Manganese in PDB 6vdf: Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium (Twinned)

The structure of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium (Twinned), PDB code: 6vdf 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)	59.90 / 1.92
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.948, 42.957, 181.209, 94.28, 94.02, 111.78
R / Rfree (%)	21.1 / 26.1

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

Manganese binding site 1 out of 3 in the Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium (Twinned)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium (Twinned) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn604 b:45.0 occ:1.00 O A:HOH852 2.3 23.6 1.0 HG23 A:THR301 2.4 14.6 1.0 H A:THR302 3.0 14.7 1.0 HD3 A:ARG451 3.0 11.7 1.0 HA A:THR301 3.2 14.2 1.0 O A:HOH853 3.4 26.4 1.0 CG2 A:THR301 3.4 12.1 1.0 N A:THR302 3.8 12.2 1.0 HG22 A:THR301 3.8 14.6 1.0 CD A:ARG451 3.8 9.7 1.0 HG21 A:THR301 3.8 14.6 1.0 HH11 A:ARG451 3.9 11.6 1.0 NE A:ARG451 4.0 9.7 1.0 CA A:THR301 4.0 11.9 1.0 OG1 A:THR302 4.0 12.3 1.0 NH1 A:ARG451 4.1 9.7 1.0 CB A:THR301 4.1 12.0 1.0 CZ A:ARG451 4.1 9.7 1.0 HD2 A:ARG451 4.1 11.7 1.0 O A:HOH838 4.2 27.0 1.0 O A:HOH829 4.2 27.7 1.0 OG1 A:THR301 4.3 12.2 1.0 HB A:THR302 4.3 14.7 1.0 HE A:ARG451 4.4 11.7 1.0 C A:THR301 4.5 11.7 1.0 HH12 A:ARG451 4.5 11.6 1.0 HG1 A:THR302 4.6 14.8 1.0 CB A:THR302 4.6 12.2 1.0 CA A:THR302 4.8 12.1 1.0 O A:ASN300 4.9 12.0 1.0 NH2 A:ARG451 4.9 9.7 1.0 HG2 A:ARG451 4.9 11.5 1.0 HD21 A:ASN403 5.0 24.7 1.0 HG1 A:THR301 5.0 14.6 1.0

Manganese binding site 2 out of 3 in the Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium (Twinned)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium (Twinned) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:65.9 occ:1.00 O B:HOH759 2.4 23.9 1.0 HH11 B:ARG451 3.7 22.2 1.0 NH1 B:ARG451 3.7 18.5 1.0 HD3 B:ARG451 3.8 21.0 1.0 HH12 B:ARG451 3.9 22.2 1.0 CZ B:ARG451 4.1 18.2 1.0 H B:THR302 4.1 18.7 1.0 O B:HOH774 4.2 27.1 1.0 HG23 B:THR301 4.3 23.9 1.0 NE B:ARG451 4.5 18.0 1.0 OG1 B:THR302 4.5 15.6 1.0 CD B:ARG451 4.6 17.5 1.0 HB B:THR302 4.6 18.6 1.0 HD21 B:ASN403 4.7 22.4 1.0 NH2 B:ARG451 4.7 18.5 1.0 HA B:THR301 4.7 22.7 1.0 HH22 B:ARG451 4.8 22.2 1.0 O B:HOH802 4.9 35.5 1.0 N B:THR302 5.0 15.6 1.0 OD1 B:ASN403 5.0 18.0 1.0 HE B:ARG451 5.0 21.6 1.0

Manganese binding site 3 out of 3 in the Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium (Twinned)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium (Twinned) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn704 b:67.2 occ:1.00 HG23 D:THR301 2.6 15.3 1.0 H D:THR302 2.8 11.6 1.0 HH11 D:ARG451 2.9 14.7 1.0 HD3 D:ARG451 3.1 14.5 1.0 NH1 D:ARG451 3.2 12.2 1.0 HG22 D:THR301 3.3 15.3 1.0 CG2 D:THR301 3.3 12.7 1.0 HB D:THR302 3.4 11.6 1.0 HH12 D:ARG451 3.4 14.7 1.0 OG1 D:THR302 3.4 9.7 1.0 N D:THR302 3.6 9.6 1.0 HG21 D:THR301 3.8 15.3 1.0 CB D:THR302 3.8 9.7 1.0 CZ D:ARG451 3.8 12.2 1.0 HA D:THR301 3.9 14.7 1.0 CD D:ARG451 4.0 12.1 1.0 HG1 D:THR302 4.0 11.6 1.0 NE D:ARG451 4.1 12.2 1.0 CA D:THR302 4.4 9.6 1.0 CA D:THR301 4.5 12.2 1.0 CB D:THR301 4.5 12.3 1.0 HD2 D:ARG451 4.5 14.5 1.0 HG2 D:ARG451 4.6 14.2 1.0 C D:THR301 4.6 11.4 1.0 H D:ASP303 4.6 14.6 1.0 NH2 D:ARG451 4.7 12.3 1.0 HE D:ARG451 4.8 14.6 1.0 HH22 D:ARG451 4.8 14.8 1.0 CG D:ARG451 4.9 11.8 1.0 HB3 D:ASP268 5.0 14.5 1.0 HA D:THR302 5.0 11.6 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