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Magnesium in PDB 6vc7: Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium

Protein crystallography data

The structure of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium, PDB code: 6vc7 was solved by U.Gabale, S.Ressl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.56 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.612, 124.899, 183.296, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.7

Other elements in 6vc7:

The structure of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium also contains other interesting chemical elements:

Potassium (K) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium (pdb code 6vc7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium, PDB code: 6vc7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6vc7

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Magnesium binding site 1 out of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1812

b:31.2
occ:1.00
 O A:HOH2078 2.7 54.2 1.0
O A:HOH2066 3.0 37.4 1.0
O A:HOH2039 3.1 30.7 1.0
N A:THR302 3.2 25.5 1.0
OG1 A:THR302 3.7 28.8 1.0
CA A:THR301 3.7 28.5 1.0
CB A:THR301 3.7 32.9 1.0
CD A:ARG451 3.7 25.8 1.0
NH1 A:ARG451 3.9 32.3 1.0
CB A:THR302 4.0 27.8 1.0
C A:THR301 4.0 26.9 1.0
NE A:ARG451 4.1 27.4 1.0
CZ A:ARG451 4.1 30.4 1.0
CA A:THR302 4.2 26.0 1.0
CG2 A:THR301 4.4 27.6 1.0
OG1 A:THR301 4.9 37.1 1.0

Magnesium binding site 2 out of 6 in 6vc7

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Magnesium binding site 2 out of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg609

b:33.7
occ:1.00
 O B:HOH885 2.6 53.4 1.0
O B:HOH855 3.1 42.3 1.0
N B:THR302 3.2 32.0 1.0
O B:HOH858 3.3 54.5 1.0
OG1 B:THR302 3.6 33.5 1.0
CD B:ARG451 3.7 35.3 1.0
NH1 B:ARG451 3.7 32.6 1.0
CB B:THR301 3.7 35.6 1.0
CA B:THR301 3.8 36.0 1.0
CB B:THR302 3.9 32.9 1.0
C B:THR301 4.0 33.7 1.0
NE B:ARG451 4.0 38.9 1.0
CZ B:ARG451 4.0 38.4 1.0
CA B:THR302 4.1 33.9 1.0
CG2 B:THR301 4.4 35.9 1.0
OG1 B:THR301 4.9 35.8 1.0
NH2 B:ARG451 4.9 34.2 1.0
CG B:ARG451 5.0 29.2 1.0

Magnesium binding site 3 out of 6 in 6vc7

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Magnesium binding site 3 out of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1709

b:33.5
occ:1.00
 O C:HOH1997 2.9 53.4 1.0
O C:HOH1980 3.0 44.9 1.0
N C:THR302 3.3 25.6 1.0
O C:HOH1937 3.4 27.1 1.0
NH1 C:ARG451 3.6 32.6 1.0
CD C:ARG451 3.7 26.6 1.0
CA C:THR301 3.7 28.4 1.0
CB C:THR301 3.8 30.7 1.0
OG1 C:THR302 3.8 28.9 1.0
CZ C:ARG451 4.0 31.3 1.0
NE C:ARG451 4.0 31.2 1.0
CB C:THR302 4.0 26.2 1.0
C C:THR301 4.0 30.0 1.0
CA C:THR302 4.2 24.7 1.0
CG2 C:THR301 4.2 25.6 1.0
NH2 C:ARG451 4.9 29.1 1.0
CG C:ARG451 5.0 25.5 1.0

Magnesium binding site 4 out of 6 in 6vc7

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Magnesium binding site 4 out of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg605

b:43.5
occ:1.00
 O D:HOH834 2.6 48.3 1.0
N D:THR302 3.1 41.2 1.0
O D:HOH789 3.4 37.6 1.0
CA D:THR301 3.7 40.6 1.0
CD D:ARG451 3.7 32.4 1.0
CB D:THR301 3.7 42.5 1.0
OG1 D:THR302 3.7 42.4 1.0
CB D:THR302 3.8 37.9 1.0
NH1 D:ARG451 3.9 40.0 1.0
C D:THR301 3.9 41.4 1.0
NE D:ARG451 4.0 34.7 1.0
CA D:THR302 4.1 38.9 1.0
CZ D:ARG451 4.1 38.9 1.0
CG2 D:THR301 4.4 44.0 1.0
O D:HOH788 4.5 51.4 1.0
OG1 D:THR301 4.8 42.8 1.0
CG D:ARG451 4.9 30.7 1.0

Magnesium binding site 5 out of 6 in 6vc7

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Magnesium binding site 5 out of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg608

b:43.8
occ:1.00
 O E:HOH826 2.2 53.8 1.0
N E:THR302 2.9 37.1 1.0
O E:HOH813 3.3 59.0 1.0
O E:HOH764 3.4 41.0 1.0
OG1 E:THR302 3.4 34.6 1.0
CD E:ARG451 3.5 34.1 1.0
CB E:THR302 3.6 34.6 1.0
CA E:THR301 3.6 36.6 1.0
NH1 E:ARG451 3.6 39.8 1.0
CB E:THR301 3.8 37.0 1.0
C E:THR301 3.8 35.1 1.0
CA E:THR302 3.9 36.7 1.0
NE E:ARG451 3.9 37.5 1.0
CZ E:ARG451 4.0 41.3 1.0
CG2 E:THR301 4.5 35.0 1.0
CG E:ARG451 4.7 37.2 1.0
N E:ASP303 4.8 36.0 1.0
OG1 E:THR301 4.9 39.9 1.0
C E:THR302 4.9 35.9 1.0
O E:THR301 5.0 34.5 1.0
N E:THR301 5.0 36.9 1.0
NH2 E:ARG451 5.0 40.7 1.0

Magnesium binding site 6 out of 6 in 6vc7

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Magnesium binding site 6 out of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg606

b:45.2
occ:1.00
 N F:THR302 3.3 40.6 1.0
O F:HOH790 3.4 44.6 1.0
CD F:ARG451 3.4 37.2 1.0
OG1 F:THR302 3.7 41.9 1.0
NE F:ARG451 3.7 40.0 1.0
NH1 F:ARG451 3.8 41.3 1.0
CA F:THR301 3.8 40.0 1.0
CB F:THR301 3.9 43.5 1.0
CZ F:ARG451 3.9 42.4 1.0
CB F:THR302 4.0 40.6 1.0
C F:THR301 4.0 39.8 1.0
CA F:THR302 4.3 38.9 1.0
CG2 F:THR301 4.3 39.5 1.0
NH2 F:ARG451 4.8 43.8 1.0
CG F:ARG451 4.8 33.1 1.0
O F:ASN300 5.0 42.3 1.0

Reference:

U.Gabale, P.A.Pena Palomino, H.Kim, W.Chen, S.Ressl. The Essential Inner Membrane Protein Yejm Is A Metalloenzyme. Sci Rep V. 10 17794 2020.
ISSN: ESSN 2045-2322
PubMed: 33082366
DOI: 10.1038/S41598-020-73660-6
Page generated: Tue Oct 1 21:27:17 2024

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