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Magnesium in PDB 2vc2: Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758

Protein crystallography data

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758, PDB code: 2vc2 was solved by T.A.Springer, J.Zhu, T.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.72 / 3.10
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 149.151, 149.151, 176.217, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 21.7

Other elements in 2vc2:

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758 also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758 (pdb code 2vc2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758, PDB code: 2vc2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2vc2

Go back to Magnesium Binding Sites List in 2vc2
Magnesium binding site 1 out of 2 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1460

b:2.0
occ:1.00
O A:HOH4023 2.7 2.0 1.0
OD1 A:ASP232 3.0 2.0 1.0
OD2 A:ASP232 3.1 2.0 1.0
O A:HOH4020 3.3 2.0 1.0
CG A:ASP232 3.4 2.0 1.0
CB B:ALA218 4.0 2.2 1.0
CB A:PHE231 4.2 2.0 1.0
CD1 A:PHE231 4.4 2.0 1.0
CG A:PHE231 4.5 2.0 1.0
C7 B:1801477 4.6 2.0 1.0
N A:ASP232 4.7 2.0 1.0
C8 B:1801477 4.7 2.0 1.0
C17 B:1801477 4.7 2.0 1.0
O A:TYR190 4.8 2.4 1.0
CB A:ASP232 4.8 2.0 1.0
N B:ALA218 4.9 2.0 1.0
C6 B:1801477 4.9 2.0 1.0
C9 B:1801477 4.9 2.0 1.0
CA A:PHE231 5.0 2.0 1.0

Magnesium binding site 2 out of 2 in 2vc2

Go back to Magnesium Binding Sites List in 2vc2
Magnesium binding site 2 out of 2 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:2.0
occ:1.00
O B:HOH4006 1.9 2.0 1.0
OE1 B:GLU220 1.9 3.6 1.0
O1 B:1801477 2.1 2.0 1.0
OG B:SER123 2.2 2.0 1.0
OG B:SER121 2.4 2.0 1.0
O B:HOH4024 2.5 2.0 1.0
CD B:GLU220 3.0 2.5 1.0
C1 B:1801477 3.2 2.0 1.0
CB B:SER123 3.2 2.0 1.0
CB B:SER121 3.2 2.0 1.0
CG B:GLU220 3.7 2.0 1.0
O B:ALA218 3.8 2.0 1.0
C2 B:1801477 3.9 2.0 1.0
C3 B:1801477 4.0 2.0 1.0
OE2 B:GLU220 4.1 2.4 1.0
N B:SER123 4.1 2.0 1.0
O2 B:1801477 4.1 2.0 1.0
O3 B:1801477 4.1 2.0 1.0
OD1 B:ASP251 4.2 6.5 1.0
CA B:SER123 4.3 2.0 1.0
ND2 B:ASN215 4.4 2.0 1.0
CB B:ALA252 4.5 4.1 1.0
CA B:SER121 4.5 2.0 1.0
C B:SER121 4.7 2.0 1.0
OD2 B:ASP119 4.7 2.0 1.0
OD1 B:ASP119 4.7 2.0 1.0
C B:ALA218 4.7 2.0 1.0
N B:TYR122 4.8 2.0 1.0
CA B:ALA218 4.8 2.0 1.0
O B:ASP217 4.9 2.0 1.0
N1 B:1801477 5.0 2.0 1.0
C4 B:1801477 5.0 2.0 1.0

Reference:

T.A.Springer, J.Zhu, T.Xiao. Structural Basis For Distinctive Recognition of Fibrinogen Gammac Peptide By the Platelet Integrin ALPHAIIBBETA3. J.Cell Biol. V. 182 791 2008.
ISSN: ISSN 0021-9525
PubMed: 18710925
DOI: 10.1083/JCB.200801146
Page generated: Mon Dec 14 07:41:31 2020

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