Manganese in PDB 3zdz: Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex

The structure of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex, PDB code: 3zdz was solved by J.H.Zhu, J.Q.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.279 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	259.620, 144.470, 104.750, 90.00, 90.00, 90.00
R / Rfree (%)	18.44 / 22.11

The structure of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex also contains other interesting chemical elements:

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

The binding sites of Manganese atom in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex (pdb code 3zdz). 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 Alphaiib BETA3 Headpiece and Rgd Peptide Complex, PDB code: 3zdz:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:47.4 occ:1.00 OD1 I:ASP495 2.1 32.6 1.0 OE2 B:GLU220 2.2 18.8 1.0 OG B:SER123 2.2 29.5 1.0 OG B:SER121 2.2 32.4 1.0 O B:HOH4009 2.2 20.8 1.0 O B:HOH4010 2.2 25.9 1.0 HB2 B:SER121 2.8 40.9 1.0 CB B:SER121 3.0 34.2 1.0 CG I:ASP495 3.1 36.2 1.0 H B:SER123 3.2 46.0 1.0 CD B:GLU220 3.2 19.5 1.0 HG3 B:GLU220 3.2 22.4 1.0 HB3 B:SER123 3.3 42.9 1.0 CB B:SER123 3.3 35.8 1.0 HB3 B:SER121 3.5 40.9 1.0 HA I:ASP495 3.5 51.0 1.0 CG B:GLU220 3.6 18.7 1.0 HG2 B:GLU220 3.7 22.4 1.0 HB2 I:ASP495 3.8 47.1 1.0 OD2 I:ASP495 3.9 38.5 1.0 CB I:ASP495 3.9 39.3 1.0 N B:SER123 3.9 38.5 1.0 HB2 B:SER123 4.0 42.9 1.0 HD22 B:ASN215 4.0 33.7 1.0 CA I:ASP495 4.1 42.6 1.0 OD1 B:ASP251 4.2 40.4 1.0 HB3 B:ALA252 4.2 29.5 1.0 CA B:SER123 4.2 38.9 1.0 HB1 B:ALA252 4.2 29.5 1.0 O B:ALA218 4.2 32.8 1.0 CA B:SER121 4.3 35.7 1.0 HG2 B:MET124 4.3 38.2 1.0 OD2 B:ASP119 4.3 34.9 1.0 OE1 B:GLU220 4.3 22.3 1.0 C B:SER121 4.4 35.3 1.0 O B:HOH4001 4.5 45.4 1.0 H B:TYR122 4.5 46.1 1.0 N B:TYR122 4.5 38.5 1.0 H B:MET124 4.6 50.9 1.0 OD1 B:ASP119 4.6 37.0 1.0 CB B:ALA252 4.6 24.6 1.0 HA B:ALA218 4.6 39.3 1.0 ND2 B:ASN215 4.7 28.2 1.0 H B:SER121 4.7 42.2 1.0 C I:ASP495 4.7 45.0 1.0 HB3 I:ASP495 4.8 47.1 1.0 HD21 B:ASN215 4.8 33.7 1.0 HB2 B:ALA252 4.9 29.5 1.0 O B:SER121 4.9 30.1 1.0 CG B:ASP119 4.9 35.8 1.0 C B:SER123 4.9 41.8 1.0 N B:MET124 4.9 42.5 1.0 HA B:SER121 4.9 42.7 1.0 HA B:SER123 5.0 46.6 1.0

Manganese binding site 2 out of 6 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:58.5 occ:1.00 OD2 B:ASP127 2.3 50.4 1.0 OD2 B:ASP251 2.4 45.1 1.0 O B:SER123 2.4 42.7 1.0 OD1 B:ASP126 2.4 68.6 1.0 O B:HOH4015 2.6 75.4 1.0 CG B:ASP126 3.3 66.0 1.0 CG B:ASP251 3.3 37.9 1.0 HB2 B:ASP251 3.3 35.9 1.0 HA I:PRO497 3.4 80.4 1.0 OD2 B:ASP126 3.4 67.3 1.0 C B:SER123 3.5 41.8 1.0 CG B:ASP127 3.5 55.0 1.0 HB2 B:SER123 3.6 42.9 1.0 HA B:MET124 3.7 50.6 1.0 HB3 B:ASP251 3.7 35.9 1.0 CB B:ASP251 3.7 30.0 1.0 OD1 B:ASP127 4.0 61.0 1.0 OXT I:PRO497 4.1 81.8 1.0 H B:ASP126 4.1 73.3 1.0 O B:HOH4088 4.2 66.9 1.0 CA I:PRO497 4.3 67.1 1.0 CB B:SER123 4.3 35.8 1.0 CA B:SER123 4.4 38.9 1.0 N B:MET124 4.4 42.5 1.0 HA B:SER123 4.4 46.6 1.0 CA B:MET124 4.4 42.3 1.0 OD1 B:ASP251 4.4 40.4 1.0 HB3 I:PRO497 4.5 72.0 1.0 HB2 B:ASP127 4.6 64.8 1.0 O B:HOH4056 4.7 44.8 1.0 C I:PRO497 4.7 76.0 1.0 CB B:ASP127 4.7 54.0 1.0 CB B:ASP126 4.7 61.7 1.0 N B:ASP126 4.8 61.1 1.0 OG B:SER123 4.9 29.5 1.0 HG22 B:THR311 4.9 53.7 1.0 H B:ASP127 4.9 66.7 1.0 N B:ASP127 4.9 55.7 1.0 H B:LYS125 4.9 72.4 1.0 C B:ASP126 5.0 58.1 1.0 CB I:PRO497 5.0 60.1 1.0

Manganese binding site 3 out of 6 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2003 b:45.7 occ:1.00 O B:PRO219 2.1 27.6 1.0 OD2 B:ASP158 2.3 35.8 1.0 OD1 B:ASP217 2.3 46.4 1.0 O B:ASP217 2.3 36.4 1.0 OD1 B:ASN215 2.3 33.9 1.0 OE1 B:GLU220 2.3 22.3 1.0 HA B:GLU220 3.0 30.3 1.0 C B:PRO219 3.2 26.8 1.0 CG B:ASP217 3.2 38.8 1.0 CD B:GLU220 3.3 19.5 1.0 CG B:ASN215 3.3 29.2 1.0 C B:ASP217 3.4 34.8 1.0 CG B:ASP158 3.4 33.2 1.0 HD22 B:ASN215 3.4 33.7 1.0 HB2 B:ASP158 3.5 43.8 1.0 H B:ASP217 3.7 35.2 1.0 OD2 B:ASP217 3.8 40.0 1.0 ND2 B:ASN215 3.8 28.2 1.0 CA B:GLU220 3.8 25.3 1.0 CB B:ASP158 3.9 36.5 1.0 OE2 B:GLU220 3.9 18.8 1.0 N B:GLU220 3.9 24.8 1.0 CA B:ASP217 4.1 31.3 1.0 C B:ALA218 4.1 33.1 1.0 N B:ASP217 4.1 29.4 1.0 HD2 B:HIS255 4.1 36.4 1.0 O B:ALA218 4.1 32.8 1.0 HB3 B:ASP158 4.1 43.8 1.0 N B:PRO219 4.1 32.6 1.0 NE2 B:HIS255 4.2 31.6 1.0 CB B:ASP217 4.2 30.9 1.0 HD2 B:PRO219 4.2 36.3 1.0 CA B:PRO219 4.3 29.7 1.0 HB3 B:TYR164 4.3 35.3 1.0 N B:ALA218 4.4 35.2 1.0 CG B:GLU220 4.4 18.7 1.0 OD1 B:ASP158 4.4 27.5 1.0 HD1 B:TYR164 4.5 42.4 1.0 CD2 B:HIS255 4.5 30.4 1.0 HB2 I:ASP495 4.5 47.1 1.0 CB B:GLU220 4.6 20.1 1.0 HB2 B:PRO219 4.6 34.2 1.0 HG2 B:GLU220 4.6 22.4 1.0 HB2 B:ASN215 4.6 32.3 1.0 CB B:ASN215 4.7 27.0 1.0 HD21 B:ASN215 4.7 33.7 1.0 CA B:ALA218 4.7 32.8 1.0 CD B:PRO219 4.7 30.3 1.0 HB3 B:GLU220 4.7 24.1 1.0 HB2 B:ASP217 4.7 37.0 1.0 H B:GLU220 4.8 29.7 1.0 HA B:ALA218 4.8 39.3 1.0 C B:GLU220 4.9 30.0 1.0 HB3 B:ASP217 4.9 37.0 1.0 H B:ARG216 4.9 41.3 1.0 CB B:PRO219 5.0 28.6 1.0 HA B:ASP217 5.0 37.4 1.0

Manganese binding site 4 out of 6 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2001 b:81.2 occ:1.00 OE2 D:GLU220 2.2 81.6 1.0 OG D:SER121 2.2 60.1 1.0 OD1 J:ASP495 2.2 95.7 1.0 O D:HOH4022 2.2 58.0 1.0 O D:HOH4010 2.2 52.2 1.0 HB2 D:SER121 2.6 76.2 1.0 HA J:ASP495 2.6 1.0 1.0 CB D:SER121 2.9 63.6 1.0 HG D:SER123 3.2 0.3 1.0 CD D:GLU220 3.2 80.5 1.0 CG J:ASP495 3.2 90.2 1.0 HB3 D:SER121 3.4 76.2 1.0 OG D:SER123 3.4 92.0 1.0 HG3 D:GLU220 3.4 93.2 1.0 CA J:ASP495 3.5 93.4 1.0 HB3 D:SER123 3.6 0.2 1.0 HD22 D:ASN215 3.6 87.4 1.0 H D:SER123 3.6 1.0 1.0 CG D:GLU220 3.8 77.7 1.0 CB J:ASP495 3.9 89.6 1.0 CB D:SER123 4.0 91.1 1.0 HD21 D:ASN215 4.0 87.4 1.0 OD2 D:ASP119 4.1 59.1 1.0 HG2 D:GLU220 4.1 93.2 1.0 CA D:SER121 4.1 74.1 1.0 O J:ASP495 4.1 0.6 1.0 HB2 J:ASP495 4.1 0.5 1.0 ND2 D:ASN215 4.1 72.9 1.0 C J:ASP495 4.1 0.4 1.0 OD2 J:ASP495 4.2 86.5 1.0 C D:SER121 4.2 92.0 1.0 OE1 D:GLU220 4.3 81.2 1.0 O J:GLY494 4.3 97.6 1.0 N D:SER123 4.4 0.6 1.0 O D:SER121 4.4 90.1 1.0 HB3 D:ALA252 4.4 94.1 1.0 HB1 D:ALA252 4.4 94.1 1.0 OD1 D:ASP119 4.5 69.2 1.0 O D:ALA218 4.6 63.8 1.0 N J:ASP495 4.6 90.1 1.0 HA D:SER121 4.7 88.8 1.0 N D:TYR122 4.7 0.5 1.0 OD1 D:ASP251 4.7 97.7 1.0 CG D:ASP119 4.7 63.8 1.0 HB3 J:ASP495 4.8 0.5 1.0 HB2 D:SER123 4.8 0.2 1.0 H D:SER121 4.8 86.2 1.0 H D:TYR122 4.8 0.1 1.0 CA D:SER123 4.8 94.9 1.0 CB D:ALA252 4.8 78.5 1.0 HG2 D:MET124 4.9 98.5 1.0 C J:GLY494 4.9 89.4 1.0

Manganese binding site 5 out of 6 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2002 b:0.8 occ:1.00 OD1 D:ASP127 2.5 96.9 1.0 O D:MET335 2.6 0.9 1.0 OD1 D:ASP126 2.6 0.6 1.0 O D:SER123 2.9 90.2 1.0 O D:HOH4026 3.0 58.0 1.0 HA D:MET124 3.2 0.4 1.0 CG D:ASP126 3.4 0.5 1.0 OD2 D:ASP126 3.4 0.4 1.0 CG D:ASP127 3.5 96.2 1.0 C D:MET335 3.7 0.7 1.0 OD2 D:ASP127 3.8 99.1 1.0 HA D:ASP336 3.9 0.9 1.0 HB3 D:MET335 3.9 0.3 1.0 C D:SER123 3.9 90.2 1.0 OD2 D:ASP251 4.1 98.6 1.0 CA D:MET124 4.1 89.6 1.0 H D:ASP127 4.2 0.7 1.0 HA D:MET335 4.3 0.1 1.0 H D:ASP126 4.3 0.2 1.0 CA D:MET335 4.5 1.0 1.0 N D:MET124 4.5 89.1 1.0 HE3 D:MET335 4.6 0.1 1.0 N D:ASP336 4.6 0.5 1.0 CB D:MET335 4.6 0.0 1.0 CA D:ASP336 4.7 95.9 1.0 N D:ASP127 4.7 99.8 1.0 C D:MET124 4.7 94.8 1.0 CB D:ASP126 4.8 0.7 1.0 CB D:ASP127 4.9 93.3 1.0 SD D:MET124 4.9 84.0 1.0 HE1 D:MET335 5.0 0.1 1.0 H D:LYS125 5.0 0.4 1.0 CG D:ASP251 5.0 97.1 1.0

Manganese binding site 6 out of 6 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2003 b:79.3 occ:1.00 O D:PRO219 2.2 55.7 1.0 OD1 D:ASP217 2.2 72.8 1.0 OE1 D:GLU220 2.3 81.2 1.0 OD2 D:ASP158 2.3 64.0 1.0 OD1 D:ASN215 2.3 64.5 1.0 O D:ASP217 2.3 69.6 1.0 CG D:ASP217 3.0 72.4 1.0 HA D:GLU220 3.1 82.1 1.0 CG D:ASN215 3.2 67.1 1.0 HD22 D:ASN215 3.2 87.4 1.0 CD D:GLU220 3.3 80.5 1.0 C D:PRO219 3.3 58.6 1.0 C D:ASP217 3.3 64.3 1.0 CG D:ASP158 3.4 60.2 1.0 OD2 D:ASP217 3.6 71.5 1.0 ND2 D:ASN215 3.6 72.9 1.0 HB2 D:ASP158 3.6 73.5 1.0 H D:ASP217 3.8 81.4 1.0 OE2 D:GLU220 3.8 81.6 1.0 CA D:GLU220 3.9 68.5 1.0 CA D:ASP217 4.0 68.6 1.0 N D:GLU220 4.0 62.5 1.0 CB D:ASP158 4.0 61.4 1.0 N D:ASP217 4.0 67.9 1.0 C D:ALA218 4.1 61.8 1.0 CB D:ASP217 4.1 71.5 1.0 O D:ALA218 4.1 63.8 1.0 N D:PRO219 4.2 62.7 1.0 NE2 D:HIS255 4.3 64.1 1.0 HB3 D:ASP158 4.3 73.5 1.0 N D:ALA218 4.3 57.1 1.0 HD2 D:PRO219 4.3 77.9 1.0 HD1 D:TYR164 4.3 75.5 1.0 CA D:PRO219 4.3 60.0 1.0 CG D:GLU220 4.4 77.7 1.0 HD21 D:ASN215 4.4 87.4 1.0 HD2 D:HIS255 4.4 77.9 1.0 OD1 D:ASP158 4.5 56.2 1.0 CB D:ASN215 4.5 64.7 1.0 HG2 D:GLU220 4.6 93.2 1.0 CB D:GLU220 4.6 73.1 1.0 HB2 D:ASP217 4.6 85.7 1.0 HB2 D:ASN215 4.6 77.6 1.0 HB3 D:TYR164 4.6 72.2 1.0 CA D:ALA218 4.6 59.4 1.0 HB3 D:GLU220 4.7 87.6 1.0 CD2 D:HIS255 4.7 65.0 1.0 H D:ARG216 4.7 79.4 1.0 HB3 D:ASP217 4.8 85.7 1.0 HA D:ALA218 4.8 71.2 1.0 CD D:PRO219 4.8 65.0 1.0 H D:GLU220 4.8 74.9 1.0 HB2 D:PRO219 4.8 71.4 1.0 C D:ARG216 4.9 69.4 1.0 HA D:ASP217 4.9 82.2 1.0 HB3 D:ASN215 4.9 77.6 1.0 H D:GLY221 5.0 75.9 1.0 CD1 D:TYR164 5.0 63.0 1.0

J.Zhu, J.Zhu, T.A.Springer. Complete Integrin Headpiece Opening in Eight Steps. J.Cell Biol. V. 201 1053 2013.
ISSN: ISSN 0021-9525
PubMed: 23798730
DOI: 10.1083/JCB.201212037