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Manganese in PDB 7uh8: Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca)

Protein crystallography data

The structure of Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca), PDB code: 7uh8 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) 49.25 / 2.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 258.69, 144.04, 104.81, 90, 90, 90
R / Rfree (%) 22.9 / 24.8

Other elements in 7uh8:

The structure of Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca) also contains other interesting chemical elements:

Calcium (Ca) 8 atoms
Chlorine (Cl) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca) (pdb code 7uh8). 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 Roxifiban (Mn/Ca), PDB code: 7uh8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7uh8

Go back to Manganese Binding Sites List in 7uh8
Manganese binding site 1 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca)


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 Roxifiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2001

b:51.8
occ:1.00
 O12 B:N9U2005 2.0 58.8 1.0
O B:HOH2104 2.1 55.3 1.0
OE2 B:GLU220 2.1 50.7 1.0
O B:HOH2117 2.1 53.5 1.0
OG B:SER121 2.2 54.6 1.0
OG B:SER123 2.2 60.7 1.0
CB B:SER121 2.9 54.4 1.0
CD B:GLU220 3.2 49.6 1.0
C10 B:N9U2005 3.3 58.8 1.0
CB B:SER123 3.5 62.1 1.0
CG B:GLU220 3.6 49.2 1.0
N B:SER123 4.1 62.2 1.0
OD2 B:ASP119 4.1 53.7 1.0
O11 B:N9U2005 4.2 58.8 1.0
O B:ALA218 4.2 49.0 1.0
CA B:SER121 4.2 55.0 1.0
C09 B:N9U2005 4.2 58.8 1.0
C13 B:N9U2005 4.3 58.8 1.0
OD1 B:ASP251 4.3 58.0 1.0
OE1 B:GLU220 4.3 49.1 1.0
OD1 B:ASP119 4.3 54.1 1.0
CA B:SER123 4.4 63.0 1.0
C B:SER121 4.4 56.6 1.0
ND2 B:ASN215 4.5 52.0 1.0
N B:TYR122 4.6 59.5 1.0
CB B:ALA252 4.6 54.8 1.0
CG B:ASP119 4.6 53.8 1.0
N B:SER121 4.9 54.6 1.0
O B:SER121 5.0 57.2 1.0

Manganese binding site 2 out of 6 in 7uh8

Go back to Manganese Binding Sites List in 7uh8
Manganese binding site 2 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca)


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 Roxifiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2002

b:79.4
occ:1.00
 O B:SER123 2.2 64.2 1.0
OD2 B:ASP251 2.2 60.7 1.0
O B:HOH2118 2.3 71.0 1.0
O B:HOH2185 2.3 79.8 1.0
CG B:ASP251 3.3 59.4 1.0
C B:SER123 3.3 63.3 1.0
CB B:ASP251 3.9 59.8 1.0
OD1 B:ASP127 4.0 77.4 1.0
OD2 B:ASP126 4.0 79.3 1.0
OD1 B:ASP126 4.1 77.9 1.0
CB B:SER123 4.1 62.1 1.0
CA B:SER123 4.2 63.0 1.0
OD1 B:ASP251 4.3 58.0 1.0
N B:MET124 4.3 65.4 1.0
CA B:MET124 4.5 65.5 1.0
CG B:ASP126 4.5 79.2 1.0
O B:MET335 4.7 83.1 1.0
SD B:MET124 4.7 63.2 1.0
CG B:ASP127 5.0 77.3 1.0

Manganese binding site 3 out of 6 in 7uh8

Go back to Manganese Binding Sites List in 7uh8
Manganese binding site 3 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca)


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 Roxifiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2003

b:51.1
occ:1.00
 O B:PRO219 2.0 48.0 1.0
OD1 B:ASP217 2.2 48.9 1.0
OD1 B:ASN215 2.2 50.6 1.0
OE1 B:GLU220 2.2 49.1 1.0
OD2 B:ASP158 2.2 48.0 1.0
O B:ASP217 2.2 50.3 1.0
CG B:ASP217 3.1 49.0 1.0
C B:PRO219 3.1 48.0 1.0
CG B:ASN215 3.2 51.3 1.0
CG B:ASP158 3.3 47.6 1.0
CD B:GLU220 3.3 49.6 1.0
C B:ASP217 3.3 51.1 1.0
ND2 B:ASN215 3.7 52.0 1.0
CA B:GLU220 3.7 47.4 1.0
OD2 B:ASP217 3.7 48.2 1.0
CB B:ASP158 3.7 48.2 1.0
N B:GLU220 3.8 47.8 1.0
OE2 B:GLU220 4.0 50.7 1.0
CA B:ASP217 4.1 51.3 1.0
N B:ASP217 4.1 51.5 1.0
C B:ALA218 4.1 49.0 1.0
NE2 B:HIS255 4.2 45.3 1.0
N B:PRO219 4.2 49.7 1.0
CB B:ASP217 4.2 50.2 1.0
O B:ALA218 4.2 49.0 1.0
CA B:PRO219 4.2 48.7 1.0
CG B:GLU220 4.3 49.2 1.0
OD1 B:ASP158 4.4 47.0 1.0
N B:ALA218 4.4 50.1 1.0
CD2 B:HIS255 4.4 44.8 1.0
CB B:GLU220 4.4 48.1 1.0
CB B:ASN215 4.5 51.7 1.0
CA B:ALA218 4.7 50.3 1.0
CD B:PRO219 4.8 49.7 1.0
C B:GLU220 4.8 46.5 1.0
CD1 B:TYR164 4.9 48.1 1.0

Manganese binding site 4 out of 6 in 7uh8

Go back to Manganese Binding Sites List in 7uh8
Manganese binding site 4 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca)


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 Roxifiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2001

b:75.9
occ:1.00
 OE2 D:GLU220 2.1 76.4 1.0
O12 D:N9U2006 2.1 79.5 1.0
O D:HOH2107 2.1 78.5 1.0
O D:HOH2130 2.2 80.4 1.0
OG D:SER121 2.2 76.7 1.0
CB D:SER121 3.0 76.2 1.0
CD D:GLU220 3.2 74.5 1.0
OG D:SER123 3.2 84.5 1.0
C10 D:N9U2006 3.3 79.5 1.0
CG D:GLU220 3.8 73.8 1.0
C13 D:N9U2006 4.0 79.5 1.0
C09 D:N9U2006 4.0 79.5 1.0
O D:ALA218 4.1 72.4 1.0
OE1 D:GLU220 4.2 73.3 1.0
O11 D:N9U2006 4.3 79.5 1.0
OD1 D:ASP251 4.3 81.3 1.0
CA D:SER121 4.4 77.7 1.0
CB D:ALA252 4.4 76.8 1.0
ND2 D:ASN215 4.4 77.7 1.0
OD2 D:ASP119 4.4 73.2 1.0
CB D:SER123 4.5 87.3 1.0
N D:TYR122 4.6 82.7 1.0
OD1 D:ASP119 4.6 74.5 1.0
N D:SER123 4.6 86.9 1.0
C D:SER121 4.7 80.3 1.0
CG D:ASP119 5.0 73.9 1.0

Manganese binding site 5 out of 6 in 7uh8

Go back to Manganese Binding Sites List in 7uh8
Manganese binding site 5 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca)


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 Roxifiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2002

b:98.7
occ:1.00
 OD1 D:ASP126 2.2 94.6 1.0
OD1 D:ASP127 2.2 93.0 1.0
O D:SER123 2.2 90.0 1.0
O D:HOH2118 2.3 93.6 1.0
O D:MET335 2.7 96.0 1.0
CG D:ASP126 3.1 97.3 1.0
OD2 D:ASP126 3.2 98.5 1.0
C D:SER123 3.4 88.7 1.0
CG D:ASP127 3.4 92.3 1.0
CA D:MET124 3.7 88.8 1.0
C D:MET335 3.9 96.7 1.0
N D:MET124 4.0 88.4 1.0
OD2 D:ASP127 4.0 91.6 1.0
OD2 D:ASP251 4.0 85.4 1.0
N D:ASP127 4.2 96.5 1.0
C D:MET124 4.3 90.9 1.0
CB D:ASP126 4.5 99.5 1.0
N D:ASP126 4.5 95.7 1.0
CA D:SER123 4.5 88.4 1.0
N D:LYS125 4.5 91.1 1.0
CB D:ASP127 4.6 92.6 1.0
CA D:MET335 4.7 96.3 1.0
SD D:MET124 4.7 84.9 1.0
N D:ASP336 4.8 92.0 1.0
CA D:ASP336 4.8 92.5 1.0
CA D:ASP126 4.9 98.0 1.0
C D:ASP126 4.9 97.0 1.0
CB D:MET124 4.9 86.4 1.0
CB D:SER123 4.9 87.3 1.0
CA D:ASP127 4.9 95.5 1.0
O D:MET124 5.0 91.2 1.0
CB D:MET335 5.0 98.3 1.0

Manganese binding site 6 out of 6 in 7uh8

Go back to Manganese Binding Sites List in 7uh8
Manganese binding site 6 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Roxifiban (Mn/Ca)


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 Roxifiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2003

b:73.0
occ:1.00
 O D:PRO219 2.0 69.9 1.0
OD1 D:ASP217 2.2 70.6 1.0
OD2 D:ASP158 2.2 69.1 1.0
OE1 D:GLU220 2.2 73.3 1.0
OD1 D:ASN215 2.2 75.0 1.0
O D:ASP217 2.2 73.6 1.0
CG D:ASP217 3.1 70.3 1.0
C D:PRO219 3.1 70.1 1.0
CG D:ASN215 3.2 76.3 1.0
C D:ASP217 3.3 74.3 1.0
CG D:ASP158 3.3 68.3 1.0
CD D:GLU220 3.4 74.5 1.0
OD2 D:ASP217 3.7 68.7 1.0
ND2 D:ASN215 3.7 77.7 1.0
CA D:GLU220 3.8 70.1 1.0
N D:GLU220 3.9 70.4 1.0
CB D:ASP158 4.0 69.5 1.0
C D:ALA218 4.0 72.1 1.0
CA D:ASP217 4.0 74.1 1.0
N D:PRO219 4.0 72.4 1.0
O D:ALA218 4.1 72.4 1.0
N D:ASP217 4.1 74.5 1.0
CB D:ASP217 4.2 72.0 1.0
NE2 D:HIS255 4.2 67.0 1.0
CA D:PRO219 4.2 71.0 1.0
OE2 D:GLU220 4.2 76.4 1.0
N D:ALA218 4.3 73.2 1.0
CG D:GLU220 4.4 73.8 1.0
OD1 D:ASP158 4.4 66.8 1.0
CB D:ASN215 4.4 76.6 1.0
CB D:GLU220 4.5 71.9 1.0
CD2 D:HIS255 4.6 66.5 1.0
CA D:ALA218 4.6 73.9 1.0
CD D:PRO219 4.6 71.8 1.0
C D:GLU220 4.9 68.5 1.0

Reference:

J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with Roxifiban To Be Published.
Page generated: Sun Oct 6 10:51:38 2024

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