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Manganese in PDB 4z7n: Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide

Protein crystallography data

The structure of Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide, PDB code: 4z7n 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) 49.19 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 256.883, 144.373, 104.639, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 25.3

Other elements in 4z7n:

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

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

Manganese Binding Sites:

The binding sites of Manganese atom in the Integrin ALPHAIIBBETA3 in Complex with Agdv Peptide (pdb code 4z7n). 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 Peptide, PDB code: 4z7n:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4z7n

Go back to Manganese Binding Sites List in 4z7n
Manganese binding site 1 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv 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 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2001

b:46.9
occ:1.00
OD1 G:ASP410 2.1 45.5 1.0
O B:HOH2114 2.2 43.6 1.0
OG B:SER121 2.2 56.7 1.0
O B:HOH2146 2.2 52.4 1.0
OE2 B:GLU220 2.2 54.7 1.0
OG B:SER123 2.2 59.9 1.0
HB2 B:SER121 2.7 67.7 1.0
CB B:SER121 2.9 56.4 1.0
HG3 B:GLU220 3.2 63.4 1.0
HB3 B:SER123 3.2 74.2 1.0
CD B:GLU220 3.2 53.3 1.0
H B:SER123 3.2 74.7 1.0
CB B:SER123 3.3 61.9 1.0
CG G:ASP410 3.3 50.4 1.0
HB3 B:SER121 3.4 67.7 1.0
CG B:GLU220 3.6 52.9 1.0
HA G:ASP410 3.7 67.6 1.0
HG2 B:GLU220 3.7 63.4 1.0
HB2 B:SER123 3.9 74.2 1.0
HD21 B:ASN215 3.9 66.2 1.0
HB2 B:ALA252 3.9 68.1 1.0
N B:SER123 4.0 62.3 1.0
OD1 B:ASP251 4.0 59.7 1.0
HB3 B:ALA252 4.0 68.1 1.0
OD2 G:ASP410 4.1 50.7 1.0
CA B:SER123 4.2 63.3 1.0
OD2 B:ASP119 4.2 54.9 1.0
CA B:SER121 4.2 57.5 1.0
HG2 B:MET124 4.2 71.7 1.0
O B:ALA218 4.3 54.2 1.0
CB G:ASP410 4.3 53.7 1.0
OE1 B:GLU220 4.3 52.5 1.0
CA G:ASP410 4.4 56.3 1.0
HB2 G:ASP410 4.4 64.5 1.0
CB B:ALA252 4.4 56.8 1.0
C B:SER121 4.4 59.6 1.0
OD1 B:ASP119 4.5 55.4 1.0
H B:MET124 4.6 75.4 1.0
HA B:ALA218 4.6 66.9 1.0
H B:SER121 4.6 68.6 1.0
H B:TYR122 4.7 72.5 1.0
N B:TYR122 4.7 60.4 1.0
ND2 B:ASN215 4.7 55.1 1.0
O G:HOH502 4.7 44.8 1.0
HB1 B:ALA252 4.7 68.1 1.0
CG B:ASP119 4.8 55.2 1.0
HD22 B:ASN215 4.8 66.2 1.0
O B:SER121 4.8 60.6 1.0
HA B:SER121 4.9 69.0 1.0
C G:ASP410 4.9 58.6 1.0
C B:SER123 4.9 63.9 1.0
N B:MET124 4.9 62.9 1.0
N B:SER121 5.0 57.2 1.0
H G:VAL411 5.0 76.6 1.0
HA B:SER123 5.0 75.9 1.0

Manganese binding site 2 out of 6 in 4z7n

Go back to Manganese Binding Sites List in 4z7n
Manganese binding site 2 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv 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 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2002

b:0.9
occ:1.00
OD2 B:ASP127 2.1 78.8 1.0
OD1 B:ASP126 2.1 97.1 1.0
OD2 B:ASP251 2.1 63.2 1.0
O B:SER123 2.2 65.4 1.0
O G:HOH501 2.2 72.9 1.0
O B:HOH2168 2.2 72.7 1.0
CG B:ASP126 3.1 0.4 1.0
CG B:ASP251 3.2 61.6 1.0
C B:SER123 3.3 63.9 1.0
HA B:MET124 3.3 76.1 1.0
CG B:ASP127 3.4 80.7 1.0
OD2 B:ASP126 3.4 1.0 1.0
HB2 B:ASP251 3.6 74.7 1.0
HB2 B:SER123 3.6 74.2 1.0
HB3 B:ASP251 3.8 74.7 1.0
CB B:ASP251 3.8 62.2 1.0
H B:ASP126 4.0 0.1 1.0
N B:MET124 4.1 62.9 1.0
CA B:MET124 4.1 63.4 1.0
OD1 B:ASP127 4.1 81.6 1.0
HB2 B:ASP127 4.1 96.8 1.0
CA B:SER123 4.2 63.3 1.0
OD1 B:ASP251 4.2 59.7 1.0
HA B:SER123 4.3 75.9 1.0
CB B:SER123 4.3 61.9 1.0
CB B:ASP127 4.4 80.7 1.0
H B:ASP127 4.4 0.8 1.0
CB B:ASP126 4.5 0.9 1.0
N B:ASP127 4.5 89.0 1.0
N B:ASP126 4.5 96.8 1.0
OXT G:VAL411 4.6 67.0 1.0
C B:ASP126 4.6 0.8 1.0
C B:MET124 4.7 65.6 1.0
OG B:SER123 4.8 59.9 1.0
CA B:ASP126 4.8 0.1 1.0
H B:LYS125 4.8 80.3 1.0
HG21 B:THR311 4.9 80.3 1.0
H B:MET124 4.9 75.4 1.0
HB3 B:ASP126 4.9 0.6 1.0
N B:LYS125 4.9 66.9 1.0
SD B:MET124 5.0 60.5 1.0

Manganese binding site 3 out of 6 in 4z7n

Go back to Manganese Binding Sites List in 4z7n
Manganese binding site 3 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv 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 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2003

b:65.0
occ:1.00
O B:PRO219 1.9 55.0 1.0
OD1 B:ASP217 2.1 52.1 1.0
OD2 B:ASP158 2.1 50.3 1.0
OD1 B:ASN215 2.2 53.3 1.0
OE1 B:GLU220 2.2 52.5 1.0
O B:ASP217 2.2 53.9 1.0
HA B:GLU220 2.9 60.6 1.0
C B:PRO219 3.0 51.2 1.0
CG B:ASP217 3.1 52.1 1.0
CG B:ASN215 3.3 54.3 1.0
CD B:GLU220 3.3 53.3 1.0
CG B:ASP158 3.3 49.8 1.0
C B:ASP217 3.3 54.6 1.0
HB2 B:ASP158 3.5 60.6 1.0
HD21 B:ASN215 3.5 66.2 1.0
HE2 B:HIS255 3.6 59.2 1.0
H B:ASP217 3.7 66.3 1.0
CA B:GLU220 3.7 50.5 1.0
OD2 B:ASP217 3.7 51.2 1.0
N B:GLU220 3.8 50.9 1.0
ND2 B:ASN215 3.8 55.1 1.0
CB B:ASP158 3.9 50.5 1.0
C B:ALA218 4.0 54.2 1.0
N B:PRO219 4.0 53.1 1.0
OE2 B:GLU220 4.0 54.7 1.0
HD2 B:HIS255 4.1 58.6 1.0
CA B:ASP217 4.1 54.9 1.0
O B:ALA218 4.1 54.2 1.0
CA B:PRO219 4.1 51.9 1.0
HB3 B:ASP158 4.1 60.6 1.0
N B:ASP217 4.1 55.2 1.0
CB B:ASP217 4.2 53.5 1.0
NE2 B:HIS255 4.2 49.4 1.0
HD2 B:PRO219 4.2 63.8 1.0
CG B:GLU220 4.3 52.9 1.0
N B:ALA218 4.3 55.4 1.0
OD1 B:ASP158 4.3 49.0 1.0
HG2 B:GLU220 4.3 63.4 1.0
HB3 B:TYR164 4.4 61.8 1.0
CB B:GLU220 4.4 51.5 1.0
CD2 B:HIS255 4.5 48.8 1.0
HB2 B:ASN215 4.5 65.9 1.0
HB2 B:PRO219 4.5 61.5 1.0
CB B:ASN215 4.5 54.9 1.0
HD1 B:TYR164 4.5 60.4 1.0
CA B:ALA218 4.5 55.7 1.0
HA B:ALA218 4.6 66.9 1.0
H B:GLU220 4.6 61.1 1.0
HB3 B:GLU220 4.6 61.8 1.0
HD22 B:ASN215 4.6 66.2 1.0
CD B:PRO219 4.7 53.2 1.0
H B:GLY221 4.7 58.9 1.0
HB2 B:ASP217 4.7 64.2 1.0
HB3 B:ASP217 4.8 64.2 1.0
HA B:PRO219 4.8 62.3 1.0
HB2 G:ASP410 4.8 64.5 1.0
C B:GLU220 4.9 49.5 1.0
CB B:PRO219 4.9 51.2 1.0
HB3 B:ASN215 5.0 65.9 1.0
HA B:ASP217 5.0 65.8 1.0

Manganese binding site 4 out of 6 in 4z7n

Go back to Manganese Binding Sites List in 4z7n
Manganese binding site 4 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv 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 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2001

b:0.3
occ:1.00
HB2 D:SER121 1.8 94.0 1.0
OD1 J:ASP410 2.1 82.2 1.0
OG D:SER121 2.1 78.7 1.0
O D:HOH2105 2.2 38.1 1.0
OE2 D:GLU220 2.2 75.8 1.0
O D:HOH2134 2.2 48.5 1.0
CB D:SER121 2.2 78.4 1.0
HB3 D:SER121 2.5 94.0 1.0
HD21 D:ASN215 3.0 93.7 1.0
CD D:GLU220 3.1 73.4 1.0
CG J:ASP410 3.1 81.9 1.0
HG3 D:GLU220 3.4 86.1 1.0
ND2 D:ASN215 3.7 78.1 1.0
HA J:ASP410 3.7 95.8 1.0
CA D:SER121 3.7 79.4 1.0
HD22 D:ASN215 3.8 93.7 1.0
CG D:GLU220 3.8 71.8 1.0
HG D:SER123 3.8 0.4 1.0
H D:SER123 3.8 0.3 1.0
OE1 D:GLU220 3.9 72.5 1.0
OG D:SER123 3.9 83.7 1.0
HB2 J:ASP410 3.9 96.8 1.0
OD2 J:ASP410 3.9 81.0 1.0
CB J:ASP410 4.0 80.7 1.0
OD2 D:ASP119 4.1 76.7 1.0
H D:TYR122 4.1 99.0 1.0
HA D:SER121 4.1 95.3 1.0
C D:SER121 4.2 81.7 1.0
HG2 D:GLU220 4.2 86.1 1.0
OD1 D:ASP119 4.3 76.9 1.0
CA J:ASP410 4.3 79.8 1.0
N D:TYR122 4.3 82.5 1.0
H D:SER121 4.4 94.8 1.0
HB3 D:SER123 4.5 0.9 1.0
N D:SER121 4.6 79.0 1.0
CG D:ASP119 4.6 76.7 1.0
N D:SER123 4.7 85.2 1.0
O D:ALA218 4.7 75.5 1.0
CB D:SER123 4.7 85.8 1.0
HB3 D:ALA252 4.8 92.7 1.0
C J:ASP410 4.8 83.2 1.0
HG13 D:VAL157 4.8 90.0 1.0
CG D:ASN215 4.8 77.2 1.0
HB3 J:ASP410 4.9 96.8 1.0
HB2 D:ALA252 4.9 92.7 1.0
O D:SER121 4.9 82.8 1.0

Manganese binding site 5 out of 6 in 4z7n

Go back to Manganese Binding Sites List in 4z7n
Manganese binding site 5 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv 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 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2002

b:0.5
occ:1.00
OD1 D:ASP127 2.1 92.0 1.0
OD1 D:ASP126 2.2 94.7 1.0
O D:HOH2136 2.2 47.0 1.0
O D:HOH2115 2.2 70.3 1.0
O D:SER123 2.2 88.8 1.0
HA D:MET124 2.7 0.0 1.0
O D:MET335 2.8 93.5 1.0
CG D:ASP126 2.9 97.0 1.0
OD2 D:ASP126 3.1 97.8 1.0
CG D:ASP127 3.2 90.9 1.0
C D:SER123 3.3 87.2 1.0
H D:ASP127 3.5 0.2 1.0
CA D:MET124 3.6 86.7 1.0
OD2 D:ASP127 3.6 89.9 1.0
N D:MET124 3.9 86.1 1.0
H D:ASP126 3.9 0.1 1.0
C D:MET335 4.0 94.1 1.0
HA D:ASP336 4.1 0.0 1.0
N D:ASP127 4.2 94.4 1.0
C D:MET124 4.2 88.4 1.0
O D:HOH2104 4.2 69.9 1.0
HB3 D:MET335 4.4 0.6 1.0
OD2 D:ASP251 4.4 85.4 1.0
CB D:ASP126 4.4 99.1 1.0
CB D:ASP127 4.4 90.9 1.0
H D:LYS125 4.4 0.5 1.0
SD D:MET124 4.5 83.8 1.0
N D:ASP126 4.5 95.1 1.0
HB2 D:ASP127 4.5 0.1 1.0
N D:LYS125 4.5 89.6 1.0
HB2 D:SER123 4.5 0.9 1.0
CA D:SER123 4.6 86.7 1.0
HA D:SER123 4.6 0.0 1.0
CB D:MET124 4.7 84.4 1.0
HA D:MET335 4.7 0.3 1.0
H D:MET124 4.7 0.4 1.0
HB3 D:MET124 4.8 0.3 1.0
HG2 D:MET124 4.8 99.3 1.0
CA D:ASP126 4.8 97.7 1.0
CA D:ASP127 4.8 93.8 1.0
O D:MET124 4.9 88.8 1.0
HB2 D:ASP126 4.9 0.9 1.0
CA D:MET335 4.9 93.6 1.0
HB3 D:ASP126 4.9 0.9 1.0
CA D:ASP336 4.9 95.9 1.0
N D:ASP336 4.9 95.4 1.0
CG D:MET124 4.9 82.8 1.0
C D:ASP126 4.9 97.0 1.0

Manganese binding site 6 out of 6 in 4z7n

Go back to Manganese Binding Sites List in 4z7n
Manganese binding site 6 out of 6 in the Integrin ALPHAIIBBETA3 in Complex with Agdv 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 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2003

b:0.5
occ:1.00
O D:PRO219 2.1 70.8 1.0
OD1 D:ASP217 2.1 73.9 1.0
OE1 D:GLU220 2.2 72.5 1.0
OD2 D:ASP158 2.2 71.5 1.0
OD1 D:ASN215 2.2 76.0 1.0
O D:ASP217 2.2 77.0 1.0
HA D:GLU220 2.9 81.9 1.0
CD D:GLU220 3.0 73.4 1.0
CG D:ASP217 3.0 73.9 1.0
C D:PRO219 3.1 70.4 1.0
C D:ASP217 3.2 78.4 1.0
CG D:ASN215 3.2 77.2 1.0
CG D:ASP158 3.4 70.7 1.0
HD21 D:ASN215 3.5 93.7 1.0
OE2 D:GLU220 3.5 75.8 1.0
OD2 D:ASP217 3.6 72.0 1.0
HB2 D:ASP158 3.6 85.5 1.0
CA D:GLU220 3.7 68.3 1.0
ND2 D:ASN215 3.7 78.1 1.0
O D:ALA218 3.8 75.5 1.0
N D:GLU220 3.8 69.1 1.0
H D:ASP217 3.8 96.1 1.0
C D:ALA218 3.8 76.2 1.0
HE2 D:HIS255 3.9 81.5 1.0
CA D:ASP217 4.0 79.2 1.0
N D:PRO219 4.0 74.5 1.0
CB D:ASP158 4.0 71.3 1.0
CB D:ASP217 4.1 76.8 1.0
N D:ASP217 4.1 80.0 1.0
CG D:GLU220 4.1 71.8 1.0
N D:ALA218 4.2 79.5 1.0
CA D:PRO219 4.2 71.8 1.0
HG2 D:GLU220 4.3 86.1 1.0
CB D:GLU220 4.3 69.3 1.0
OD1 D:ASP158 4.3 69.5 1.0
HD2 D:PRO219 4.4 90.2 1.0
HB2 D:ASN215 4.4 93.7 1.0
HB3 D:ASP158 4.4 85.5 1.0
HD2 D:HIS255 4.4 79.5 1.0
CA D:ALA218 4.4 79.3 1.0
HA D:ALA218 4.4 95.1 1.0
CB D:ASN215 4.4 78.1 1.0
HB3 D:GLU220 4.4 83.2 1.0
NE2 D:HIS255 4.5 67.9 1.0
HB2 D:ASP217 4.5 92.1 1.0
HD22 D:ASN215 4.6 93.7 1.0
H D:GLU220 4.6 82.9 1.0
HD1 D:TYR164 4.7 86.3 1.0
H D:GLY221 4.8 78.6 1.0
CD D:PRO219 4.8 75.1 1.0
CD2 D:HIS255 4.8 66.3 1.0
HB3 D:ASP217 4.8 92.1 1.0
HB3 D:TYR164 4.8 87.1 1.0
HA D:PRO219 4.8 86.2 1.0
HB2 D:PRO219 4.8 85.1 1.0
HB3 D:ASN215 4.9 93.7 1.0
HB2 J:ASP410 4.9 96.8 1.0
HA D:ASP217 4.9 95.1 1.0
C D:GLU220 4.9 66.1 1.0
HG3 D:GLU220 4.9 86.1 1.0
H D:ALA218 4.9 95.4 1.0

Reference:

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
Page generated: Tue Dec 15 04:34:13 2020

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