Magnesium in PDB 6rp4: Cdt of Sidd, Deampylase From Legionella Pneumophila

Protein crystallography data

The structure of Cdt of Sidd, Deampylase From Legionella Pneumophila, PDB code: 6rp4 was solved by I.Tascon, M.Lucas, A.L.Rojas, A.Hierro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.80 / 2.50
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 165.579, 165.579, 68.712, 90.00, 90.00, 120.00
R / Rfree (%) 26.3 / 29.6

Other elements in 6rp4:

The structure of Cdt of Sidd, Deampylase From Legionella Pneumophila also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cdt of Sidd, Deampylase From Legionella Pneumophila (pdb code 6rp4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cdt of Sidd, Deampylase From Legionella Pneumophila, PDB code: 6rp4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6rp4

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Magnesium binding site 1 out of 4 in the Cdt of Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cdt of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:51.0
occ:1.00
O A:ASP414 2.1 46.2 1.0
O A:LEU411 2.5 44.7 1.0
O A:HOH718 2.5 36.1 1.0
OG1 A:THR421 2.5 47.2 1.0
OG1 A:THR417 2.7 47.4 1.0
O A:VAL412 2.7 46.6 1.0
C A:ASP414 3.1 46.6 1.0
C A:VAL412 3.2 47.2 1.0
N A:ASP414 3.4 47.2 1.0
O A:THR417 3.5 39.6 1.0
C A:LEU411 3.6 48.2 1.0
CA A:VAL412 3.6 44.6 1.0
CA A:ASP414 3.7 47.8 1.0
CB A:THR421 3.7 43.4 1.0
C A:SER413 4.0 47.4 1.0
C A:THR417 4.0 40.5 1.0
CB A:THR417 4.0 44.6 1.0
CB A:ASP414 4.0 49.1 1.0
N A:VAL412 4.1 46.1 1.0
N A:SER413 4.1 43.9 1.0
CG2 A:THR421 4.1 43.6 1.0
N A:SER415 4.3 48.6 1.0
N A:THR417 4.3 43.1 1.0
CA A:THR417 4.3 41.0 1.0
CA A:SER413 4.5 42.4 1.0
O A:SER413 4.5 51.4 1.0
CA A:SER415 4.7 54.7 1.0
N A:PRO418 4.8 40.3 1.0
CD2 A:LEU411 4.8 44.7 1.0
CA A:LEU411 4.9 46.7 1.0
CA A:THR421 5.0 41.3 1.0
CG2 A:THR417 5.0 44.1 1.0
C A:SER415 5.0 54.1 1.0
CB A:VAL412 5.0 37.8 1.0

Magnesium binding site 2 out of 4 in 6rp4

Go back to Magnesium Binding Sites List in 6rp4
Magnesium binding site 2 out of 4 in the Cdt of Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cdt of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:61.1
occ:1.00
O B:ASP414 2.2 68.7 1.0
CG2 B:THR421 2.6 60.0 1.0
O B:LEU411 2.7 52.1 1.0
OG1 B:THR417 2.7 63.0 1.0
O B:VAL412 2.9 58.1 1.0
O B:THR417 3.3 60.6 1.0
C B:ASP414 3.4 63.4 1.0
C B:VAL412 3.5 57.5 1.0
CB B:THR421 3.6 61.6 1.0
OG1 B:THR421 3.7 63.5 1.0
C B:THR417 3.7 63.5 1.0
CA B:VAL412 3.8 55.1 1.0
C B:LEU411 3.8 55.8 1.0
CB B:THR417 4.0 59.7 1.0
N B:ASP414 4.1 57.9 1.0
CA B:THR417 4.2 58.4 1.0
N B:THR417 4.2 59.4 1.0
CA B:ASP414 4.2 58.4 1.0
N B:VAL412 4.3 54.2 1.0
N B:SER415 4.4 57.3 1.0
CB B:ASP414 4.5 55.6 1.0
NZ B:LYS433 4.5 62.5 1.0
N B:PRO418 4.5 66.5 1.0
C B:SER413 4.5 56.1 1.0
CA B:SER415 4.5 61.6 1.0
N B:SER413 4.6 55.0 1.0
CD2 B:LEU411 4.8 58.4 1.0
CA B:PRO418 4.8 65.1 1.0
C B:SER415 4.8 69.4 1.0
O B:HOH705 4.9 56.9 1.0
CG2 B:THR417 4.9 58.4 1.0
CA B:THR421 4.9 62.2 1.0
CE B:LYS433 5.0 57.7 1.0
O B:SER413 5.0 58.3 1.0

Magnesium binding site 3 out of 4 in 6rp4

Go back to Magnesium Binding Sites List in 6rp4
Magnesium binding site 3 out of 4 in the Cdt of Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cdt of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:62.4
occ:1.00
OG1 C:THR421 2.6 57.2 1.0
O C:ASP414 2.6 65.9 1.0
O C:VAL412 2.9 57.6 1.0
O C:THR417 3.0 63.3 1.0
CB C:THR421 3.1 62.8 1.0
CG2 C:THR421 3.6 58.9 1.0
C C:THR417 3.6 59.1 1.0
OG1 C:THR417 3.6 60.8 1.0
NZ C:LYS433 3.6 54.5 1.0
C C:ASP414 3.8 59.5 1.0
C C:VAL412 3.8 57.2 1.0
O C:LEU411 3.8 57.8 1.0
CA C:PRO418 3.9 64.1 1.0
N C:PRO418 4.0 59.6 1.0
CE C:LYS433 4.1 49.2 1.0
CA C:VAL412 4.2 58.1 1.0
CA C:THR417 4.5 62.0 1.0
CA C:SER415 4.6 59.4 1.0
CA C:THR421 4.6 64.5 1.0
N C:ASP414 4.6 59.0 1.0
N C:SER415 4.6 56.4 1.0
CB C:THR417 4.7 59.1 1.0
N C:THR417 4.7 63.7 1.0
C C:SER413 4.7 57.4 1.0
CA C:ASP414 4.7 56.8 1.0
C C:PRO418 4.8 63.6 1.0
C C:LEU411 4.9 56.5 1.0
CB C:PRO418 4.9 64.0 1.0
N C:SER413 4.9 56.9 1.0
N C:THR421 4.9 65.7 1.0
O C:SER413 5.0 55.8 1.0
O C:PRO418 5.0 67.5 1.0

Magnesium binding site 4 out of 4 in 6rp4

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Magnesium binding site 4 out of 4 in the Cdt of Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cdt of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:49.0
occ:1.00
O D:ASP414 2.1 46.1 1.0
O D:VAL412 2.4 44.5 1.0
OG1 D:THR421 2.6 47.1 1.0
O D:LEU411 2.6 45.4 1.0
O D:HOH717 2.7 44.7 1.0
OG1 D:THR417 2.8 45.0 1.0
C D:VAL412 3.1 42.6 1.0
C D:ASP414 3.2 44.1 1.0
N D:ASP414 3.4 46.7 1.0
O D:THR417 3.6 47.8 1.0
CA D:VAL412 3.6 41.1 1.0
CA D:ASP414 3.7 44.5 1.0
C D:LEU411 3.7 45.7 1.0
CB D:THR421 3.7 48.4 1.0
C D:SER413 3.8 44.4 1.0
N D:SER413 4.0 43.4 1.0
C D:THR417 4.0 48.6 1.0
CG2 D:THR421 4.1 50.5 1.0
CB D:THR417 4.1 47.2 1.0
CB D:ASP414 4.1 43.0 1.0
N D:VAL412 4.1 44.0 1.0
NZ D:LYS433 4.2 43.6 1.0
N D:SER415 4.3 48.5 1.0
N D:THR417 4.3 40.1 1.0
CA D:THR417 4.3 45.7 1.0
O D:SER413 4.3 43.7 1.0
CA D:SER413 4.4 40.5 1.0
CE D:LYS433 4.6 40.6 1.0
CA D:SER415 4.7 50.3 1.0
N D:PRO418 4.7 46.6 1.0
O D:HOH709 4.9 43.8 1.0
CB D:VAL412 5.0 43.0 1.0

Reference:

I.Tascon, X.Li, M.Lucas, D.Nelson, A.Vidaurrazaga, Y.H.Lin, A.L.Rojas, A.Hierro, M.P.Machner. Structural Insight Into the Membrane Targeting Domain of the Legionella Deampylase Sidd. Plos Pathog. V. 16 08734 2020.
ISSN: ESSN 1553-7374
PubMed: 32853279
DOI: 10.1371/JOURNAL.PPAT.1008734
Page generated: Tue Dec 15 00:00:47 2020

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