Magnesium in PDB 6vat: Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium

The structure of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium, PDB code: 6vat 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)	59.65 / 2.35
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.799, 113.799, 299.777, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 24.9

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

Calcium

(Ca)

3 atoms

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

Magnesium binding site 1 out of 5 in the Structure 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 Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:26.7 occ:1.00 O A:HOH819 3.1 43.1 1.0 N A:THR302 3.3 28.7 1.0 OG1 A:THR302 3.6 28.9 1.0 CD A:ARG451 3.7 25.5 1.0 NH1 A:ARG451 3.8 26.8 1.0 CA A:THR301 3.8 29.7 1.0 CB A:THR301 3.9 28.3 1.0 CB A:THR302 3.9 29.8 1.0 NE A:ARG451 4.0 25.9 1.0 CZ A:ARG451 4.0 26.9 1.0 C A:THR301 4.1 25.4 1.0 CA A:THR302 4.2 27.8 1.0 CG2 A:THR301 4.6 30.1 1.0 NH2 A:ARG451 4.9 29.3 1.0 CG A:ARG451 5.0 20.3 1.0 OG1 A:THR301 5.0 36.5 1.0

Magnesium binding site 2 out of 5 in the Structure 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 Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:30.1 occ:1.00 O B:HOH826 3.0 31.5 1.0 N B:THR302 3.2 31.8 1.0 OG1 B:THR302 3.7 28.7 1.0 CD B:ARG451 3.7 29.7 1.0 CB B:THR301 3.7 27.6 1.0 CA B:THR301 3.7 32.6 1.0 CB B:THR302 3.9 24.3 1.0 NH1 B:ARG451 3.9 31.4 1.0 NE B:ARG451 3.9 29.9 1.0 C B:THR301 4.0 31.0 1.0 CZ B:ARG451 4.0 29.9 1.0 CA B:THR302 4.1 26.6 1.0 CG2 B:THR301 4.4 29.1 1.0 OG1 B:THR301 4.8 33.7 1.0 NH2 B:ARG451 4.9 35.2 1.0

Magnesium binding site 3 out of 5 in the Structure 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 Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg607 b:35.0 occ:1.00 O C:HOH804 3.2 29.0 1.0 N C:THR302 3.4 26.4 1.0 CD C:ARG451 3.6 30.9 1.0 NH1 C:ARG451 3.6 33.6 1.0 OG1 C:THR302 3.8 31.1 1.0 NE C:ARG451 3.8 36.0 1.0 CA C:THR301 3.8 29.6 1.0 CZ C:ARG451 3.8 34.5 1.0 CB C:THR301 3.9 31.2 1.0 CB C:THR302 4.1 34.4 1.0 C C:THR301 4.1 26.4 1.0 CG2 C:THR301 4.3 27.9 1.0 CA C:THR302 4.4 37.6 1.0 NH2 C:ARG451 4.7 30.3 1.0 CG C:ARG451 4.9 27.9 1.0

Magnesium binding site 4 out of 5 in the Structure 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 Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg605 b:37.5 occ:1.00 O D:HOH782 3.2 24.1 1.0 N D:THR302 3.4 27.9 1.0 CD D:ARG451 3.6 27.5 1.0 CA D:THR301 3.8 29.7 1.0 CB D:THR301 3.8 30.0 1.0 NE D:ARG451 3.8 30.3 1.0 OG1 D:THR302 3.8 28.2 1.0 NH1 D:ARG451 3.9 32.2 1.0 CZ D:ARG451 4.0 34.7 1.0 C D:THR301 4.1 29.6 1.0 CB D:THR302 4.1 28.2 1.0 CG2 D:THR301 4.3 27.6 1.0 CA D:THR302 4.4 30.6 1.0 NH2 D:ARG451 4.8 36.2 1.0 CG D:ARG451 4.9 29.4 1.0 O D:ASN300 5.0 26.6 1.0

Magnesium binding site 5 out of 5 in the Structure 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 Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg703 b:49.6 occ:1.00 O F:HOH840 2.5 50.2 1.0 N F:THR302 3.4 63.5 1.0 NH1 F:ARG451 3.7 65.8 1.0 CD F:ARG451 3.8 66.2 1.0 OG1 F:THR302 3.8 64.1 1.0 CB F:THR302 4.0 61.7 1.0 CG2 F:THR301 4.0 64.9 1.0 CA F:THR301 4.1 66.5 1.0 CZ F:ARG451 4.1 68.9 1.0 NE F:ARG451 4.1 69.1 1.0 C F:THR301 4.3 63.4 1.0 CA F:THR302 4.4 60.7 1.0 CB F:THR301 4.5 66.3 1.0 OG1 F:THR301 4.6 69.7 1.0 O F:ASN300 4.8 73.5 1.0 CG F:ARG451 5.0 63.6 1.0

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