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Magnesium in PDB 3nif: The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening

Protein crystallography data

The structure of The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening, PDB code: 3nif 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 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 259.530, 144.280, 104.350, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.6

Other elements in 3nif:

The structure of The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - 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 Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening (pdb code 3nif). 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 Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening, PDB code: 3nif:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3nif

Go back to Magnesium Binding Sites List in 3nif
Magnesium binding site 1 out of 2 in the The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - 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 Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:53.5
occ:1.00
O B:HOH726 2.1 7.4 1.0
OE2 B:GLU220 2.4 25.4 1.0
O B:HOH499 2.5 7.3 1.0
O B:HOH728 2.5 16.8 1.0
O B:HOH727 2.7 13.6 1.0
OG B:SER121 3.0 20.2 1.0
CB B:SER121 3.3 16.5 1.0
CD B:GLU220 3.4 23.1 1.0
CG B:GLU220 3.9 16.0 1.0
OG B:SER123 4.1 16.9 1.0
O B:HOH610 4.3 2.0 1.0
O B:ALA218 4.3 17.9 1.0
O B:HOH729 4.4 34.1 1.0
CB B:ALA252 4.5 14.7 1.0
OE1 B:GLU220 4.5 20.3 1.0
ND2 B:ASN215 4.6 14.8 1.0
OD1 B:ASP251 4.6 24.2 1.0
CA B:SER121 4.8 15.2 1.0
OD2 B:ASP119 4.8 17.4 1.0
O B:ASP217 4.9 20.0 1.0
OD1 B:ASP119 4.9 16.7 1.0

Magnesium binding site 2 out of 2 in 3nif

Go back to Magnesium Binding Sites List in 3nif
Magnesium binding site 2 out of 2 in the The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - 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 Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:82.8
occ:1.00
O D:HOH790 1.9 16.2 1.0
O D:HOH561 2.3 2.0 1.0
OE2 D:GLU220 2.4 34.2 1.0
O D:HOH495 2.6 19.0 1.0
O D:HOH497 2.8 11.2 1.0
O D:HOH791 3.1 33.7 1.0
OG D:SER121 3.1 35.6 1.0
CB D:SER121 3.4 27.2 1.0
CD D:GLU220 3.5 33.4 1.0
O D:HOH476 3.9 2.0 1.0
CG D:GLU220 4.1 27.8 1.0
OG D:SER123 4.2 32.1 1.0
ND2 D:ASN215 4.3 25.9 1.0
OE1 D:GLU220 4.3 31.1 1.0
O D:ALA218 4.4 21.7 1.0
O D:ASP217 4.7 26.6 1.0
CA D:SER121 4.8 26.9 1.0
CB D:ALA252 4.9 22.3 1.0
N D:TYR122 5.0 27.7 1.0

Reference:

J.Zhu, J.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 08:28:38 2020

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