 0.5 1.0 CB D:ASP126 3.9 0.5 1.0 H D:ASP127 3.9 0.1 1.0 HE3 D:MET335 4.0 82.5 1.0 H D:ASP126 4.0 0.9 1.0 HB3 D:MET335 4.1 0.4 1.0 N D:ASP127 4.1 95.9 1.0 HB2 D:ASP126 4.2 0.2 1.0 CA D:ASP336 4.3 76.5 1.0 N D:ASP336 4.3 83.9 1.0 O D:HOH637 4.4 81.7 1.0 HB3 D:ASP126 4.4 0.2 1.0 C D:ASP126 4.4 92.6 1.0 CB D:ASP127 4.5 89.8 1.0 N D:ASP126 4.5 0.8 1.0 CA D:ASP126 4.5 0.5 1.0 HA D:MET335 4.5 0.6 1.0 CA D:MET124 4.5 83.8 1.0 CA D:MET335 4.5 87.2 1.0 C D:SER123 4.6 85.5 1.0 HB3 D:ASP336 4.6 88.0 1.0 OD2 D:ASP251 4.7 1.0 1.0 HB2 D:ASP127 4.7 0.8 1.0 HA D:ASP127 4.7 0.3 1.0 CA D:ASP127 4.7 96.9 1.0 CB D:MET335 4.8 0.7 1.0 C D:MET124 4.9 86.4 1.0 CE D:MET335 4.9 68.8 1.0 H D:LYS125 4.9 0.6 1.0

Manganese binding site 5 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn502 b:81.2 occ:1.00 O D:PRO219 2.2 49.1 1.0 OD1 D:ASP217 2.2 62.1 1.0 OD2 D:ASP158 2.2 93.0 1.0 OD1 D:ASN215 2.2 91.2 1.0 OE1 D:GLU220 2.2 70.9 1.0 O D:ASP217 2.2 80.5 1.0 HA D:GLU220 2.9 70.1 1.0 CG D:ASP217 3.1 67.9 1.0 C D:PRO219 3.2 54.1 1.0 C D:ASP217 3.3 62.9 1.0 CG D:ASN215 3.3 83.0 1.0 CG D:ASP158 3.3 79.1 1.0 CD D:GLU220 3.4 64.3 1.0 HB2 D:ASP158 3.4 94.1 1.0 H D:ASP217 3.6 81.7 1.0 OD2 D:ASP217 3.6 71.4 1.0 HE2 D:HIS255 3.7 78.0 1.0 HD21 D:ASN215 3.7 0.5 1.0 CA D:GLU220 3.7 58.5 1.0 CB D:ASP158 3.9 78.4 1.0 N D:GLU220 3.9 50.2 1.0 ND2 D:ASN215 3.9 99.6 1.0 CA D:ASP217 4.0 68.8 1.0 N D:ASP217 4.1 68.1 1.0 CB D:ASP217 4.1 72.2 1.0 HB3 D:ASP158 4.1 94.1 1.0 C D:ALA218 4.1 53.2 1.0 OE2 D:GLU220 4.1 79.1 1.0 N D:PRO219 4.2 54.9 1.0 O D:ALA218 4.2 52.2 1.0 NE2 D:HIS255 4.3 65.0 1.0 N D:ALA218 4.3 55.4 1.0 HB2 D:ASN215 4.3 96.7 1.0 HD2 D:HIS255 4.3 82.9 1.0 CG D:GLU220 4.3 59.3 1.0 CA D:PRO219 4.3 58.0 1.0 OD1 D:ASP158 4.4 54.8 1.0 HD2 D:PRO219 4.4 74.0 1.0 HG2 D:GLU220 4.4 71.2 1.0 CB D:ASN215 4.4 80.6 1.0 CB D:GLU220 4.5 63.2 1.0 HB3 D:TYR164 4.5 64.5 1.0 HD1 D:TYR164 4.6 66.5 1.0 HB2 D:ASP217 4.6 86.7 1.0 HB3 D:GLU220 4.6 75.9 1.0 CD2 D:HIS255 4.6 69.1 1.0 CA D:ALA218 4.6 63.2 1.0 HA D:ALA218 4.7 75.8 1.0 H D:GLU220 4.7 60.3 1.0 HB2 D:PRO219 4.8 79.0 1.0 HD22 D:ASN215 4.8 0.5 1.0 HB3 D:ASP217 4.8 86.7 1.0 H D:GLY221 4.8 88.3 1.0 HB2 I:ASP410 4.8 89.5 1.0 C D:GLU220 4.8 60.1 1.0 CD D:PRO219 4.9 61.6 1.0 HB3 D:ASN215 4.9 96.7 1.0 HA D:ASP217 4.9 82.5 1.0

Manganese binding site 6 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Integrin ALPHAIIBBETA3 in Complex with Agdv-NH2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn509 b:0.1 occ:1.00 OD1 I:ASP410 1.3 0.2 1.0 CG I:ASP410 1.8 95.4 1.0 HB2 D:SER121 1.8 72.4 1.0 O D:HOH601 2.1 29.3 1.0 OD2 I:ASP410 2.1 83.1 1.0 O I:HOH2101 2.2 33.4 1.0 OE2 D:GLU220 2.2 79.1 1.0 OG D:SER121 2.2 55.1 1.0 OG D:SER123 2.2 0.8 1.0 CB D:SER121 2.4 60.3 1.0 H D:SER123 2.8 87.8 1.0 HD21 D:ASN215 2.9 0.5 1.0 HB3 D:SER121 3.0 72.4 1.0 CB I:ASP410 3.1 74.6 1.0 HB2 I:ASP410 3.3 89.5 1.0 HA I:ASP410 3.3 90.2 1.0 H D:TYR122 3.4 92.6 1.0 CD D:GLU220 3.4 64.3 1.0 CA D:SER121 3.5 59.9 1.0 ND2 D:ASN215 3.6 99.6 1.0 N D:SER123 3.6 73.2 1.0 CB D:SER123 3.6 0.5 1.0 N D:TYR122 3.6 77.2 1.0 C D:SER121 3.7 62.7 1.0 HD22 D:ASN215 3.7 0.5 1.0 CA I:ASP410 3.7 75.2 1.0 HB3 I:ASP410 3.8 89.5 1.0 HA D:SER121 4.0 71.9 1.0 HB2 D:SER123 4.0 0.5 1.0 O D:HOH646 4.1 57.5 1.0 C I:ASP410 4.2 85.2 1.0 HG3 D:GLU220 4.2 71.2 1.0 HB3 D:SER123 4.2 0.5 1.0 OE1 D:GLU220 4.2 70.9 1.0 CA D:SER123 4.2 89.3 1.0 O D:SER121 4.4 62.4 1.0 CG D:GLU220 4.4 59.3 1.0 O I:ASP410 4.4 79.0 1.0 H D:SER121 4.6 68.8 1.0 HB3 D:TYR122 4.6 89.0 1.0 C D:TYR122 4.6 61.4 1.0 CA D:TYR122 4.6 67.5 1.0 N D:SER121 4.6 57.4 1.0 OD1 D:ASP119 4.7 67.5 1.0 N I:VAL411 4.8 0.3 1.0 CG D:ASN215 4.8 83.0 1.0 HG2 D:GLU220 4.8 71.2 1.0 H D:ASN215 4.8 87.2 1.0 HA D:SER123 4.8 0.2 1.0 HG13 D:VAL157 4.8 75.5 1.0 H I:VAL411 4.9 0.6 1.0 OD2 D:ASP119 4.9 61.6 1.0

F.Y.Lin, J.Zhu, E.T.Eng, N.E.Hudson, T.A.Springer. Beta-Subunit Binding Is Sufficient For Ligands to Open the Integrin Alpha Iib Beta 3 Headpiece. J.Biol.Chem. V. 291 4537 2016.
ISSN: ESSN 1083-351X
PubMed: 26631735
DOI: 10.1074/JBC.M115.705624