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Magnesium in PDB 3nid: The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening

Protein crystallography data

The structure of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening, PDB code: 3nid was solved by J.H.Zhu, J.Q.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.21 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 258.970, 144.490, 104.200, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.5

Other elements in 3nid:

The structure of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening (pdb code 3nid). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening, PDB code: 3nid:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3nid

Go back to Magnesium Binding Sites List in 3nid
Magnesium binding site 1 out of 2 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:26.9
occ:0.50
O B:HOH493 2.1 5.0 1.0
O B:HOH492 2.2 8.9 1.0
O B:HOH495 2.3 7.7 1.0
OE2 B:GLU220 2.4 20.8 1.0
OG B:SER121 2.7 16.2 1.0
O B:HOH494 2.7 8.3 1.0
CB B:SER121 3.2 20.7 1.0
CD B:GLU220 3.4 22.2 1.0
O B:HOH496 3.5 21.1 1.0
CG B:GLU220 3.6 16.6 1.0
OG B:SER123 3.9 24.0 1.0
O B:ALA218 4.1 19.7 1.0
O B:HOH572 4.2 32.2 1.0
OD2 B:ASP119 4.3 18.1 1.0
CB B:ALA252 4.3 14.2 1.0
OD1 B:ASP251 4.4 18.5 1.0
OE1 B:GLU220 4.5 18.9 1.0
O B:HOH478 4.5 2.0 1.0
OD1 B:ASP119 4.6 19.5 1.0
CA B:SER121 4.7 16.2 1.0
O B:HOH821 4.7 21.9 1.0
ND2 B:ASN215 4.8 16.1 1.0
CG B:ASP119 4.9 20.1 1.0

Magnesium binding site 2 out of 2 in 3nid

Go back to Magnesium Binding Sites List in 3nid
Magnesium binding site 2 out of 2 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:41.5
occ:0.50
O D:HOH488 1.9 8.8 1.0
O D:HOH483 2.1 14.9 1.0
O D:HOH482 2.1 5.4 1.0
OE2 D:GLU220 2.2 25.2 1.0
O D:HOH481 2.4 18.3 1.0
OG D:SER121 2.4 31.9 1.0
CB D:SER121 2.9 25.6 1.0
CD D:GLU220 3.4 32.2 1.0
O D:HOH489 3.4 16.0 1.0
O D:HOH984 3.7 32.5 1.0
OG D:SER123 3.8 28.1 1.0
CG D:GLU220 4.0 24.9 1.0
O D:HOH484 4.0 2.0 1.0
OE1 D:GLU220 4.4 22.5 1.0
CA D:SER121 4.4 23.1 1.0
ND2 D:ASN215 4.5 29.8 1.0
O D:ALA218 4.5 21.7 1.0
OD2 D:ASP119 4.5 25.1 1.0
OD1 D:ASP251 4.6 22.1 1.0
OD1 D:ASP119 4.7 30.6 1.0
N D:TYR122 4.7 22.3 1.0
CB D:ALA252 4.8 19.2 1.0
C D:SER121 4.8 22.9 1.0
CB D:SER123 5.0 24.9 1.0

Reference:

J.H.Zhu, J.Q.Zhu, A.Negri, D.Provasi, M.Filizola, B.S.Coller, T.A.Springer. Closed Headpiece of Integrin {Alpha}Iib{Beta}3 and Its Complex with An {Alpha}Iib{Beta}3-Specific Antagonist That Does Not Induce Opening. Blood V. 116 5050 2010.
ISSN: ISSN 0006-4971
PubMed: 20679525
DOI: 10.1182/BLOOD-2010-04-281154
Page generated: Mon Dec 14 08:28:35 2020

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