Manganese in PDB 5zr6: Manganese-Dependent Transcriptional Repressor Complex with Manganese

The structure of Manganese-Dependent Transcriptional Repressor Complex with Manganese, PDB code: 5zr6 was solved by X.Y.Cong, S.J.Xu, J.B.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.29 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.120, 47.459, 88.468, 90.00, 116.04, 90.00
R / Rfree (%)	23.7 / 26.9

The binding sites of Manganese atom in the Manganese-Dependent Transcriptional Repressor Complex with Manganese (pdb code 5zr6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Manganese-Dependent Transcriptional Repressor Complex with Manganese, PDB code: 5zr6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Manganese-Dependent Transcriptional Repressor Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Manganese-Dependent Transcriptional Repressor Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:25.2 occ:1.00 ND1 A:HIS105 2.1 18.4 1.0 OE2 A:GLU90 2.1 25.0 1.0 NE2 A:HIS86 2.3 43.1 1.0 O A:HOH410 2.4 19.6 1.0 OD2 A:ASP170 2.4 24.3 1.0 CE1 A:HIS105 2.5 19.0 1.0 CD A:GLU90 3.1 24.1 1.0 CD2 A:HIS86 3.2 43.2 1.0 MN A:MN302 3.2 38.7 1.0 CE1 A:HIS86 3.3 42.8 1.0 CG A:HIS105 3.4 17.7 1.0 CG A:ASP170 3.4 22.3 1.0 OE1 A:GLU90 3.5 23.9 1.0 OD1 A:ASP170 3.7 20.6 1.0 NE2 A:HIS105 3.8 18.8 1.0 CB A:HIS105 4.1 19.1 1.0 CD2 A:HIS105 4.2 17.9 1.0 CG A:GLU90 4.3 22.8 1.0 CG A:HIS86 4.4 42.8 1.0 ND1 A:HIS86 4.4 43.3 1.0 OD2 A:ASP137 4.5 45.8 1.0 OD2 A:ASP133 4.6 43.9 1.0 CA A:HIS105 4.6 20.9 1.0 CE1 A:HIS135 4.7 39.4 1.0 ND1 A:HIS135 4.7 40.4 1.0 CB A:ASP170 4.7 24.5 1.0

Manganese binding site 2 out of 6 in the Manganese-Dependent Transcriptional Repressor Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Manganese-Dependent Transcriptional Repressor Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:38.7 occ:1.00 OD2 A:ASP133 1.7 43.9 1.0 OD2 A:ASP137 2.4 45.8 1.0 OE1 A:GLU90 2.5 23.9 1.0 ND1 A:HIS135 2.7 40.4 1.0 CG A:ASP133 2.9 46.0 1.0 O A:HOH410 3.1 19.6 1.0 CD A:GLU90 3.2 24.1 1.0 MN A:MN301 3.2 25.2 1.0 CG A:ASP137 3.3 45.4 1.0 OE2 A:GLU90 3.5 25.0 1.0 CE1 A:HIS135 3.5 39.4 1.0 OD2 A:ASP170 3.6 24.3 1.0 CB A:ASP133 3.7 47.5 1.0 CB A:ASP137 3.7 43.1 1.0 CG A:HIS135 3.8 41.5 1.0 OD1 A:ASP133 3.9 48.3 1.0 CB A:HIS135 4.2 44.0 1.0 CG A:ASP170 4.3 22.3 1.0 OD1 A:ASP137 4.4 46.6 1.0 CG A:GLU90 4.5 22.8 1.0 CG A:ARG87 4.6 31.1 1.0 NE2 A:HIS135 4.7 40.1 1.0 NE2 A:HIS86 4.8 43.1 1.0 CD2 A:HIS135 4.8 40.5 1.0 CB A:GLU90 4.9 21.0 1.0 CD2 A:HIS86 4.9 43.2 1.0 OD1 A:ASP170 4.9 20.6 1.0 NE A:ARG87 4.9 31.1 1.0 CB A:ASP170 5.0 24.5 1.0 CD A:ARG87 5.0 32.1 1.0

Manganese binding site 3 out of 6 in the Manganese-Dependent Transcriptional Repressor Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Manganese-Dependent Transcriptional Repressor Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:32.6 occ:1.00 OE1 A:GLU112 2.0 31.1 1.0 O A:GLU109 2.1 28.8 1.0 OE2 A:GLU109 2.4 36.5 1.0 NE2 A:HIS113 2.4 27.7 1.0 OD1 A:ASP16 2.5 37.4 1.0 CD A:GLU112 3.0 31.5 1.0 CD A:GLU109 3.1 34.1 1.0 CE1 A:HIS113 3.1 28.6 1.0 OD2 A:ASP16 3.2 37.5 1.0 CG A:ASP16 3.2 38.6 1.0 C A:GLU109 3.3 26.3 1.0 CG A:GLU109 3.3 29.8 1.0 CD2 A:HIS113 3.5 28.1 1.0 CG A:GLU112 3.6 31.7 1.0 CA A:GLU109 3.8 26.5 1.0 OE2 A:GLU112 4.0 30.4 1.0 CB A:GLU109 4.2 27.7 1.0 OE1 A:GLU109 4.2 36.2 1.0 ND1 A:HIS113 4.3 28.7 1.0 NZ A:LYS19 4.4 22.3 1.0 N A:VAL110 4.4 24.8 1.0 CG A:HIS113 4.5 28.9 1.0 CB A:ASP16 4.7 41.7 1.0 CA A:VAL110 4.7 23.8 1.0

Manganese binding site 4 out of 6 in the Manganese-Dependent Transcriptional Repressor Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Manganese-Dependent Transcriptional Repressor Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:40.6 occ:1.00 OD2 B:ASP133 2.2 41.2 1.0 OD2 B:ASP137 2.2 44.0 1.0 OE1 B:GLU90 2.5 39.9 1.0 ND1 B:HIS135 2.8 42.5 1.0 MN B:MN302 3.1 46.7 1.0 O B:HOH404 3.2 23.8 1.0 CG B:ASP133 3.3 41.1 1.0 CD B:GLU90 3.3 38.5 1.0 CG B:ASP137 3.3 44.6 1.0 CE1 B:HIS135 3.6 42.9 1.0 OE2 B:GLU90 3.6 41.2 1.0 CG B:HIS135 3.7 42.7 1.0 OD1 B:ASP133 3.7 43.0 1.0 CB B:HIS135 3.9 41.7 1.0 CB B:ASP137 3.9 42.6 1.0 OD2 B:ASP170 4.0 41.3 1.0 OD1 B:ASP137 4.4 45.4 1.0 CG B:ASP170 4.4 41.2 1.0 CG B:GLU90 4.5 35.2 1.0 CB B:ASP133 4.5 38.1 1.0 NE B:ARG87 4.6 24.8 1.0 NE2 B:HIS86 4.7 26.6 1.0 CD B:ARG87 4.7 23.1 1.0 CG B:ARG87 4.7 24.6 1.0 NE2 B:HIS135 4.7 43.7 1.0 CB B:GLU90 4.7 31.5 1.0 CD2 B:HIS135 4.8 43.4 1.0 CD2 B:HIS86 4.8 26.4 1.0 N B:HIS135 4.8 40.8 1.0 CB B:ASP170 4.9 40.2 1.0 CA B:HIS135 5.0 41.5 1.0

Manganese binding site 5 out of 6 in the Manganese-Dependent Transcriptional Repressor Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Manganese-Dependent Transcriptional Repressor Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:46.7 occ:1.00 OE2 B:GLU90 2.1 41.2 1.0 NE2 B:HIS86 2.4 26.6 1.0 OD2 B:ASP170 2.5 41.3 1.0 O B:HOH404 2.6 23.8 1.0 ND1 B:HIS105 2.7 23.8 1.0 CD B:GLU90 3.0 38.5 1.0 MN B:MN301 3.1 40.6 1.0 CD2 B:HIS86 3.3 26.4 1.0 OE1 B:GLU90 3.3 39.9 1.0 CE1 B:HIS86 3.5 26.6 1.0 CG B:ASP170 3.5 41.2 1.0 CE1 B:HIS105 3.5 24.1 1.0 CG B:HIS105 3.8 24.4 1.0 OD1 B:ASP170 4.0 42.2 1.0 CB B:HIS105 4.1 26.0 1.0 CG B:GLU90 4.3 35.2 1.0 ND1 B:HIS135 4.4 42.5 1.0 CE1 B:HIS135 4.5 42.9 1.0 CG B:HIS86 4.5 26.3 1.0 ND1 B:HIS86 4.5 26.0 1.0 CA B:HIS105 4.6 28.2 1.0 OD2 B:ASP137 4.6 44.0 1.0 CB B:ASP170 4.7 40.2 1.0 NE2 B:HIS105 4.7 24.9 1.0 CD2 B:HIS105 4.9 25.1 1.0 OD2 B:ASP133 4.9 41.2 1.0

Manganese binding site 6 out of 6 in the Manganese-Dependent Transcriptional Repressor Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Manganese-Dependent Transcriptional Repressor Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:48.0 occ:1.00 OD1 B:ASP16 2.2 47.9 1.0 OE1 B:GLU109 2.3 46.7 1.0 OE2 B:GLU112 2.3 37.9 1.0 NE2 B:HIS113 2.4 42.6 1.0 O B:GLU109 2.4 28.5 1.0 OD2 B:ASP16 2.8 49.1 1.0 CG B:ASP16 2.8 49.2 1.0 CD B:GLU112 3.1 36.9 1.0 CD2 B:HIS113 3.1 41.6 1.0 CD B:GLU109 3.3 43.4 1.0 CE1 B:HIS113 3.4 42.4 1.0 CG B:GLU112 3.6 34.2 1.0 C B:GLU109 3.6 29.2 1.0 CG B:GLU109 3.6 37.8 1.0 OE1 B:GLU112 4.0 37.5 1.0 CA B:GLU109 4.1 31.4 1.0 CB B:ASP16 4.3 50.7 1.0 CG B:HIS113 4.3 40.4 1.0 ND1 B:HIS113 4.4 42.0 1.0 OE2 B:GLU109 4.4 46.0 1.0 CB B:GLU109 4.5 33.6 1.0 O B:HOH401 4.5 56.8 1.0 NZ B:LYS19 4.6 28.6 1.0 N B:VAL110 4.7 27.4 1.0 CA B:ASP16 4.9 48.9 1.0

X.Y.Cong, Z.L.Yuan, Z.Wang, B.Wei, S.J.Xu, J.B.Wang. Crystal Structures of Manganese-Dependent Transcriptional Repressor Mntr (RV2788) From Mycobacterium Tuberculosis in Apo and Manganese Bound Forms. Biochem. Biophys. Res. V. 501 423 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 29730293
DOI: 10.1016/J.BBRC.2018.05.005