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Manganese in PDB 7ufh: Integrin ALAPHIIBBETA3 Complex with Fradafiban (Mn/Ca)

Protein crystallography data

The structure of Integrin ALAPHIIBBETA3 Complex with Fradafiban (Mn/Ca), PDB code: 7ufh 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) 42.05 / 3.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 258.581, 144.453, 104.764, 90, 90, 90
R / Rfree (%) 22.5 / 24.5

Other elements in 7ufh:

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

Calcium (Ca) 8 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 6 in 7ufh

Go back to Manganese Binding Sites List in 7ufh
Manganese binding site 1 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Fradafiban (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 Fradafiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2001

b:62.5
occ:1.00
 O27 B:MWX2005 2.1 68.7 1.0
O B:HOH2112 2.1 60.8 1.0
OE2 B:GLU220 2.1 59.9 1.0
O B:HOH2114 2.2 63.4 1.0
OG B:SER123 2.2 67.2 1.0
OG B:SER121 2.2 62.9 1.0
CB B:SER121 2.9 63.0 1.0
CD B:GLU220 3.2 58.7 1.0
C25 B:MWX2005 3.2 68.7 1.0
CB B:SER123 3.5 69.0 1.0
CG B:GLU220 3.6 58.0 1.0
O26 B:MWX2005 4.0 68.7 1.0
OD2 B:ASP119 4.1 61.1 1.0
N B:SER123 4.2 69.4 1.0
C02 B:MWX2005 4.2 68.7 1.0
CA B:SER121 4.2 63.8 1.0
C24 B:MWX2005 4.2 68.7 1.0
OD1 B:ASP251 4.2 66.2 1.0
OE1 B:GLU220 4.3 58.2 1.0
O B:ALA218 4.3 58.1 1.0
C B:SER121 4.4 65.5 1.0
CA B:SER123 4.5 70.1 1.0
OD1 B:ASP119 4.5 61.3 1.0
ND2 B:ASN215 4.6 62.2 1.0
CG B:ASP119 4.7 61.1 1.0
CB B:ALA252 4.7 64.4 1.0
N B:TYR122 4.7 67.0 1.0
O B:SER121 4.8 66.0 1.0
C01 B:MWX2005 4.9 68.7 1.0
N B:SER121 5.0 63.1 1.0

Manganese binding site 2 out of 6 in 7ufh

Go back to Manganese Binding Sites List in 7ufh
Manganese binding site 2 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Fradafiban (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 Fradafiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2002

b:104.5
occ:1.00
 O B:SER123 2.2 70.9 1.0
OD2 B:ASP251 2.2 68.7 1.0
CG B:ASP251 3.4 67.5 1.0
C B:SER123 3.4 70.1 1.0
OD1 B:ASP127 3.6 80.8 1.0
O B:MET335 3.9 87.4 1.0
CB B:ASP251 4.0 67.8 1.0
OD1 B:ASP126 4.1 80.5 0.4
N B:MET124 4.2 71.1 1.0
CA B:MET124 4.3 71.0 1.0
CA B:SER123 4.3 70.1 1.0
CB B:SER123 4.3 69.0 1.0
SD B:MET124 4.4 68.2 1.0
OD1 B:ASP251 4.4 66.2 1.0
CG B:ASP127 4.7 80.6 1.0
CG B:MET124 5.0 67.9 1.0
C B:MET335 5.0 88.0 1.0
OD2 B:ASP127 5.0 80.8 1.0

Manganese binding site 3 out of 6 in 7ufh

Go back to Manganese Binding Sites List in 7ufh
Manganese binding site 3 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Fradafiban (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 Fradafiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2003

b:61.2
occ:1.00
 O B:PRO219 1.9 56.7 1.0
OD1 B:ASP217 2.2 59.1 1.0
OD1 B:ASN215 2.2 60.7 1.0
OE1 B:GLU220 2.2 58.2 1.0
OD2 B:ASP158 2.2 57.0 1.0
O B:ASP217 2.2 60.2 1.0
CG B:ASP217 2.9 59.0 1.0
C B:PRO219 3.0 56.5 1.0
CG B:ASN215 3.3 61.6 1.0
CD B:GLU220 3.3 58.7 1.0
OD2 B:ASP217 3.3 58.1 1.0
C B:ASP217 3.3 61.1 1.0
CG B:ASP158 3.3 56.5 1.0
CA B:GLU220 3.6 56.1 1.0
N B:GLU220 3.7 56.5 1.0
ND2 B:ASN215 3.8 62.2 1.0
CB B:ASP217 3.9 60.4 1.0
CA B:ASP217 4.0 61.5 1.0
CB B:ASP158 4.0 57.2 1.0
OE2 B:GLU220 4.0 59.9 1.0
N B:PRO219 4.1 58.5 1.0
N B:ASP217 4.1 62.0 1.0
C B:ALA218 4.1 58.3 1.0
CA B:PRO219 4.1 57.2 1.0
NE2 B:HIS255 4.2 54.3 1.0
CG B:GLU220 4.2 58.0 1.0
O B:ALA218 4.3 58.1 1.0
CB B:GLU220 4.3 56.7 1.0
OD1 B:ASP158 4.3 55.8 1.0
N B:ALA218 4.4 59.9 1.0
CD2 B:HIS255 4.5 53.5 1.0
CB B:ASN215 4.5 62.3 1.0
CA B:ALA218 4.7 59.8 1.0
CD B:PRO219 4.7 58.7 1.0
C B:GLU220 4.8 55.2 1.0
CD1 B:TYR164 4.9 56.5 1.0
CB B:PRO219 4.9 56.7 1.0
N B:GLY221 4.9 56.2 1.0

Manganese binding site 4 out of 6 in 7ufh

Go back to Manganese Binding Sites List in 7ufh
Manganese binding site 4 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Fradafiban (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 Fradafiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2001

b:97.4
occ:1.00
 O27 D:MWX2005 2.1 93.0 1.0
OE2 D:GLU220 2.1 93.3 1.0
OG D:SER121 2.1 95.8 1.0
O D:HOH2104 2.1 98.2 1.0
O D:HOH2109 2.2 91.0 1.0
CB D:SER121 2.6 95.0 1.0
C25 D:MWX2005 3.2 93.0 1.0
CD D:GLU220 3.3 91.6 1.0
OG D:SER123 3.4 103.8 1.0
CB D:SER123 3.8 105.1 1.0
O26 D:MWX2005 3.9 93.0 1.0
CG D:GLU220 3.9 91.6 1.0
CA D:SER121 4.0 96.2 1.0
N D:SER123 4.1 105.0 1.0
OD1 D:ASP119 4.1 94.9 1.0
OD2 D:ASP119 4.1 94.5 1.0
OD1 D:ASP251 4.3 101.7 1.0
N D:TYR122 4.3 100.6 1.0
C24 D:MWX2005 4.3 93.0 1.0
OE1 D:GLU220 4.3 90.1 1.0
C D:SER121 4.3 98.6 1.0
C02 D:MWX2005 4.3 93.0 1.0
ND2 D:ASN215 4.5 93.8 1.0
CG D:ASP119 4.5 94.9 1.0
CA D:SER123 4.6 106.5 1.0
O D:ALA218 4.7 88.6 1.0
N D:SER121 4.8 96.4 1.0

Manganese binding site 5 out of 6 in 7ufh

Go back to Manganese Binding Sites List in 7ufh
Manganese binding site 5 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Fradafiban (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 Fradafiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2002

b:129.5
occ:1.00
 OD1 D:ASP127 2.2 113.7 1.0
OD1 D:ASP126 2.2 117.8 1.0
O D:SER123 2.2 109.0 1.0
O D:HOH2112 2.6 111.5 1.0
O D:MET335 3.0 120.1 1.0
CG D:ASP126 3.2 120.3 1.0
C D:SER123 3.3 107.6 1.0
CG D:ASP127 3.4 113.2 1.0
OD2 D:ASP126 3.5 121.6 1.0
CA D:MET124 3.6 108.2 1.0
N D:MET124 3.8 107.1 1.0
OD2 D:ASP127 3.9 112.5 1.0
C D:MET335 4.2 121.3 1.0
N D:ASP127 4.3 116.8 1.0
C D:MET124 4.3 109.8 1.0
N D:LYS125 4.5 111.3 1.0
CB D:ASP127 4.5 113.5 1.0
CA D:SER123 4.5 106.5 1.0
N D:ASP126 4.6 118.5 1.0
CB D:MET124 4.6 106.3 1.0
CB D:ASP126 4.6 122.3 1.0
SD D:MET124 4.6 105.4 1.0
OD2 D:ASP251 4.7 104.7 1.0
CG D:MET124 4.8 104.5 1.0
CA D:ASP336 4.9 115.5 1.0
C D:ASP126 4.9 120.5 1.0
CA D:ASP126 4.9 121.0 1.0
CA D:ASP127 5.0 116.3 1.0
N D:ASP336 5.0 115.1 1.0

Manganese binding site 6 out of 6 in 7ufh

Go back to Manganese Binding Sites List in 7ufh
Manganese binding site 6 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Fradafiban (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 Fradafiban (Mn/Ca) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2003

b:88.7
occ:1.00
 O D:PRO219 2.1 86.7 1.0
OD1 D:ASP217 2.1 86.5 1.0
OE1 D:GLU220 2.2 90.1 1.0
OD2 D:ASP158 2.2 84.6 1.0
O D:ASP217 2.2 89.9 1.0
OD1 D:ASN215 2.2 91.1 1.0
CG D:ASP217 2.8 86.0 1.0
C D:ASP217 3.2 90.0 1.0
C D:PRO219 3.2 87.3 1.0
CG D:ASN215 3.2 92.2 1.0
OD2 D:ASP217 3.3 84.9 1.0
CG D:ASP158 3.4 83.9 1.0
CD D:GLU220 3.4 91.6 1.0
ND2 D:ASN215 3.8 93.8 1.0
CA D:ASP217 3.9 88.9 1.0
CA D:GLU220 3.9 88.0 1.0
CB D:ASP217 3.9 86.8 1.0
N D:ASP217 3.9 89.2 1.0
N D:GLU220 4.0 88.2 1.0
CB D:ASP158 4.0 84.8 1.0
C D:ALA218 4.1 87.8 1.0
N D:PRO219 4.1 88.7 1.0
O D:ALA218 4.1 88.6 1.0
OE2 D:GLU220 4.1 93.3 1.0
N D:ALA218 4.3 87.6 1.0
CA D:PRO219 4.3 87.9 1.0
OD1 D:ASP158 4.4 82.7 1.0
CG D:GLU220 4.4 91.6 1.0
CB D:ASN215 4.5 92.0 1.0
NE2 D:HIS255 4.5 82.2 1.0
CB D:GLU220 4.6 89.9 1.0
CA D:ALA218 4.6 88.8 1.0
CD D:PRO219 4.8 87.7 1.0
CD2 D:HIS255 4.8 82.2 1.0

Reference:

J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with BMS4-1 To Be Published.
Page generated: Sun Oct 6 10:50:45 2024

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