Cobalt in PDB 1fx7: Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis

The structure of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis, PDB code: 1fx7 was solved by M.D.Feese, B.P.Ingason, J.Goranson-Siekierke, R.K.Holmes, W.J.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.309, 113.970, 236.210, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 27.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis (pdb code 1fx7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 13 binding sites of Cobalt where determined in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis, PDB code: 1fx7:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2001 b:21.3 occ:1.00 OE2 A:GLU83 2.0 23.7 1.0 OE1 A:GLU172 2.0 20.8 1.0 OE1 A:GLN175 2.1 23.2 1.0 ND1 A:HIS98 2.1 19.1 1.0 NE2 A:HIS79 2.1 17.9 1.0 CD A:GLU83 2.9 23.8 1.0 CE1 A:HIS98 3.0 20.3 1.0 CD A:GLN175 3.1 20.9 1.0 CD A:GLU172 3.1 19.5 1.0 CE1 A:HIS79 3.1 22.2 1.0 CD2 A:HIS79 3.1 20.1 1.0 CG A:HIS98 3.2 23.3 1.0 OE1 A:GLU83 3.3 18.7 1.0 CB A:HIS98 3.6 21.4 1.0 OE2 A:GLU172 3.6 23.2 1.0 NE2 A:GLN175 3.6 18.4 1.0 O A:HOH2010 3.8 19.9 1.0 CA A:HIS98 3.9 26.3 1.0 NE2 A:HIS98 4.2 24.2 1.0 CG A:GLU83 4.2 19.2 1.0 ND1 A:HIS79 4.2 20.3 1.0 CD2 A:HIS98 4.3 25.3 1.0 CG A:HIS79 4.3 23.3 1.0 CG A:GLN175 4.3 22.2 1.0 CG A:GLU172 4.3 22.6 1.0 CB A:GLN175 4.3 18.7 1.0 CB A:GLU172 4.6 20.0 1.0 O A:HIS98 4.7 19.0 1.0 CE1 A:PHE128 4.7 24.3 1.0 CD1 A:PHE128 4.7 23.0 1.0 CA A:GLU172 4.7 22.3 1.0 C A:HIS98 4.8 21.6 1.0

Cobalt binding site 2 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2002 b:23.3 occ:1.00 OE2 A:GLU105 2.0 23.9 1.0 O A:CYS102 2.1 21.2 1.0 NE2 A:HIS106 2.2 20.9 1.0 O A:HOH2011 2.3 24.0 1.0 SG A:CYS102 2.4 23.0 1.0 SD A:MET10 2.5 19.1 1.0 CD A:GLU105 3.0 22.2 1.0 C A:CYS102 3.1 23.2 1.0 CE1 A:HIS106 3.1 20.4 1.0 CD2 A:HIS106 3.1 19.9 1.0 CE A:MET10 3.4 24.4 1.0 CA A:CYS102 3.5 17.3 1.0 CG A:MET10 3.5 18.8 1.0 CB A:CYS102 3.5 22.4 1.0 CG A:GLU105 3.6 21.6 1.0 OE1 A:GLU105 4.1 24.5 1.0 NH1 A:ARG13 4.1 20.3 1.0 ND1 A:HIS106 4.2 20.6 1.0 CG A:HIS106 4.2 18.5 1.0 N A:ARG103 4.2 22.9 1.0 O A:HOH2012 4.3 30.9 1.0 O A:LEU4 4.4 24.8 1.0 CA A:ARG103 4.8 24.5 1.0 N A:CYS102 4.9 23.4 1.0 CB A:MET10 4.9 19.4 1.0

Cobalt binding site 3 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2009 b:29.2 occ:1.00 O A:HOH2013 1.9 26.2 1.0 O A:HOH2015 1.9 29.8 1.0 NE2 A:HIS219 2.1 24.4 1.0 NE2 A:HIS223 2.1 24.6 1.0 O A:HOH2016 2.2 27.6 1.0 O A:HOH2014 2.2 38.5 1.0 CE1 A:HIS219 2.9 28.4 1.0 CE1 A:HIS223 3.1 28.9 1.0 CD2 A:HIS223 3.1 24.1 1.0 CD2 A:HIS219 3.2 24.1 1.0 ND1 A:HIS219 4.1 26.1 1.0 ND1 A:HIS223 4.2 22.7 1.0 CG A:HIS219 4.3 26.8 1.0 CG A:HIS223 4.3 22.7 1.0 O3 A:SO41004 4.3 30.9 1.0 O4 A:SO41004 4.3 38.4 1.0 O A:HOH2118 4.4 42.0 1.0 O A:HOH2077 4.4 37.6 1.0 O A:HOH2081 4.5 38.7 1.0 S A:SO41004 4.8 31.4 1.0 CG1 A:VAL23 4.9 30.4 1.0

Cobalt binding site 4 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2003 b:27.5 occ:1.00 ND1 B:HIS98 1.9 19.0 1.0 OE2 B:GLU83 1.9 26.3 1.0 OE2 B:GLU172 2.1 29.8 1.0 OE1 B:GLN175 2.1 29.1 1.0 NE2 B:HIS79 2.2 25.5 1.0 CE1 B:HIS98 2.8 26.5 1.0 CD B:GLU83 3.0 26.6 1.0 CG B:HIS98 3.1 23.9 1.0 CD B:GLN175 3.1 30.8 1.0 CE1 B:HIS79 3.1 28.9 1.0 CD B:GLU172 3.1 26.4 1.0 CD2 B:HIS79 3.2 22.9 1.0 OE1 B:GLU83 3.5 27.9 1.0 CB B:HIS98 3.5 23.6 1.0 OE1 B:GLU172 3.6 25.9 1.0 NE2 B:GLN175 3.6 26.1 1.0 O B:HOH2011 3.8 26.3 1.0 CA B:HIS98 3.9 29.6 1.0 NE2 B:HIS98 4.0 20.7 1.0 CD2 B:HIS98 4.1 21.8 1.0 CG B:GLU83 4.2 23.6 1.0 ND1 B:HIS79 4.3 29.0 1.0 CG B:HIS79 4.3 24.9 1.0 CG B:GLN175 4.3 22.9 1.0 CG B:GLU172 4.4 26.5 1.0 CB B:GLN175 4.4 27.5 1.0 CB B:GLU172 4.6 27.4 1.0 O B:HIS98 4.6 23.4 1.0 C B:HIS98 4.8 28.8 1.0 CA B:GLU172 4.8 30.1 1.0 CD1 B:PHE128 4.9 32.7 1.0 CE1 B:PHE128 4.9 35.2 1.0 N B:HIS98 4.9 23.3 1.0

Cobalt binding site 5 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2004 b:26.9 occ:1.00 O B:HOH2012 1.9 26.3 1.0 OE2 B:GLU105 2.0 21.0 1.0 NE2 B:HIS106 2.1 31.3 1.0 O B:CYS102 2.3 28.8 1.0 SG B:CYS102 2.5 29.5 1.0 SD B:MET10 2.5 26.1 1.0 CE1 B:HIS106 3.0 27.1 1.0 CD B:GLU105 3.1 25.9 1.0 CD2 B:HIS106 3.1 22.0 1.0 C B:CYS102 3.2 30.4 1.0 CE B:MET10 3.5 27.5 1.0 CG B:MET10 3.5 30.5 1.0 CA B:CYS102 3.5 27.2 1.0 CB B:CYS102 3.6 28.9 1.0 CG B:GLU105 3.6 19.9 1.0 ND1 B:HIS106 4.1 26.1 1.0 NH2 B:ARG13 4.1 26.0 1.0 OE1 B:GLU105 4.2 27.0 1.0 CG B:HIS106 4.2 30.4 1.0 O B:HOH2013 4.3 40.9 1.0 N B:ARG103 4.3 27.0 1.0 O B:LEU4 4.4 23.8 1.0 CA B:ARG103 4.8 21.5 1.0 CB B:MET10 4.9 24.3 1.0 N B:CYS102 4.9 23.3 1.0

Cobalt binding site 6 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2010 b:44.9 occ:1.00 O B:HOH2014 2.0 42.8 1.0 O B:HOH2016 2.1 41.5 1.0 NE2 B:HIS223 2.1 38.0 1.0 NE2 B:HIS219 2.2 38.8 1.0 O B:HOH2015 2.2 45.0 1.0 CD2 B:HIS223 3.0 32.8 1.0 CE1 B:HIS219 3.0 37.6 1.0 CE1 B:HIS223 3.3 41.8 1.0 CD2 B:HIS219 3.3 33.8 1.0 O3 B:SO41005 4.0 65.2 1.0 ND1 B:HIS219 4.2 42.6 1.0 CG B:HIS223 4.2 38.6 1.0 ND1 B:HIS223 4.3 36.0 1.0 CG B:HIS219 4.3 39.0 1.0 O B:HOH2134 4.6 50.8 1.0 O B:HOH2164 4.6 56.0 1.0 CG2 B:THR155 4.8 44.5 1.0 O4 B:SO41005 4.9 52.8 1.0 S B:SO41005 4.9 58.5 1.0

Cobalt binding site 7 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ C:Co2005 b:32.0 occ:1.00 ND1 C:HIS98 2.0 26.8 1.0 OE1 C:GLU172 2.0 32.4 1.0 OE1 C:GLN175 2.1 39.4 1.0 NE2 C:HIS79 2.1 36.0 1.0 OE1 C:GLU83 2.2 29.0 1.0 CE1 C:HIS98 2.8 28.4 1.0 CE1 C:HIS79 3.0 24.4 1.0 CD C:GLU83 3.0 38.3 1.0 CD C:GLN175 3.1 29.4 1.0 CD C:GLU172 3.1 31.9 1.0 CD2 C:HIS79 3.2 33.5 1.0 CG C:HIS98 3.3 25.3 1.0 OE2 C:GLU83 3.3 27.1 1.0 NE2 C:GLN175 3.5 27.4 1.0 OE2 C:GLU172 3.6 29.9 1.0 O C:HOH2012 3.7 26.8 1.0 CB C:HIS98 3.8 24.8 1.0 CA C:HIS98 4.0 28.1 1.0 NE2 C:HIS98 4.0 27.2 1.0 ND1 C:HIS79 4.2 31.4 1.0 CG C:GLU83 4.2 29.6 1.0 CD2 C:HIS98 4.2 26.2 1.0 CG C:GLU172 4.3 28.3 1.0 CG C:HIS79 4.3 30.8 1.0 CG C:GLN175 4.3 33.7 1.0 CB C:GLN175 4.4 30.9 1.0 CB C:GLU172 4.5 31.8 1.0 O C:HIS98 4.6 32.2 1.0 CA C:GLU172 4.7 37.1 1.0 C C:HIS98 4.8 24.1 1.0 CD1 C:PHE128 4.9 35.8 1.0

Cobalt binding site 8 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ C:Co2006 b:31.1 occ:1.00 OE2 C:GLU105 1.9 22.6 1.0 O C:HOH2013 2.1 34.6 1.0 NE2 C:HIS106 2.2 32.3 1.0 O C:CYS102 2.3 29.1 1.0 SD C:MET10 2.5 28.6 1.0 SG C:CYS102 2.6 32.5 1.0 CD C:GLU105 3.0 37.6 1.0 C C:CYS102 3.1 31.1 1.0 CD2 C:HIS106 3.1 22.1 1.0 CE1 C:HIS106 3.2 28.3 1.0 CE C:MET10 3.3 35.5 1.0 CG C:MET10 3.5 32.4 1.0 CA C:CYS102 3.5 27.7 1.0 CG C:GLU105 3.5 28.2 1.0 CB C:CYS102 3.6 31.4 1.0 OE1 C:GLU105 4.0 30.4 1.0 NH2 C:ARG13 4.1 35.8 1.0 CG C:HIS106 4.3 27.6 1.0 ND1 C:HIS106 4.3 32.8 1.0 N C:ARG103 4.3 32.1 1.0 O C:LEU4 4.3 31.0 1.0 O C:HOH2014 4.4 36.6 1.0 CA C:ARG103 4.8 31.6 1.0 CB C:MET10 4.9 27.0 1.0 N C:CYS102 4.9 31.5 1.0

Cobalt binding site 9 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ C:Co2011 b:44.4 occ:1.00 O C:HOH2018 1.9 31.7 1.0 NE2 C:HIS219 2.0 27.8 1.0 O C:HOH2015 2.1 39.8 1.0 O C:HOH2017 2.2 51.3 1.0 NE2 C:HIS223 2.3 32.7 1.0 O C:HOH2016 2.5 51.1 1.0 CE1 C:HIS219 2.7 35.9 1.0 CD2 C:HIS223 3.0 30.3 1.0 CD2 C:HIS219 3.2 33.5 1.0 CE1 C:HIS223 3.5 38.0 1.0 ND1 C:HIS219 3.9 35.0 1.0 CG C:HIS219 4.2 32.3 1.0 CG C:HIS223 4.2 40.6 1.0 O C:HOH2077 4.4 52.1 1.0 ND1 C:HIS223 4.4 45.9 1.0 O1 C:SO41003 4.5 53.5 1.0 O4 C:SO41003 4.6 41.2 1.0 O C:HOH2075 4.8 50.3 1.0 CG2 C:THR155 5.0 36.9 1.0 CG1 C:VAL23 5.0 52.2 1.0

Cobalt binding site 10 out of 13 in the Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of the Iron-Dependent Regulator (Ider) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ D:Co2007 b:30.5 occ:1.00 OE1 D:GLU172 2.0 32.9 1.0 OE1 D:GLU83 2.0 28.4 1.0 NE2 D:HIS79 2.1 34.4 1.0 OE1 D:GLN175 2.1 36.0 1.0 ND1 D:HIS98 2.2 24.6 1.0 CD D:GLU83 2.9 39.8 1.0 CE1 D:HIS98 3.0 25.4 1.0 CD D:GLU172 3.1 29.2 1.0 CD2 D:HIS79 3.1 35.8 1.0 CD D:GLN175 3.1 33.5 1.0 CE1 D:HIS79 3.1 36.2 1.0 OE2 D:GLU83 3.3 31.7 1.0 CG D:HIS98 3.3 26.3 1.0 OE2 D:GLU172 3.6 31.1 1.0 O D:HOH2014 3.6 33.3 1.0 NE2 D:GLN175 3.6 29.4 1.0 CB D:HIS98 3.7 23.9 1.0 CA D:HIS98 4.0 27.4 1.0 NE2 D:HIS98 4.2 31.5 1.0 CG D:GLU83 4.2 30.9 1.0 CG D:GLU172 4.2 31.6 1.0 ND1 D:HIS79 4.2 30.6 1.0 CG D:HIS79 4.3 32.7 1.0 CD2 D:HIS98 4.3 23.9 1.0 CG D:GLN175 4.4 35.5 1.0 CB D:GLN175 4.5 30.3 1.0 CB D:GLU172 4.6 31.9 1.0 CA D:GLU172 4.7 33.9 1.0 O D:HIS98 4.8 29.2 1.0 C D:HIS98 4.9 31.8 1.0 CD1 D:PHE128 4.9 31.8 1.0 N D:HIS98 5.0 33.1 1.0

M.D.Feese, B.P.Ingason, J.Goranson-Siekierke, R.K.Holmes, W.G.Hol. Crystal Structure of the Iron-Dependent Regulator From Mycobacterium Tuberculosis at 2.0-A Resolution Reveals the Src Homology Domain 3-Like Fold and Metal Binding Function of the Third Domain. J.Biol.Chem. V. 276 5959 2001.
ISSN: ISSN 0021-9258
PubMed: 11053439
DOI: 10.1074/JBC.M007531200