Cobalt in PDB 7b1v: Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt

The structure of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt, PDB code: 7b1v was solved by D.Maurer, F.J.Marcos-Torres, J.J.Griese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.10 / 2.04
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.888, 45.564, 66.275, 109.12, 93.2, 113.98
R / Rfree (%)	21.8 / 25.5

The binding sites of Cobalt atom in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt (pdb code 7b1v). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt, PDB code: 7b1v:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:18.9 occ:1.00 OE2 A:GLU105 1.9 18.6 1.0 O A:HOH406 2.0 22.9 1.0 O A:CSD102 2.0 19.0 1.0 OD1 A:CSD102 2.1 21.2 1.0 NE2 A:HIS106 2.2 20.6 1.0 SD A:MET10 2.5 25.3 1.0 C A:CSD102 3.0 19.9 1.0 CD A:GLU105 3.0 18.9 1.0 CD2 A:HIS106 3.1 20.8 1.0 CE1 A:HIS106 3.2 20.7 1.0 SG A:CSD102 3.4 22.3 1.0 CA A:CSD102 3.5 20.2 1.0 CE A:MET10 3.5 25.7 1.0 CG A:MET10 3.5 26.7 1.0 CG A:GLU105 3.6 19.0 1.0 CB A:CSD102 3.8 20.8 1.0 OD2 A:CSD102 3.9 21.6 1.0 OE1 A:GLU105 4.1 19.2 1.0 O A:LEU4 4.1 29.3 1.0 CG A:HIS106 4.2 20.7 1.0 N A:ARG103 4.2 19.4 1.0 ND1 A:HIS106 4.3 20.5 1.0 NH1 A:ARG13 4.4 29.5 1.0 CA A:ARG103 4.7 19.5 1.0 N A:CSD102 4.8 19.7 1.0 CB A:MET10 4.9 27.2 1.0 O A:ALA101 5.0 19.9 1.0

Cobalt binding site 2 out of 4 in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:23.0 occ:1.00 OE1 A:GLU172 1.8 23.0 1.0 OE2 A:GLU83 1.9 23.1 1.0 NE2 A:HIS79 2.1 17.8 1.0 ND1 A:HIS98 2.1 23.8 1.0 OE1 A:GLN175 2.3 22.8 1.0 CD A:GLU83 2.9 23.4 1.0 CD A:GLU172 2.9 24.4 1.0 CE1 A:HIS98 3.0 24.0 1.0 CE1 A:HIS79 3.0 17.8 1.0 CD2 A:HIS79 3.1 18.0 1.0 CG A:HIS98 3.2 24.1 1.0 OE1 A:GLU83 3.3 24.1 1.0 CD A:GLN175 3.3 23.0 1.0 OE2 A:GLU172 3.4 24.4 1.0 CB A:HIS98 3.6 24.5 1.0 O A:HOH404 3.7 26.0 1.0 NE2 A:GLN175 3.9 22.6 1.0 CA A:HIS98 4.1 25.1 1.0 CG A:GLU83 4.2 23.6 1.0 ND1 A:HIS79 4.2 17.8 1.0 NE2 A:HIS98 4.2 23.8 1.0 CG A:GLU172 4.2 25.0 1.0 CG A:HIS79 4.2 18.1 1.0 CD2 A:HIS98 4.3 23.8 1.0 CB A:GLN175 4.5 24.6 1.0 CG A:GLN175 4.5 23.9 1.0 CB A:GLU172 4.5 25.8 1.0 CA A:GLU172 4.6 26.3 1.0 CD2 A:TYR128 4.6 33.8 1.0 CE2 A:TYR128 4.7 35.0 1.0 O A:HIS98 4.8 25.0 1.0 C A:HIS98 4.9 25.0 1.0

Cobalt binding site 3 out of 4 in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:20.3 occ:1.00 OE2 B:GLU105 1.9 18.5 1.0 O B:CSD102 2.1 21.6 1.0 NE2 B:HIS106 2.1 21.4 1.0 OD1 B:CSD102 2.1 23.1 1.0 O B:HOH422 2.1 28.0 1.0 SD B:MET10 2.5 28.0 1.0 CD B:GLU105 3.0 18.7 1.0 CE1 B:HIS106 3.0 21.9 1.0 CD2 B:HIS106 3.1 21.4 1.0 C B:CSD102 3.1 21.1 1.0 SG B:CSD102 3.5 23.8 1.0 CG B:GLU105 3.5 19.0 1.0 CG B:MET10 3.5 28.3 1.0 CE B:MET10 3.6 28.6 1.0 CA B:CSD102 3.6 21.2 1.0 CB B:CSD102 3.9 22.3 1.0 OE1 B:GLU105 4.1 18.8 1.0 OD2 B:CSD102 4.1 23.9 1.0 ND1 B:HIS106 4.1 21.6 1.0 O B:LEU4 4.2 34.1 1.0 CG B:HIS106 4.2 21.5 1.0 NH1 B:ARG13 4.2 26.4 1.0 N B:ARG103 4.3 20.7 1.0 CA B:ARG103 4.7 20.5 1.0 N B:CSD102 4.9 20.3 1.0 CB B:MET10 5.0 28.4 1.0 O B:ALA101 5.0 19.3 1.0

Cobalt binding site 4 out of 4 in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:22.1 occ:1.00 OE2 B:GLU83 1.9 22.9 1.0 ND1 B:HIS98 2.0 22.9 1.0 OE1 B:GLU172 2.0 26.4 1.0 NE2 B:HIS79 2.1 19.0 1.0 OE1 B:GLN175 2.2 23.7 1.0 CE1 B:HIS98 2.8 23.0 1.0 CD B:GLU83 2.9 23.3 1.0 CG B:HIS98 3.1 23.7 1.0 CE1 B:HIS79 3.1 19.2 1.0 CD B:GLU172 3.1 28.0 1.0 CD2 B:HIS79 3.1 19.4 1.0 CD B:GLN175 3.2 24.6 1.0 OE1 B:GLU83 3.3 23.0 1.0 O B:HOH404 3.5 21.6 1.0 CB B:HIS98 3.6 23.7 1.0 OE2 B:GLU172 3.6 28.9 1.0 NE2 B:GLN175 3.8 24.3 1.0 NE2 B:HIS98 4.0 23.5 1.0 CA B:HIS98 4.0 24.0 1.0 CD2 B:HIS98 4.1 23.8 1.0 CG B:GLU83 4.2 23.7 1.0 ND1 B:HIS79 4.2 19.4 1.0 CG B:HIS79 4.3 19.4 1.0 CG B:GLU172 4.4 27.9 1.0 CG B:GLN175 4.4 25.8 1.0 CB B:GLN175 4.4 27.0 1.0 CB B:GLU172 4.6 28.1 1.0 CD2 B:TYR128 4.6 27.5 1.0 CE2 B:TYR128 4.7 27.3 1.0 CA B:GLU172 4.7 28.7 1.0 O B:HIS98 4.7 24.4 1.0 C B:HIS98 4.9 24.5 1.0

F.J.Marcos-Torres, D.Maurer, J.J.Griese. The Bacterial Iron Sensor Ider Recognizes Its Dna Targets By Indirect Readout Biorxiv 2021.
DOI: 10.1101/2021.02.12.430932