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Magnesium in PDB 3v4v: Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376

Protein crystallography data

The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376, PDB code: 3v4v was solved by Y.Yu, J.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.580, 123.530, 154.160, 90.00, 112.63, 90.00
R / Rfree (%) 19.7 / 23.1

Other elements in 3v4v:

The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Calcium (Ca) 10 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 (pdb code 3v4v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376, PDB code: 3v4v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3v4v

Go back to Magnesium Binding Sites List in 3v4v
Magnesium binding site 1 out of 2 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:49.5
occ:1.00
O B:HOH504 2.8 73.6 1.0
OE2 B:GLU240 2.9 51.9 1.0
OG B:SER144 2.9 0.0 1.0
O29 B:0DU4000 2.9 87.4 1.0
OG B:SER142 3.0 73.0 1.0
O B:HOH505 3.0 75.5 1.0
CB B:SER144 3.3 0.8 1.0
OD1 B:ASP270 3.3 92.8 1.0
CB B:SER142 3.8 90.0 1.0
CD B:GLU240 3.9 0.4 1.0
C27 B:0DU4000 4.0 89.2 1.0
OD2 B:ASP270 4.1 0.5 1.0
CG B:ASP270 4.1 0.7 1.0
OD2 B:ASP140 4.1 95.7 1.0
CG B:GLU240 4.3 0.6 1.0
N B:SER144 4.3 0.2 1.0
CA B:SER144 4.4 0.3 1.0
O B:SER238 4.4 73.5 1.0
C14 B:0DU4000 4.5 73.3 1.0
C15 B:0DU4000 4.5 56.0 1.0
CB B:ASP271 4.7 89.7 1.0
OE1 B:GLU240 4.8 0.5 1.0
O28 B:0DU4000 4.9 0.3 1.0
C B:SER144 5.0 0.8 1.0

Magnesium binding site 2 out of 2 in 3v4v

Go back to Magnesium Binding Sites List in 3v4v
Magnesium binding site 2 out of 2 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:61.4
occ:1.00
O D:HOH504 2.8 85.1 1.0
OE2 D:GLU240 2.9 64.7 1.0
O D:HOH505 2.9 67.3 1.0
OG D:SER144 2.9 0.9 1.0
OG D:SER142 3.0 78.4 1.0
O29 D:0DU4000 3.0 89.1 1.0
CB D:SER144 3.3 0.8 1.0
O D:HOH506 3.4 76.7 1.0
OD1 D:ASP270 3.5 0.2 1.0
CB D:SER142 3.7 87.8 1.0
CD D:GLU240 3.9 0.8 1.0
C27 D:0DU4000 3.9 0.4 1.0
C14 D:0DU4000 4.2 55.8 1.0
OD2 D:ASP270 4.2 0.3 1.0
N D:SER144 4.2 0.8 1.0
OD2 D:ASP140 4.2 95.0 1.0
CG D:ASP270 4.3 0.9 1.0
CA D:SER144 4.3 0.3 1.0
CG D:GLU240 4.4 0.5 1.0
C15 D:0DU4000 4.4 79.9 1.0
O D:SER238 4.4 87.4 1.0
O28 D:0DU4000 4.7 0.7 1.0
CB D:ASP271 4.8 77.1 1.0
OE1 D:GLU240 4.8 0.7 1.0
CA D:SER142 4.9 81.8 1.0
C D:SER144 4.9 0.8 1.0
C D:SER142 5.0 91.4 1.0

Reference:

Y.Yu, J.Zhu, L.Z.Mi, T.Walz, H.Sun, J.Chen, T.A.Springer. Structural Specializations of A4B7, An Integrin That Mediates Rolling Adhesion J.Cell Biol. V. 196 131 2012.
ISSN: ISSN 0021-9525
PubMed: 22232704
DOI: 10.1083/JCB.201110023
Page generated: Mon Dec 14 08:58:00 2020

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