Magnesium in PDB 6dus: Structure of Salmonella Effector SSEK3 E258Q Mutant

Protein crystallography data

The structure of Structure of Salmonella Effector SSEK3 E258Q Mutant, PDB code: 6dus was solved by I.Y.W.Chung, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.73 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.490, 107.120, 74.730, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Salmonella Effector SSEK3 E258Q Mutant (pdb code 6dus). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Salmonella Effector SSEK3 E258Q Mutant, PDB code: 6dus:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6dus

Go back to Magnesium Binding Sites List in 6dus
Magnesium binding site 1 out of 2 in the Structure of Salmonella Effector SSEK3 E258Q Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Salmonella Effector SSEK3 E258Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:31.4
occ:1.00
OD2 A:ASP228 1.9 34.6 1.0
O1A A:UDP501 2.0 29.2 1.0
OD1 A:ASP325 2.1 34.0 1.0
O1B A:UDP501 2.1 36.1 1.0
OG A:SER327 2.2 38.2 1.0
O A:HOH608 2.3 35.5 1.0
CG A:ASP228 2.9 34.1 1.0
CG A:ASP325 3.2 32.9 1.0
OD1 A:ASP228 3.3 32.8 1.0
CB A:SER327 3.3 34.7 1.0
PA A:UDP501 3.3 26.3 1.0
PB A:UDP501 3.4 27.1 1.0
O A:HOH604 3.6 40.1 1.0
O3A A:UDP501 3.7 34.2 1.0
CA A:ASP325 3.9 33.0 1.0
OD2 A:ASP325 4.0 39.8 1.0
OD2 A:ASP226 4.0 35.7 1.0
CB A:ASP325 4.1 30.3 1.0
O A:HOH696 4.1 33.1 1.0
O A:HOH640 4.1 33.5 1.0
N A:SER327 4.1 39.0 1.0
O2A A:UDP501 4.1 39.5 1.0
CB A:ASP228 4.1 30.2 1.0
CA A:SER327 4.2 39.0 1.0
O2B A:UDP501 4.3 34.2 1.0
C A:ASP325 4.4 35.6 1.0
O5' A:UDP501 4.4 34.9 1.0
O3B A:UDP501 4.4 33.5 1.0
C5' A:UDP501 4.7 26.3 1.0
O A:ASP325 4.8 39.7 1.0
O A:HOH620 4.8 24.3 1.0
N A:THR326 4.8 32.5 1.0
C A:SER327 4.9 36.9 1.0
OH A:TYR75 4.9 29.0 1.0
CG A:ASP226 4.9 35.6 1.0

Magnesium binding site 2 out of 2 in 6dus

Go back to Magnesium Binding Sites List in 6dus
Magnesium binding site 2 out of 2 in the Structure of Salmonella Effector SSEK3 E258Q Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Salmonella Effector SSEK3 E258Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:24.2
occ:1.00
O1B B:UDP501 2.0 21.3 1.0
OD1 B:ASP325 2.0 23.7 1.0
O1A B:UDP501 2.1 24.8 1.0
O B:HOH610 2.1 27.9 1.0
OD2 B:ASP228 2.1 31.1 1.0
OG B:SER327 2.2 31.4 1.0
CG B:ASP228 3.1 32.4 1.0
CG B:ASP325 3.2 28.7 1.0
PA B:UDP501 3.2 29.9 1.0
CB B:SER327 3.3 26.9 1.0
PB B:UDP501 3.3 26.3 1.0
OD1 B:ASP228 3.5 28.4 1.0
O3A B:UDP501 3.5 33.0 1.0
O B:HOH606 3.6 28.7 1.0
O B:HOH612 3.6 20.9 1.0
O2A B:UDP501 4.0 34.1 1.0
OD2 B:ASP325 4.0 28.9 1.0
CA B:ASP325 4.0 29.7 1.0
OD2 B:ASP226 4.1 30.3 1.0
N B:SER327 4.1 28.9 1.0
CB B:ASP325 4.1 21.5 1.0
CA B:SER327 4.2 30.0 1.0
O2B B:UDP501 4.2 32.4 1.0
O3B B:UDP501 4.3 29.3 1.0
CB B:ASP228 4.3 26.9 1.0
C B:ASP325 4.4 28.3 1.0
O B:HOH613 4.4 31.3 1.0
O5' B:UDP501 4.4 33.4 1.0
O B:HOH601 4.6 38.7 1.0
C B:SER327 4.7 28.5 1.0
C5' B:UDP501 4.7 23.7 1.0
O B:ASP325 4.7 24.5 1.0
OH B:TYR75 4.7 27.0 1.0
N B:SER328 4.8 31.0 1.0
N B:THR326 4.9 29.7 1.0

Reference:

J.P.M.Newson, N.E.Scott, I.Yeuk Wah Chung, T.Wong Fok Lung, C.Giogha, J.Gan, N.Wang, R.A.Strugnell, N.F.Brown, M.Cygler, J.S.Pearson, E.L.Hartland. Salmonella Effectors SSEK1 and SSEK3 Target Death Domain Proteins in the Tnf and Trail Signaling Pathways. Mol.Cell Proteomics V. 18 1138 2019.
ISSN: ESSN 1535-9484
PubMed: 30902834
DOI: 10.1074/MCP.RA118.001093
Page generated: Mon Dec 14 22:37:14 2020

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