Manganese in PDB 8pw0: Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Manganese and Bound to DR1709 Promotor

The structure of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Manganese and Bound to DR1709 Promotor, PDB code: 8pw0 was solved by C.Mota, D.De Sanctis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.88 / 2.20
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.71, 67.71, 158.137, 90, 90, 90
R / Rfree (%)	18.3 / 22.7

The binding sites of Manganese atom in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Manganese and Bound to DR1709 Promotor (pdb code 8pw0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Manganese and Bound to DR1709 Promotor, PDB code: 8pw0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Manganese and Bound to DR1709 Promotor


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 DR2539 Complexed with Manganese and Bound to DR1709 Promotor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:44.5 occ:1.00 OE2 A:GLU105 2.1 47.0 1.0 OE2 A:GLU102 2.2 49.3 1.0 NE2 A:HIS106 2.2 48.7 1.0 O A:HOH304 2.2 41.5 1.0 OD1 A:ASP11 2.2 40.0 1.0 O A:GLU102 2.3 45.9 1.0 CE1 A:HIS106 3.0 37.3 1.0 CG A:ASP11 3.1 44.1 1.0 CD A:GLU102 3.1 62.8 1.0 CD A:GLU105 3.2 55.5 1.0 OD2 A:ASP11 3.2 39.0 1.0 CD2 A:HIS106 3.2 35.2 1.0 C A:GLU102 3.4 49.1 1.0 CG A:GLU102 3.6 45.9 1.0 CG A:GLU105 3.8 45.6 1.0 NZ A:LYS14 3.8 58.8 1.0 CA A:GLU102 4.0 37.6 1.0 ND1 A:HIS106 4.1 39.4 1.0 OE1 A:GLU105 4.2 46.1 1.0 OE1 A:GLU102 4.2 57.1 1.0 CG A:HIS106 4.3 36.0 1.0 O A:HOH320 4.4 55.0 1.0 CB A:GLU102 4.4 46.5 1.0 O A:HOH343 4.5 56.6 1.0 N A:ALA103 4.5 43.5 1.0 CB A:ASP11 4.5 42.6 1.0 CE A:LYS14 4.8 54.3 1.0 CA A:ALA103 4.9 38.5 1.0

Manganese binding site 2 out of 4 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Manganese and Bound to DR1709 Promotor


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 DR2539 Complexed with Manganese and Bound to DR1709 Promotor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:52.1 occ:1.00 NE2 A:HIS78 2.1 60.0 1.0 OE2 A:GLU110 2.2 47.4 1.0 OE1 A:GLU113 2.2 60.1 1.0 OE1 A:GLU110 2.2 54.6 1.0 O A:HOH314 2.3 59.9 1.0 OE2 A:GLU74 2.3 79.6 1.0 CD A:GLU110 2.5 67.9 1.0 CE1 A:HIS78 3.0 52.7 1.0 CD A:GLU113 3.1 54.7 1.0 CD2 A:HIS78 3.2 45.7 1.0 CD A:GLU74 3.3 65.9 1.0 OE2 A:GLU113 3.3 50.4 1.0 CG A:GLU74 3.6 66.0 1.0 CG A:GLU110 4.0 64.2 1.0 ND1 A:HIS78 4.2 51.3 1.0 O A:HOH301 4.3 57.5 1.0 CG A:HIS78 4.3 48.6 1.0 OE1 A:GLU74 4.4 85.2 1.0 CG A:GLU113 4.4 51.2 1.0 CD1 A:LEU135 4.7 65.3 1.0 CA A:GLU110 4.8 50.0 1.0 CB A:GLU110 4.8 49.1 1.0 CB A:GLU113 4.8 47.3 1.0 CB A:GLU74 4.9 49.0 1.0 O A:GLU74 5.0 43.0 1.0

Manganese binding site 3 out of 4 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Manganese and Bound to DR1709 Promotor


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 DR2539 Complexed with Manganese and Bound to DR1709 Promotor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:62.5 occ:1.00 OE2 A:GLU83 2.1 63.6 1.0 ND1 A:HIS98 2.2 48.1 1.0 NE2 A:HIS79 2.2 67.5 1.0 O A:HOH319 2.3 69.6 1.0 O A:HOH341 2.6 46.4 1.0 CE1 A:HIS98 2.9 73.3 1.0 CD A:GLU83 3.1 59.8 1.0 CE1 A:HIS79 3.1 54.3 1.0 CD2 A:HIS79 3.3 51.8 1.0 CG A:HIS98 3.3 50.1 1.0 MN A:MN204 3.4 81.1 1.0 OE1 A:GLU83 3.4 76.6 1.0 CB A:HIS98 3.8 50.2 1.0 NE2 A:HIS98 4.1 50.4 1.0 CA A:HIS98 4.3 48.0 1.0 ND1 A:HIS79 4.3 43.6 1.0 CD2 A:HIS98 4.3 38.6 1.0 CG A:GLU83 4.3 46.7 1.0 CG A:HIS79 4.4 47.2 1.0 CE1 A:HIS128 4.5 83.7 1.0 O A:HOH338 4.5 50.8 1.0 ND1 A:HIS128 4.6 102.6 1.0 OD2 A:ASP130 4.9 94.5 1.0

Manganese binding site 4 out of 4 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Manganese and Bound to DR1709 Promotor


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 DR2539 Complexed with Manganese and Bound to DR1709 Promotor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:81.1 occ:1.00 OD2 A:ASP130 2.2 94.5 1.0 OE1 A:GLU83 2.2 76.6 1.0 OD2 A:ASP126 2.2 77.3 1.0 ND1 A:HIS128 2.4 102.6 1.0 O A:HOH341 3.1 46.4 1.0 CD A:GLU83 3.2 59.8 1.0 CE1 A:HIS128 3.3 83.7 1.0 CG A:ASP126 3.3 88.6 1.0 CG A:ASP130 3.4 105.6 1.0 MN A:MN203 3.4 62.5 1.0 OE2 A:GLU83 3.4 63.6 1.0 CG A:HIS128 3.5 100.5 1.0 O A:HOH319 3.5 69.6 1.0 OD1 A:ASP126 3.6 85.7 1.0 CB A:HIS128 3.8 62.5 1.0 CB A:ASP130 4.0 88.5 1.0 CG A:ARG80 4.3 54.2 1.0 OD1 A:ASP130 4.4 84.8 1.0 NE2 A:HIS128 4.4 81.2 1.0 CG A:GLU83 4.6 46.7 1.0 CD2 A:HIS128 4.6 88.0 1.0 CB A:ASP126 4.6 61.2 1.0 NE2 A:HIS79 4.6 67.5 1.0 NE A:ARG80 4.6 91.0 1.0 CD2 A:HIS79 4.8 51.8 1.0 N A:HIS128 4.9 75.5 1.0 CB A:GLU83 4.9 56.1 1.0 CA A:HIS128 5.0 87.4 1.0 CD A:ARG80 5.0 48.5 1.0

C.Mota, M.Webster, M.Saidi, U.Kapp, C.Zubieta, G.Giachin, J.A.Manso, D.De Sanctis. Metal Ion Activation and Dna Recognition By the Deinococcus Radiodurans Manganese Sensor DR2539. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38652591
DOI: 10.1111/FEBS.17140