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Magnesium in PDB 3fcu: Structure of Headpiece of Integrin AIIBB3 in Open Conformation

Protein crystallography data

The structure of Structure of Headpiece of Integrin AIIBB3 in Open Conformation, PDB code: 3fcu was solved by J.Zhu, B.-H.Luo, T.Xiao, C.Zhang, N.Nishida, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.59 / 2.90
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 332.093, 332.093, 88.288, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 19.7

Other elements in 3fcu:

The structure of Structure of Headpiece of Integrin AIIBB3 in Open Conformation also contains other interesting chemical elements:

Arsenic (As) 3 atoms
Calcium (Ca) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation (pdb code 3fcu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation, PDB code: 3fcu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3fcu

Go back to Magnesium Binding Sites List in 3fcu
Magnesium binding site 1 out of 6 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg458

b:61.5
occ:1.00
 O C:HOH472 2.0 47.3 1.0
O C:HOH470 2.0 78.5 1.0
O C:HOH468 2.2 58.4 1.0
O C:HOH467 2.4 54.3 1.0
O C:HOH469 2.5 48.3 1.0
O A:SER99 3.4 43.8 1.0
O C:HOH471 3.4 58.1 1.0
OD2 A:ASP24 3.8 47.2 1.0
OD1 A:ASP24 4.2 49.1 1.0
CG A:ASP24 4.4 48.5 1.0
O A:PHE25 4.5 50.9 1.0
C A:SER99 4.5 43.2 1.0

Magnesium binding site 2 out of 6 in 3fcu

Go back to Magnesium Binding Sites List in 3fcu
Magnesium binding site 2 out of 6 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:39.7
occ:1.00
 O1 B:CAC462 1.7 0.5 1.0
O C:HOH464 1.9 29.2 1.0
OE1 B:GLU220 2.0 45.4 1.0
OG B:SER123 2.1 51.9 1.0
O C:HOH463 2.2 27.0 1.0
OG B:SER121 2.3 51.0 1.0
AS B:CAC462 3.1 0.6 1.0
CB B:SER123 3.1 52.8 1.0
CD B:GLU220 3.2 49.3 1.0
CB B:SER121 3.3 51.8 1.0
C1 B:CAC462 3.4 0.8 1.0
N B:SER123 3.8 52.8 1.0
CG B:GLU220 3.9 50.4 1.0
CA B:SER123 4.0 52.6 1.0
OD1 B:ASP251 4.1 60.0 1.0
OE2 B:GLU220 4.2 46.7 1.0
O B:ALA218 4.2 56.9 1.0
O2 B:CAC462 4.3 0.5 1.0
CA B:SER121 4.4 52.7 1.0
C2 B:CAC462 4.4 0.0 1.0
C B:SER121 4.4 53.9 1.0
OD2 B:ASP119 4.5 51.0 1.0
OD1 B:ASP119 4.5 58.4 1.0
N B:TYR122 4.5 54.1 1.0
CB B:ALA252 4.6 54.0 1.0
C B:SER123 4.7 53.8 1.0
N B:MET124 4.8 57.1 1.0
ND2 B:ASN215 4.8 52.5 1.0
O B:SER121 4.9 57.0 1.0
CG B:ASP119 4.9 55.8 1.0
C B:TYR122 5.0 53.2 1.0

Magnesium binding site 3 out of 6 in 3fcu

Go back to Magnesium Binding Sites List in 3fcu
Magnesium binding site 3 out of 6 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg458

b:72.1
occ:1.00
 O C:HOH478 1.9 55.2 1.0
O A:HOH605 2.0 51.4 1.0
O C:HOH473 2.0 57.4 1.0
O C:HOH475 2.0 49.4 1.0
O C:HOH477 2.1 60.6 1.0
O C:HOH474 2.2 50.2 1.0
OD2 C:ASP24 3.6 47.4 1.0
OD1 C:ASP24 3.7 47.4 1.0
O C:SER99 4.0 44.6 1.0
O C:HOH476 4.0 70.4 1.0
CG C:ASP24 4.1 49.1 1.0
O C:PHE25 4.4 51.0 1.0

Magnesium binding site 4 out of 6 in 3fcu

Go back to Magnesium Binding Sites List in 3fcu
Magnesium binding site 4 out of 6 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:43.0
occ:1.00
 O2 D:CAC462 1.7 96.1 1.0
O C:HOH460 1.9 32.1 1.0
O C:HOH459 2.0 40.3 1.0
OG D:SER123 2.0 52.8 1.0
OE1 D:GLU220 2.1 45.1 1.0
OG D:SER121 2.2 49.6 1.0
CB D:SER121 3.1 51.5 1.0
AS D:CAC462 3.2 99.8 1.0
CB D:SER123 3.2 52.3 1.0
CD D:GLU220 3.3 49.9 1.0
C2 D:CAC462 3.7 1.0 1.0
N D:SER123 3.8 51.8 1.0
CG D:GLU220 3.8 50.2 1.0
OD1 D:ASP251 4.0 59.2 1.0
CA D:SER123 4.0 52.3 1.0
O C:HOH461 4.1 41.9 1.0
O D:ALA218 4.2 55.2 1.0
O1 D:CAC462 4.2 91.3 1.0
CA D:SER121 4.3 52.6 1.0
OE2 D:GLU220 4.3 47.3 1.0
C D:SER121 4.3 53.4 1.0
N D:TYR122 4.5 54.0 1.0
C1 D:CAC462 4.5 99.4 1.0
OD1 D:ASP119 4.5 58.8 1.0
OD2 D:ASP119 4.5 52.2 1.0
CB D:ALA252 4.7 53.8 1.0
C D:SER123 4.8 54.3 1.0
O D:SER121 4.8 57.5 1.0
ND2 D:ASN215 4.8 52.7 1.0
N D:MET124 4.8 56.2 1.0
CG D:ASP119 4.9 56.6 1.0
C D:TYR122 5.0 53.2 1.0

Magnesium binding site 5 out of 6 in 3fcu

Go back to Magnesium Binding Sites List in 3fcu
Magnesium binding site 5 out of 6 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg458

b:68.0
occ:1.00
 O A:HOH607 2.1 46.6 1.0
O C:HOH484 2.2 53.0 1.0
O A:HOH608 2.5 43.8 1.0
O A:HOH606 2.6 71.4 1.0
O A:HOH609 2.7 63.7 1.0
OD1 E:ASP24 3.8 48.3 1.0
O A:HOH610 3.8 52.7 1.0
OD2 E:ASP24 4.1 46.5 1.0
O E:SER99 4.3 44.5 1.0
CG E:ASP24 4.4 49.5 1.0
O E:PHE25 5.0 51.3 1.0

Magnesium binding site 6 out of 6 in 3fcu

Go back to Magnesium Binding Sites List in 3fcu
Magnesium binding site 6 out of 6 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:37.5
occ:1.00
 O2 F:CAC462 1.7 0.2 1.0
O C:HOH465 2.0 42.3 1.0
OG F:SER123 2.1 51.6 1.0
OE1 F:GLU220 2.1 45.6 1.0
O C:HOH466 2.1 43.3 1.0
OG F:SER121 2.3 49.6 1.0
CB F:SER121 3.1 51.5 1.0
CB F:SER123 3.1 52.4 1.0
AS F:CAC462 3.2 0.8 1.0
CD F:GLU220 3.3 49.5 1.0
C2 F:CAC462 3.7 0.4 1.0
N F:SER123 3.8 52.1 1.0
CG F:GLU220 3.8 50.4 1.0
OD1 F:ASP251 4.0 60.4 1.0
CA F:SER123 4.0 52.1 1.0
O1 F:CAC462 4.2 0.0 1.0
OE2 F:GLU220 4.3 46.4 1.0
CA F:SER121 4.3 52.6 1.0
C F:SER121 4.4 54.0 1.0
O F:ALA218 4.4 55.8 1.0
OD2 F:ASP119 4.4 52.9 1.0
OD1 F:ASP119 4.5 59.4 1.0
N F:TYR122 4.5 54.2 1.0
C1 F:CAC462 4.5 0.5 1.0
CB F:ALA252 4.8 54.9 1.0
N F:MET124 4.8 56.8 1.0
ND2 F:ASN215 4.8 52.1 1.0
C F:SER123 4.8 54.3 1.0
O F:SER121 4.8 57.1 1.0
CG F:ASP119 4.9 56.6 1.0
C F:TYR122 5.0 53.3 1.0
CG F:ASP251 5.0 57.2 1.0

Reference:

J.Zhu, B.H.Luo, T.Xiao, C.Zhang, N.Nishida, T.A.Springer. Structure of A Complete Integrin Ectodomain in A Physiologic Resting State and Activation and Deactivation By Applied Forces. Mol.Cell V. 32 849 2008.
ISSN: ISSN 1097-2765
PubMed: 19111664
DOI: 10.1016/J.MOLCEL.2008.11.018
Page generated: Wed Aug 14 13:41:29 2024

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