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Manganese in PDB 7uko: Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)

Protein crystallography data

The structure of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn), PDB code: 7uko was solved by F.-Y.Lin, J.Zhu, J.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.29 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 258.388, 144.599, 104.854, 90, 90, 90
R / Rfree (%) 21.4 / 23.9

Other elements in 7uko:

The structure of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn) 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 ALAPHIIBBETA3 Complex with Sibrafiban (Mn) (pdb code 7uko). 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 ALAPHIIBBETA3 Complex with Sibrafiban (Mn), PDB code: 7uko:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7uko

Go back to Manganese Binding Sites List in 7uko
Manganese binding site 1 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2001

b:29.4
occ:1.00
 O B:HOH2123 2.1 31.6 1.0
OE2 B:GLU220 2.2 31.0 1.0
O03 B:XQS2005 2.2 33.8 1.0
O B:HOH2140 2.2 33.0 1.0
OG B:SER121 2.3 34.6 1.0
OG B:SER123 2.4 39.3 1.0
CB B:SER121 3.0 34.5 1.0
CD B:GLU220 3.2 30.2 1.0
C20 B:XQS2005 3.4 33.8 1.0
CG B:GLU220 3.6 29.9 1.0
O01 B:XQS2005 3.7 33.8 1.0
CB B:SER123 3.8 40.5 1.0
O B:HOH2229 4.1 40.0 1.0
OD2 B:ASP119 4.2 32.5 1.0
C17 B:XQS2005 4.2 33.8 1.0
O B:ALA218 4.2 30.7 1.0
OD1 B:ASP251 4.3 36.5 1.0
N B:SER123 4.3 40.6 1.0
O05 B:XQS2005 4.3 33.8 1.0
CA B:SER121 4.3 35.0 1.0
OE1 B:GLU220 4.3 29.8 1.0
OD1 B:ASP119 4.4 32.7 1.0
CB B:ALA252 4.5 33.6 1.0
C B:SER121 4.6 36.2 1.0
ND2 B:ASN215 4.6 31.9 1.0
N B:TYR122 4.7 37.3 1.0
CA B:SER123 4.7 41.2 1.0
CG B:ASP119 4.7 32.6 1.0
C10 B:XQS2005 4.9 33.8 1.0

Manganese binding site 2 out of 6 in 7uko

Go back to Manganese Binding Sites List in 7uko
Manganese binding site 2 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2002

b:66.8
occ:1.00
 OD1 B:ASP126 2.1 50.1 0.5
OD2 B:ASP126 2.2 50.5 0.5
O B:SER123 2.3 42.4 1.0
OD1 B:ASP127 2.3 49.3 1.0
CG B:ASP126 2.4 50.7 0.5
O B:HOH2109 2.4 50.0 1.0
O B:HOH2137 2.5 45.4 1.0
CA B:MET124 3.3 43.9 1.0
C B:SER123 3.3 41.5 1.0
CG B:ASP127 3.5 48.9 1.0
O B:HOH2101 3.5 44.3 1.0
C B:MET124 3.6 44.8 1.0
O B:MET335 3.6 50.4 1.0
N B:MET124 3.7 43.7 1.0
N B:ASP126 3.7 49.8 0.5
N B:ASP126 3.7 49.8 0.5
CB B:ASP126 3.7 51.8 0.5
N B:LYS125 3.8 46.8 1.0
CB B:ASP126 4.0 52.0 0.5
N B:ASP127 4.0 50.6 1.0
OD2 B:ASP127 4.1 48.7 1.0
CA B:ASP126 4.2 50.9 0.5
O B:MET124 4.2 44.9 1.0
CA B:ASP126 4.2 51.0 0.5
OD2 B:ASP251 4.5 38.4 1.0
C B:ASP126 4.5 50.3 0.5
C B:ASP126 4.5 50.3 0.5
CB B:MET124 4.5 42.7 1.0
CB B:ASP127 4.6 48.8 1.0
CA B:SER123 4.6 41.2 1.0
C B:LYS125 4.7 48.9 1.0
CG B:ASP126 4.7 53.1 0.5
OD2 B:ASP126 4.7 53.7 0.5
CA B:LYS125 4.8 47.8 1.0
O B:HOH2103 4.8 48.4 1.0
C B:MET335 4.9 51.1 1.0
CA B:ASP127 4.9 50.1 1.0

Manganese binding site 3 out of 6 in 7uko

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Manganese binding site 3 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2003

b:32.8
occ:1.00
 O B:PRO219 2.1 28.3 1.0
OD1 B:ASP217 2.2 29.5 1.0
OD1 B:ASN215 2.2 30.9 1.0
OD2 B:ASP158 2.2 29.9 1.0
OE1 B:GLU220 2.2 29.8 1.0
O B:ASP217 2.2 30.7 1.0
CG B:ASP217 3.1 29.6 1.0
CG B:ASN215 3.2 31.5 1.0
C B:PRO219 3.3 28.3 1.0
CG B:ASP158 3.3 29.6 1.0
C B:ASP217 3.3 31.1 1.0
CD B:GLU220 3.4 30.2 1.0
OD2 B:ASP217 3.7 29.1 1.0
ND2 B:ASN215 3.7 31.9 1.0
CB B:ASP158 3.8 30.1 1.0
CA B:GLU220 3.8 28.6 1.0
N B:GLU220 4.0 28.8 1.0
CA B:ASP217 4.0 31.3 1.0
N B:ASP217 4.1 31.6 1.0
OE2 B:GLU220 4.1 31.0 1.0
C B:ALA218 4.1 30.8 1.0
CB B:ASP217 4.1 30.6 1.0
NE2 B:HIS255 4.2 28.0 1.0
O B:ALA218 4.2 30.7 1.0
N B:PRO219 4.2 29.5 1.0
N B:ALA218 4.3 31.6 1.0
CA B:PRO219 4.4 28.8 1.0
CG B:GLU220 4.4 29.9 1.0
OD1 B:ASP158 4.4 29.1 1.0
CD2 B:HIS255 4.5 27.6 1.0
CB B:ASN215 4.5 31.9 1.0
CB B:GLU220 4.5 29.1 1.0
CA B:ALA218 4.7 31.7 1.0
CD B:PRO219 4.9 29.6 1.0
C B:GLU220 4.9 27.9 1.0
CB B:TYR164 5.0 30.0 1.0
CD1 B:TYR164 5.0 29.3 1.0

Manganese binding site 4 out of 6 in 7uko

Go back to Manganese Binding Sites List in 7uko
Manganese binding site 4 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2001

b:44.8
occ:1.00
 O D:HOH2145 2.1 46.3 1.0
O03 D:XQS2005 2.1 48.5 1.0
OE2 D:GLU220 2.2 45.6 1.0
O D:HOH2106 2.2 47.4 1.0
OG D:SER121 2.3 47.9 1.0
CB D:SER121 3.1 47.8 1.0
OG D:SER123 3.1 53.6 1.0
C20 D:XQS2005 3.3 48.5 1.0
CD D:GLU220 3.4 44.6 1.0
O01 D:XQS2005 3.6 48.5 1.0
CG D:GLU220 3.9 44.0 1.0
C17 D:XQS2005 4.1 48.5 1.0
O05 D:XQS2005 4.2 48.5 1.0
OD1 D:ASP251 4.3 47.0 1.0
OD2 D:ASP119 4.3 45.2 1.0
O D:ALA218 4.4 43.0 1.0
CA D:SER121 4.4 48.6 1.0
OE1 D:GLU220 4.4 44.1 1.0
CB D:SER123 4.5 54.6 1.0
N D:TYR122 4.5 52.7 1.0
OD1 D:ASP119 4.5 45.8 1.0
CB D:ALA252 4.6 43.9 1.0
N D:SER123 4.6 54.5 1.0
ND2 D:ASN215 4.6 45.5 1.0
C D:SER121 4.7 49.7 1.0
C12 D:XQS2005 4.7 48.5 1.0
C10 D:XQS2005 4.7 48.5 1.0
CG D:ASP119 4.8 45.6 1.0

Manganese binding site 5 out of 6 in 7uko

Go back to Manganese Binding Sites List in 7uko
Manganese binding site 5 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2002

b:65.6
occ:1.00
 OD1 D:ASP126 2.2 60.0 1.0
OD1 D:ASP127 2.2 58.0 1.0
O D:SER123 2.3 56.6 1.0
O D:HOH2142 2.3 58.9 1.0
O D:HOH2120 2.4 54.8 1.0
O D:MET335 2.6 57.0 1.0
CG D:ASP126 3.0 61.3 1.0
OD2 D:ASP126 3.2 61.8 1.0
CG D:ASP127 3.4 58.0 1.0
C D:SER123 3.5 55.7 1.0
O D:HOH2121 3.8 53.6 1.0
C D:MET335 3.8 57.4 1.0
CA D:MET124 3.8 55.7 1.0
OD2 D:ASP127 4.0 57.9 1.0
N D:MET124 4.1 55.3 1.0
N D:ASP127 4.1 60.1 1.0
CB D:ASP126 4.4 62.4 1.0
C D:MET124 4.4 56.8 1.0
CB D:ASP127 4.5 58.3 1.0
CA D:ASP336 4.5 55.1 1.0
O D:HOH2107 4.5 59.8 1.0
OD2 D:ASP251 4.6 49.2 1.0
N D:ASP126 4.6 60.6 1.0
N D:ASP336 4.6 54.9 1.0
CA D:SER123 4.6 55.2 1.0
SD D:MET124 4.7 53.9 1.0
CA D:MET335 4.7 57.3 1.0
N D:LYS125 4.7 59.0 1.0
CA D:ASP127 4.8 59.9 1.0
C D:ASP126 4.8 61.7 1.0
CA D:ASP126 4.9 61.9 1.0
CB D:SER123 4.9 54.6 1.0
CB D:MET124 5.0 54.7 1.0

Manganese binding site 6 out of 6 in 7uko

Go back to Manganese Binding Sites List in 7uko
Manganese binding site 6 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2003

b:45.3
occ:1.00
 OD1 D:ASP217 2.1 42.7 1.0
O D:PRO219 2.2 41.4 1.0
OE1 D:GLU220 2.2 44.1 1.0
OD1 D:ASN215 2.2 44.4 1.0
OD2 D:ASP158 2.2 42.1 1.0
O D:ASP217 2.3 44.0 1.0
CG D:ASP217 3.1 42.7 1.0
CG D:ASN215 3.2 45.2 1.0
C D:PRO219 3.3 41.3 1.0
CG D:ASP158 3.3 41.9 1.0
CD D:GLU220 3.3 44.6 1.0
C D:ASP217 3.3 44.4 1.0
ND2 D:ASN215 3.6 45.5 1.0
OD2 D:ASP217 3.7 41.9 1.0
CB D:ASP158 3.8 42.7 1.0
CA D:GLU220 3.8 42.4 1.0
N D:GLU220 4.0 42.5 1.0
OE2 D:GLU220 4.0 45.6 1.0
CA D:ASP217 4.1 44.8 1.0
C D:ALA218 4.1 43.0 1.0
O D:ALA218 4.1 43.0 1.0
N D:ASP217 4.1 45.3 1.0
CB D:ASP217 4.2 43.8 1.0
N D:PRO219 4.2 42.7 1.0
NE2 D:HIS255 4.3 40.4 1.0
CG D:GLU220 4.3 44.0 1.0
N D:ALA218 4.3 44.1 1.0
OD1 D:ASP158 4.4 41.2 1.0
CA D:PRO219 4.4 41.8 1.0
CB D:GLU220 4.5 43.1 1.0
CB D:ASN215 4.5 46.0 1.0
CD2 D:HIS255 4.5 39.9 1.0
CA D:ALA218 4.7 44.1 1.0
C D:GLU220 4.9 41.6 1.0
CD D:PRO219 4.9 42.6 1.0

Reference:

J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with Sibrafiban (Mn) To Be Published.
Page generated: Sun Oct 6 10:53:05 2024

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