Magnesium in PDB 7l8p: Integrin ALPHAIIBBETA3 in Complex with Sibrafiban

Protein crystallography data

The structure of Integrin ALPHAIIBBETA3 in Complex with Sibrafiban, PDB code: 7l8p was solved by F.-Y.Lin, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.22 / 2.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 257.5, 144.68, 104.68, 90, 90, 90
R / Rfree (%) 20.4 / 24.5

Other elements in 7l8p:

The structure of Integrin ALPHAIIBBETA3 in Complex with Sibrafiban also contains other interesting chemical elements:

Calcium (Ca) 12 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Integrin ALPHAIIBBETA3 in Complex with Sibrafiban (pdb code 7l8p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Integrin ALPHAIIBBETA3 in Complex with Sibrafiban, PDB code: 7l8p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7l8p

Go back to Magnesium Binding Sites List in 7l8p
Magnesium binding site 1 out of 2 in the Integrin ALPHAIIBBETA3 in Complex with Sibrafiban


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Integrin ALPHAIIBBETA3 in Complex with Sibrafiban within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:30.9
occ:1.00
O03 B:XQS2005 2.0 35.5 1.0
O B:HOH2148 2.1 30.9 1.0
OE2 B:GLU220 2.1 42.4 1.0
O B:HOH2103 2.1 58.2 1.0
OG B:SER121 2.1 47.3 1.0
O B:HOH2173 2.2 30.9 1.0
HB2 B:SER121 2.8 38.8 1.0
CB B:SER121 2.9 32.3 1.0
CD B:GLU220 3.2 32.0 1.0
HG3 B:GLU220 3.2 36.9 1.0
HB3 B:SER121 3.2 38.8 1.0
C20 B:XQS2005 3.2 30.9 1.0
CG B:GLU220 3.6 30.7 1.0
HG2 B:GLU220 3.8 36.9 1.0
O01 B:XQS2005 3.9 59.4 1.0
OG B:SER123 3.9 62.6 1.0
HD21 B:ASN215 3.9 48.8 1.0
HB2 B:ALA252 4.0 38.9 1.0
O05 B:XQS2005 4.0 36.8 1.0
H B:SER123 4.1 42.5 1.0
C17 B:XQS2005 4.2 30.9 1.0
OE1 B:GLU220 4.3 32.6 1.0
CA B:SER121 4.3 34.0 1.0
HG B:SER123 4.3 75.1 1.0
OD2 B:ASP119 4.3 32.2 1.0
H B:TYR122 4.3 42.5 1.0
HB3 B:ALA252 4.3 38.9 1.0
O B:ALA218 4.4 36.4 1.0
OD1 B:ASP119 4.4 32.2 1.0
OD1 B:ASP251 4.5 34.8 1.0
HD22 B:ASN215 4.5 48.8 1.0
ND2 B:ASN215 4.5 40.6 1.0
H172 B:XQS2005 4.5 37.1 1.0
CB B:ALA252 4.5 32.4 1.0
C B:SER121 4.6 33.1 1.0
H122 B:XQS2005 4.6 37.1 1.0
N B:TYR122 4.7 35.5 1.0
H B:SER121 4.7 38.0 1.0
HB1 B:ALA252 4.7 38.9 1.0
HA B:ALA218 4.8 37.9 1.0
HB3 B:SER123 4.8 54.5 1.0
CG B:ASP119 4.8 37.3 1.0
HA B:SER121 4.9 40.8 1.0
CB B:SER123 4.9 45.4 1.0
N B:SER123 4.9 35.4 1.0
H171 B:XQS2005 5.0 37.1 1.0
C10 B:XQS2005 5.0 33.4 1.0

Magnesium binding site 2 out of 2 in 7l8p

Go back to Magnesium Binding Sites List in 7l8p
Magnesium binding site 2 out of 2 in the Integrin ALPHAIIBBETA3 in Complex with Sibrafiban


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Integrin ALPHAIIBBETA3 in Complex with Sibrafiban within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:30.9
occ:1.00
O03 C:XQS510 2.0 46.5 1.0
O D:HOH2135 2.1 30.9 1.0
OG D:SER121 2.1 40.3 1.0
OE2 D:GLU220 2.1 49.5 1.0
O D:HOH2154 2.1 30.9 1.0
O D:HOH2122 2.2 39.8 1.0
HB2 D:SER121 2.8 48.7 1.0
CB D:SER121 2.9 40.6 1.0
HB3 D:SER121 3.2 48.7 1.0
C20 C:XQS510 3.3 44.8 1.0
CD D:GLU220 3.3 39.0 1.0
HG3 D:GLU220 3.4 44.9 1.0
CG D:GLU220 3.8 37.5 1.0
O01 C:XQS510 3.8 70.6 1.0
HD21 D:ASN215 3.9 48.5 1.0
HG D:SER123 3.9 64.4 1.0
HB2 D:ALA252 3.9 54.5 1.0
HG2 D:GLU220 4.0 44.9 1.0
OG D:SER123 4.0 53.7 1.0
O05 C:XQS510 4.1 36.7 1.0
H D:TYR122 4.2 53.8 1.0
C17 C:XQS510 4.2 32.5 1.0
H D:SER123 4.2 58.8 1.0
CA D:SER121 4.3 40.4 1.0
OE1 D:GLU220 4.3 50.4 1.0
OD2 D:ASP119 4.3 47.5 1.0
HB3 D:ALA252 4.3 54.5 1.0
O D:ALA218 4.4 44.5 1.0
H122 C:XQS510 4.4 53.2 1.0
OD1 D:ASP251 4.5 42.3 1.0
HD22 D:ASN215 4.5 48.5 1.0
H172 C:XQS510 4.5 39.0 1.0
ND2 D:ASN215 4.5 40.4 1.0
CB D:ALA252 4.5 45.5 1.0
OD1 D:ASP119 4.5 46.2 1.0
N D:TYR122 4.6 44.8 1.0
C D:SER121 4.7 42.8 1.0
HA D:ALA218 4.7 48.9 1.0
HB1 D:ALA252 4.7 54.5 1.0
H D:SER121 4.7 47.5 1.0
O D:HOH2281 4.8 53.5 1.0
CG D:ASP119 4.9 45.3 1.0
C10 C:XQS510 4.9 41.7 1.0
HA D:SER121 4.9 48.5 1.0
C12 C:XQS510 5.0 44.3 1.0
H121 C:XQS510 5.0 53.2 1.0
H171 C:XQS510 5.0 39.0 1.0

Reference:

F.-Y.Lin, T.A.Springer. Small, Closure-Stabilizing Integrin Antagonists and Their Mechanism of Action To Be Published.
Page generated: Wed Apr 5 13:17:05 2023

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