Magnesium in PDB 6h4f: Tarp-3RBOP

Protein crystallography data

The structure of Tarp-3RBOP, PDB code: 6h4f was solved by Y.Guo, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.75 / 2.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.610, 217.270, 123.990, 90.00, 91.38, 90.00
R / Rfree (%) 17.2 / 20.5

Other elements in 6h4f:

The structure of Tarp-3RBOP also contains other interesting chemical elements:

Chlorine (Cl) 17 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tarp-3RBOP (pdb code 6h4f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tarp-3RBOP, PDB code: 6h4f:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6h4f

Go back to Magnesium Binding Sites List in 6h4f
Magnesium binding site 1 out of 4 in the Tarp-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tarp-3RBOP within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:80.5
occ:1.00
OD2 B:ASP316 3.7 59.6 1.0
OD2 C:ASP316 3.9 43.5 1.0
OD2 F:ASP316 4.3 45.4 1.0
OD1 B:ASP316 4.3 44.8 1.0
CG B:ASP316 4.4 45.7 1.0
OD1 C:ASP316 4.5 49.4 1.0
CG C:ASP316 4.6 37.9 1.0
CB B:ALA319 4.7 33.3 1.0
CB B:LEU318 4.9 33.8 1.0
N B:ALA319 4.9 30.8 1.0
CB C:LEU318 5.0 33.4 1.0
CB C:ALA319 5.0 30.5 1.0
OD1 F:ASP316 5.0 46.9 1.0

Magnesium binding site 2 out of 4 in 6h4f

Go back to Magnesium Binding Sites List in 6h4f
Magnesium binding site 2 out of 4 in the Tarp-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tarp-3RBOP within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg402

b:65.7
occ:1.00
OD2 Q:ASP316 3.7 54.4 1.0
OD2 E:ASP316 4.0 67.3 1.0
OD2 G:ASP316 4.2 48.8 1.0
OD1 Q:ASP316 4.4 59.7 1.0
CG Q:ASP316 4.4 50.9 1.0
OD1 E:ASP316 4.4 45.1 1.0
CB Q:ALA319 4.5 35.0 1.0
CB E:LEU318 4.6 33.6 1.0
CG E:ASP316 4.6 42.8 1.0
CD1 E:LEU318 4.9 37.2 1.0
N Q:ALA319 4.9 33.6 1.0
CA Q:ALA319 5.0 35.2 1.0

Magnesium binding site 3 out of 4 in 6h4f

Go back to Magnesium Binding Sites List in 6h4f
Magnesium binding site 3 out of 4 in the Tarp-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tarp-3RBOP within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:66.8
occ:1.00
OD2 D:ASP316 3.8 47.9 1.0
OD2 A:ASP316 4.0 57.9 1.0
OD1 D:ASP316 4.4 52.1 1.0
CG D:ASP316 4.5 46.3 1.0
OD2 P:ASP316 4.5 60.0 1.0
OD1 A:ASP316 4.6 49.5 1.0
CG A:ASP316 4.6 44.5 1.0
CB D:ALA319 4.7 31.4 1.0
CB A:ALA319 4.8 34.7 1.0
CB D:LEU318 4.9 36.5 1.0
N D:ALA319 5.0 31.7 1.0

Magnesium binding site 4 out of 4 in 6h4f

Go back to Magnesium Binding Sites List in 6h4f
Magnesium binding site 4 out of 4 in the Tarp-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tarp-3RBOP within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg402

b:74.2
occ:1.00
OD2 H:ASP316 4.0 61.3 1.0
OD2 I:ASP316 4.3 40.9 1.0
OD1 H:ASP316 4.4 46.9 1.0
CB H:ALA319 4.5 34.8 1.0
OD2 O:ASP316 4.5 47.7 1.0
CG H:ASP316 4.5 46.9 1.0
N H:ALA319 4.7 29.3 1.0
CB H:LEU318 4.7 30.3 1.0
OD1 I:ASP316 4.8 41.7 1.0
CD1 H:ILE322 4.8 27.7 1.0
CA H:ALA319 4.8 31.4 1.0
CB I:ALA319 4.9 28.8 1.0
CG I:ASP316 4.9 39.6 1.0
CD1 I:ILE322 4.9 35.2 1.0
CB I:LEU318 4.9 33.2 1.0

Reference:

D.Gerlach, Y.Guo, C.De Castro, S.H.Kim, K.Schlatterer, F.F.Xu, C.Pereira, P.H.Seeberger, S.Ali, J.Codee, W.Sirisarn, B.Schulte, C.Wolz, J.Larsen, A.Molinaro, B.L.Lee, G.Xia, T.Stehle, A.Peschel. Methicillin-Resistant Staphylococcus Aureus Alters Cell Wall Glycosylation to Evade Immunity. Nature V. 563 705 2018.
ISSN: ESSN 1476-4687
PubMed: 30464342
DOI: 10.1038/S41586-018-0730-X
Page generated: Mon Dec 14 22:47:28 2020

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