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Manganese in PDB 7u9f: Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+

Protein crystallography data

The structure of Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+, PDB code: 7u9f 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) 46.09 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 259.397, 144.292, 104.923, 90, 90, 90
R / Rfree (%) 21.7 / 23.7

Other elements in 7u9f:

The structure of Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+ also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+ (pdb code 7u9f). 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 Bms Compound 4 in MN2+, PDB code: 7u9f:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7u9f

Go back to Manganese Binding Sites List in 7u9f
Manganese binding site 1 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2001

b:36.0
occ:1.00
 OE2 B:GLU220 2.1 39.6 1.0
O B:HOH2115 2.2 42.7 1.0
O B:HOH2138 2.2 33.3 1.0
O2 B:I7R2005 2.2 46.7 1.0
O B:HOH2179 2.2 36.9 1.0
OG B:SER121 2.3 41.0 1.0
CB B:SER121 2.8 41.2 1.0
CD B:GLU220 3.2 38.6 1.0
C22 B:I7R2005 3.3 46.7 1.0
CG B:GLU220 3.7 38.1 1.0
O3 B:I7R2005 3.9 46.7 1.0
CA B:SER121 4.2 41.8 1.0
O B:HOH2182 4.2 43.9 1.0
ND2 B:ASN215 4.3 41.2 1.0
OG B:SER123 4.3 44.5 1.0
OE1 B:GLU220 4.3 38.1 1.0
OD2 B:ASP119 4.4 38.1 1.0
O B:ALA218 4.5 37.5 1.0
OD1 B:ASP119 4.5 38.5 1.0
C21 B:I7R2005 4.5 46.7 1.0
O B:HOH2308 4.6 41.1 1.0
N6 B:I7R2005 4.6 46.7 1.0
OD1 B:ASP251 4.6 40.9 1.0
C B:SER121 4.6 43.2 1.0
N B:TYR122 4.6 45.0 1.0
CB B:ALA252 4.6 40.1 1.0
C19 B:I7R2005 4.7 46.7 1.0
CG B:ASP119 4.9 38.3 1.0
N B:SER121 5.0 41.1 1.0

Manganese binding site 2 out of 6 in 7u9f

Go back to Manganese Binding Sites List in 7u9f
Manganese binding site 2 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2002

b:64.4
occ:1.00
 OD1 B:ASP126 2.2 51.5 0.6
OD1 B:ASP127 2.2 50.6 1.0
OD2 B:ASP126 2.2 52.9 0.6
O B:SER123 2.2 47.1 1.0
O B:HOH2190 2.3 50.8 1.0
O B:HOH2156 2.3 48.5 1.0
CG B:ASP126 2.4 52.6 0.6
O B:MET335 2.8 52.9 1.0
CG B:ASP127 3.4 50.0 1.0
C B:SER123 3.4 46.2 1.0
CA B:MET124 3.8 47.7 1.0
O B:HOH2101 3.8 49.9 1.0
CB B:ASP126 3.9 54.0 0.6
O B:HOH2132 4.0 50.8 1.0
C B:MET335 4.0 53.5 1.0
N B:MET124 4.0 47.8 1.0
OD2 B:ASP127 4.0 49.9 1.0
N B:ASP127 4.1 52.1 1.0
CB B:ASP126 4.1 54.2 0.5
C B:MET124 4.3 48.7 1.0
N B:ASP126 4.3 51.9 0.5
N B:ASP126 4.3 51.9 0.6
CB B:ASP127 4.5 49.8 1.0
CA B:ASP336 4.5 50.6 1.0
CA B:ASP126 4.5 53.0 0.6
CA B:SER123 4.6 46.4 1.0
OD2 B:ASP251 4.6 43.2 1.0
CA B:ASP126 4.6 53.0 0.5
N B:LYS125 4.6 50.5 1.0
C B:ASP126 4.7 52.1 0.5
C B:ASP126 4.7 52.1 0.6
N B:ASP336 4.7 50.9 1.0
SD B:MET124 4.7 45.6 1.0
CA B:ASP127 4.8 51.3 1.0
OD2 B:ASP126 4.8 56.2 0.5
O B:MET124 4.9 48.7 1.0
CB B:SER123 4.9 46.0 1.0
CG B:ASP126 4.9 55.6 0.5
CB B:MET124 5.0 46.1 1.0

Manganese binding site 3 out of 6 in 7u9f

Go back to Manganese Binding Sites List in 7u9f
Manganese binding site 3 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2003

b:42.8
occ:1.00
 O B:PRO219 2.1 36.0 1.0
OD1 B:ASP217 2.1 37.0 1.0
OD1 B:ASN215 2.2 40.1 1.0
OE1 B:GLU220 2.2 38.1 1.0
OD2 B:ASP158 2.2 37.5 1.0
O B:ASP217 2.2 38.0 1.0
CG B:ASP217 3.1 37.0 1.0
C B:PRO219 3.2 35.9 1.0
CD B:GLU220 3.3 38.6 1.0
CG B:ASP158 3.3 37.1 1.0
C B:ASP217 3.3 38.7 1.0
CG B:ASN215 3.3 40.8 1.0
OD2 B:ASP217 3.6 36.3 1.0
CB B:ASP158 3.8 37.7 1.0
CA B:GLU220 3.9 36.5 1.0
ND2 B:ASN215 3.9 41.2 1.0
N B:GLU220 4.0 36.8 1.0
CA B:ASP217 4.0 39.2 1.0
OE2 B:GLU220 4.0 39.6 1.0
N B:ASP217 4.0 39.5 1.0
CB B:ASP217 4.1 38.2 1.0
C B:ALA218 4.1 37.7 1.0
N B:PRO219 4.2 37.5 1.0
NE2 B:HIS255 4.2 35.3 1.0
O B:ALA218 4.3 37.5 1.0
CG B:GLU220 4.3 38.1 1.0
CA B:PRO219 4.3 36.5 1.0
OD1 B:ASP158 4.3 36.5 1.0
N B:ALA218 4.4 38.9 1.0
CD2 B:HIS255 4.5 34.8 1.0
CB B:GLU220 4.5 37.1 1.0
CB B:ASN215 4.5 41.4 1.0
CA B:ALA218 4.7 38.9 1.0
CD B:PRO219 4.9 37.6 1.0
CB B:TYR164 4.9 37.2 1.0
CD1 B:TYR164 4.9 36.2 1.0

Manganese binding site 4 out of 6 in 7u9f

Go back to Manganese Binding Sites List in 7u9f
Manganese binding site 4 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2001

b:64.7
occ:1.00
 OE2 D:GLU220 2.1 65.6 1.0
O D:HOH2151 2.2 66.0 1.0
O2 D:I7R2006 2.2 69.6 1.0
O D:HOH2175 2.2 61.6 1.0
O D:HOH2116 2.2 64.8 1.0
OG D:SER121 2.2 64.0 1.0
CB D:SER121 2.6 64.3 1.0
CD D:GLU220 3.2 63.9 1.0
C22 D:I7R2006 3.4 69.6 1.0
CG D:GLU220 3.9 62.9 1.0
O3 D:I7R2006 4.0 69.6 1.0
OG D:SER123 4.0 70.1 1.0
CA D:SER121 4.1 65.8 1.0
OE1 D:GLU220 4.1 63.0 1.0
OD2 D:ASP119 4.1 62.4 1.0
ND2 D:ASN215 4.2 65.6 1.0
O D:HOH2191 4.3 65.2 1.0
OD1 D:ASP119 4.4 63.5 1.0
N6 D:I7R2006 4.4 69.6 1.0
C21 D:I7R2006 4.5 69.6 1.0
C D:SER121 4.5 68.4 1.0
N D:TYR122 4.5 69.7 1.0
C19 D:I7R2006 4.6 69.6 1.0
OD1 D:ASP251 4.6 67.7 1.0
O D:ALA218 4.6 62.2 1.0
CG D:ASP119 4.7 62.8 1.0
CB D:ALA252 4.8 64.0 1.0
N D:SER121 4.8 65.1 1.0
O D:HOH2231 4.9 63.9 1.0
N D:SER123 4.9 72.6 1.0

Manganese binding site 5 out of 6 in 7u9f

Go back to Manganese Binding Sites List in 7u9f
Manganese binding site 5 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2002

b:74.0
occ:1.00
 OD1 D:ASP126 2.2 78.7 1.0
OD1 D:ASP127 2.2 75.2 1.0
O D:SER123 2.2 75.1 1.0
O D:HOH2117 2.3 72.9 1.0
O D:HOH2204 2.3 72.2 1.0
O D:MET335 2.5 76.9 1.0
CG D:ASP126 3.0 81.2 1.0
OD2 D:ASP126 3.2 82.1 1.0
CG D:ASP127 3.3 74.4 1.0
C D:SER123 3.4 73.8 1.0
C D:MET335 3.7 77.6 1.0
OD2 D:ASP127 3.8 73.4 1.0
CA D:MET124 3.9 74.5 1.0
O D:HOH2198 4.0 70.5 1.0
O D:HOH2124 4.1 72.5 1.0
N D:MET124 4.1 74.4 1.0
N D:ASP127 4.3 78.8 1.0
OD2 D:ASP251 4.3 71.7 1.0
CB D:ASP126 4.5 83.4 1.0
C D:MET124 4.5 76.7 1.0
CA D:SER123 4.5 73.8 1.0
CB D:ASP127 4.6 74.7 1.0
N D:ASP126 4.6 80.2 1.0
N D:ASP336 4.6 78.8 1.0
CA D:ASP336 4.6 79.4 1.0
CA D:MET335 4.6 77.2 1.0
SD D:MET124 4.6 70.4 1.0
N D:LYS125 4.7 75.3 1.0
CB D:SER123 4.8 72.7 1.0
C D:ASP126 4.9 80.7 1.0
CA D:ASP126 4.9 82.1 1.0
CB D:MET335 4.9 79.3 1.0
CA D:ASP127 4.9 77.5 1.0
CE D:MET335 5.0 75.9 1.0

Manganese binding site 6 out of 6 in 7u9f

Go back to Manganese Binding Sites List in 7u9f
Manganese binding site 6 out of 6 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2003

b:62.5
occ:1.00
 OD1 D:ASP217 2.1 60.3 1.0
OE1 D:GLU220 2.2 63.0 1.0
OD1 D:ASN215 2.2 62.6 1.0
OD2 D:ASP158 2.2 59.9 1.0
O D:ASP217 2.2 63.1 1.0
O D:PRO219 2.2 59.6 1.0
CG D:ASP217 3.0 59.9 1.0
C D:ASP217 3.2 63.6 1.0
C D:PRO219 3.3 59.6 1.0
CG D:ASN215 3.3 64.3 1.0
CG D:ASP158 3.3 59.3 1.0
CD D:GLU220 3.4 63.9 1.0
OD2 D:ASP217 3.5 58.3 1.0
ND2 D:ASN215 3.8 65.6 1.0
CA D:GLU220 3.9 59.5 1.0
CB D:ASP158 3.9 60.7 1.0
CA D:ASP217 3.9 63.7 1.0
N D:GLU220 4.0 59.6 1.0
N D:ASP217 4.0 64.6 1.0
CB D:ASP217 4.0 61.5 1.0
C D:ALA218 4.0 62.0 1.0
O D:ALA218 4.1 62.2 1.0
OE2 D:GLU220 4.1 65.6 1.0
N D:PRO219 4.1 61.7 1.0
NE2 D:HIS255 4.2 58.1 1.0
N D:ALA218 4.2 63.6 1.0
CA D:PRO219 4.3 60.1 1.0
OD1 D:ASP158 4.4 57.8 1.0
CG D:GLU220 4.4 62.9 1.0
CD2 D:HIS255 4.5 57.5 1.0
CB D:ASN215 4.5 65.2 1.0
CA D:ALA218 4.6 63.9 1.0
CB D:GLU220 4.6 61.0 1.0
CD D:PRO219 4.8 61.3 1.0
C D:GLU220 5.0 57.8 1.0

Reference:

J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with Bms Compound 4 in MN2+. To Be Published.
Page generated: Sun Oct 6 10:46:51 2024

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