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Manganese in PDB 7ukp: Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog

Protein crystallography data

The structure of Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog, PDB code: 7ukp 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) 48.25 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 259.322, 144.495, 104.848, 90, 90, 90
R / Rfree (%) 21.9 / 24.1

Other elements in 7ukp:

The structure of Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog 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 A Gantofiban Analog (pdb code 7ukp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog, PDB code: 7ukp:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7ukp

Go back to Manganese Binding Sites List in 7ukp
Manganese binding site 1 out of 4 in the Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog


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 A Gantofiban Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2001

b:66.7
occ:1.00
O B:HOH2120 2.0 65.5 1.0
O4 B:NJ92004 2.1 73.5 1.0
OG B:SER123 2.1 69.8 1.0
OE2 B:GLU220 2.2 65.9 1.0
OG B:SER121 2.2 66.8 1.0
O B:HOH2109 2.2 62.6 1.0
CB B:SER121 2.7 67.4 1.0
C18 B:NJ92004 3.2 73.5 1.0
CD B:GLU220 3.3 64.5 1.0
CB B:SER123 3.4 71.4 1.0
CG B:GLU220 3.7 63.7 1.0
O3 B:NJ92004 3.9 73.5 1.0
N B:SER123 4.1 72.1 1.0
CA B:SER121 4.1 68.2 1.0
C8 B:NJ92004 4.1 73.5 1.0
OD2 B:ASP119 4.2 65.0 1.0
OD1 B:ASP251 4.2 68.9 1.0
OD1 B:ASP119 4.3 65.5 1.0
C17 B:NJ92004 4.3 73.5 1.0
O B:ALA218 4.3 63.7 1.0
CA B:SER123 4.4 72.8 1.0
C B:SER121 4.4 70.2 1.0
OE1 B:GLU220 4.4 64.1 1.0
ND2 B:ASN215 4.5 66.2 1.0
CG B:ASP119 4.6 65.2 1.0
N B:TYR122 4.7 71.2 1.0
CB B:ALA252 4.7 67.3 1.0
N B:SER121 4.8 67.4 1.0
O B:SER121 4.9 70.8 1.0

Manganese binding site 2 out of 4 in 7ukp

Go back to Manganese Binding Sites List in 7ukp
Manganese binding site 2 out of 4 in the Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog


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 A Gantofiban Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2002

b:65.5
occ:1.00
O B:PRO219 2.0 62.7 1.0
OD1 B:ASP217 2.2 63.5 1.0
OD1 B:ASN215 2.2 64.8 1.0
OD2 B:ASP158 2.2 63.2 1.0
OE1 B:GLU220 2.2 64.1 1.0
O B:ASP217 2.2 64.8 1.0
CG B:ASP217 3.1 63.6 1.0
C B:PRO219 3.2 62.4 1.0
CG B:ASN215 3.2 65.7 1.0
CG B:ASP158 3.3 62.8 1.0
CD B:GLU220 3.3 64.5 1.0
C B:ASP217 3.4 65.8 1.0
OD2 B:ASP217 3.7 62.6 1.0
ND2 B:ASN215 3.7 66.2 1.0
CB B:ASP158 3.8 63.6 1.0
CA B:GLU220 3.8 61.6 1.0
N B:GLU220 3.9 62.0 1.0
CA B:ASP217 4.0 66.4 1.0
N B:ASP217 4.1 67.0 1.0
OE2 B:GLU220 4.1 65.9 1.0
CB B:ASP217 4.1 65.2 1.0
C B:ALA218 4.2 63.9 1.0
N B:PRO219 4.2 64.4 1.0
NE2 B:HIS255 4.2 60.1 1.0
O B:ALA218 4.2 63.7 1.0
CA B:PRO219 4.3 63.0 1.0
CG B:GLU220 4.3 63.7 1.0
OD1 B:ASP158 4.4 62.0 1.0
N B:ALA218 4.4 65.8 1.0
CB B:GLU220 4.5 62.3 1.0
CB B:ASN215 4.5 66.6 1.0
CD2 B:HIS255 4.5 59.3 1.0
CA B:ALA218 4.8 65.7 1.0
CD B:PRO219 4.9 64.7 1.0
C B:GLU220 4.9 60.5 1.0
CD1 B:TYR164 4.9 63.3 1.0

Manganese binding site 3 out of 4 in 7ukp

Go back to Manganese Binding Sites List in 7ukp
Manganese binding site 3 out of 4 in the Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog


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 A Gantofiban Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2001

b:98.4
occ:1.00
OE2 D:GLU220 2.1 99.5 1.0
O4 D:NJ92004 2.2 100.1 1.0
O D:HOH2106 2.2 102.1 1.0
O D:HOH2113 2.2 99.4 1.0
OG D:SER121 2.2 100.0 1.0
OG D:SER123 2.4 105.1 1.0
CB D:SER121 2.8 99.2 1.0
C18 D:NJ92004 3.2 100.1 1.0
CD D:GLU220 3.3 97.5 1.0
C8 D:NJ92004 3.5 100.1 1.0
CB D:SER123 3.9 108.0 1.0
CG D:GLU220 3.9 97.2 1.0
C17 D:NJ92004 3.9 100.1 1.0
O3 D:NJ92004 4.1 100.1 1.0
CA D:SER121 4.1 100.9 1.0
N D:SER123 4.2 108.0 1.0
OE1 D:GLU220 4.2 95.8 1.0
OD2 D:ASP119 4.3 98.0 1.0
C D:SER121 4.4 103.7 1.0
ND2 D:ASN215 4.4 98.9 1.0
OD1 D:ASP251 4.4 104.8 1.0
N D:TYR122 4.5 106.3 1.0
O D:ALA218 4.5 96.7 1.0
OD1 D:ASP119 4.5 98.3 1.0
CA D:SER123 4.6 109.7 1.0
N2 D:NJ92004 4.8 100.1 1.0
CB D:ALA252 4.8 99.4 1.0
CG D:ASP119 4.8 98.5 1.0
O D:SER121 4.9 105.5 1.0
N D:SER121 5.0 100.9 1.0

Manganese binding site 4 out of 4 in 7ukp

Go back to Manganese Binding Sites List in 7ukp
Manganese binding site 4 out of 4 in the Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog


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 A Gantofiban Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2002

b:98.1
occ:1.00
OD1 D:ASP217 2.1 92.6 1.0
OD2 D:ASP158 2.2 91.0 1.0
OD1 D:ASN215 2.2 95.7 1.0
O D:PRO219 2.2 92.2 1.0
OE1 D:GLU220 2.2 95.8 1.0
O D:ASP217 2.2 96.3 1.0
CG D:ASN215 3.1 97.1 1.0
CG D:ASP217 3.1 92.2 1.0
C D:PRO219 3.3 92.8 1.0
CG D:ASP158 3.3 90.2 1.0
CD D:GLU220 3.3 97.5 1.0
C D:ASP217 3.4 96.7 1.0
ND2 D:ASN215 3.5 98.9 1.0
OD2 D:ASP217 3.8 90.8 1.0
CA D:GLU220 3.8 93.2 1.0
CB D:ASP158 3.9 91.3 1.0
N D:GLU220 4.0 93.5 1.0
CA D:ASP217 4.1 95.9 1.0
N D:ASP217 4.1 96.1 1.0
OE2 D:GLU220 4.1 99.5 1.0
C D:ALA218 4.1 96.0 1.0
O D:ALA218 4.2 96.7 1.0
CB D:ASP217 4.2 93.5 1.0
N D:PRO219 4.2 94.8 1.0
CG D:GLU220 4.3 97.2 1.0
CB D:ASN215 4.3 97.0 1.0
OD1 D:ASP158 4.3 88.8 1.0
NE2 D:HIS255 4.4 87.9 1.0
CA D:PRO219 4.4 93.6 1.0
N D:ALA218 4.4 96.3 1.0
CB D:GLU220 4.5 95.2 1.0
CA D:ALA218 4.7 97.5 1.0
CD2 D:HIS255 4.7 87.7 1.0
CD D:PRO219 4.9 93.9 1.0
C D:GLU220 4.9 91.6 1.0

Reference:

J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with A Gantofiban Analog To Be Published.
Page generated: Sun Oct 6 10:54:01 2024

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