Zinc in PDB 4mtd: Zinc Uptake Regulator Complexed with Zinc and Dna

The structure of Zinc Uptake Regulator Complexed with Zinc and Dna, PDB code: 4mtd was solved by B.A.Gilston, A.Mondragon, T.V.O'halloran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.34 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	193.324, 80.470, 98.770, 90.00, 120.15, 90.00
R / Rfree (%)	23.4 / 27.1

The binding sites of Zinc atom in the Zinc Uptake Regulator Complexed with Zinc and Dna (pdb code 4mtd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Zinc Uptake Regulator Complexed with Zinc and Dna, PDB code: 4mtd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Zinc Uptake Regulator Complexed with Zinc and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc Uptake Regulator Complexed with Zinc and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:53.6 occ:1.00 SG A:CYS146 2.3 53.0 1.0 SG A:CYS103 2.3 52.0 1.0 SG A:CYS143 2.3 63.6 1.0 SG A:CYS106 2.3 53.2 1.0 CB A:CYS103 3.2 47.1 1.0 CB A:CYS146 3.3 54.1 1.0 CB A:CYS106 3.4 48.8 1.0 CB A:CYS143 3.5 60.0 1.0 N A:CYS143 3.9 60.3 1.0 N A:CYS106 4.0 50.3 1.0 CA A:CYS143 4.3 61.3 1.0 CA A:CYS106 4.3 49.3 1.0 N A:CYS146 4.3 56.6 1.0 CA A:CYS146 4.4 55.5 1.0 CA A:CYS103 4.7 45.9 1.0 O A:CYS143 4.8 63.0 1.0 CB A:ALA108 4.8 44.7 1.0 C A:CYS143 4.8 61.5 1.0 CB A:ARG105 4.8 54.5 1.0 C A:CYS106 5.0 46.8 1.0

Zinc binding site 2 out of 8 in the Zinc Uptake Regulator Complexed with Zinc and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc Uptake Regulator Complexed with Zinc and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:63.3 occ:1.00 OE1 A:GLU111 2.0 53.9 1.0 NE2 A:HIS77 2.1 55.2 1.0 NE2 A:HIS96 2.1 73.2 1.0 SG A:CYS88 2.3 61.8 1.0 OE2 A:GLU111 2.6 49.5 1.0 CD A:GLU111 2.6 52.3 1.0 CE1 A:HIS77 2.9 52.8 1.0 CE1 A:HIS96 2.9 76.2 1.0 CD2 A:HIS77 3.2 51.8 1.0 CD2 A:HIS96 3.2 74.5 1.0 CB A:CYS88 3.3 60.5 1.0 CA A:CYS88 4.0 59.6 1.0 OE1 A:GLN93 4.0 0.0 1.0 ND1 A:HIS77 4.1 53.2 1.0 ND1 A:HIS96 4.1 76.4 1.0 CG A:GLU111 4.1 53.6 1.0 ND1 A:HIS89 4.2 75.5 1.0 CG A:HIS77 4.2 50.3 1.0 CG A:HIS96 4.3 76.4 1.0 OG A:SER98 4.5 74.0 1.0 N A:HIS89 4.5 67.8 1.0 C A:CYS88 4.6 61.4 1.0 CE1 A:HIS89 4.6 75.8 1.0 O A:LEU90 4.8 76.8 1.0 CB A:SER98 4.9 69.8 1.0

Zinc binding site 3 out of 8 in the Zinc Uptake Regulator Complexed with Zinc and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc Uptake Regulator Complexed with Zinc and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:54.5 occ:1.00 OE1 B:GLU111 2.0 48.5 1.0 NE2 B:HIS77 2.1 50.8 1.0 NE2 B:HIS96 2.1 75.2 1.0 SG B:CYS88 2.3 53.8 1.0 CE1 B:HIS96 2.6 81.5 1.0 CD B:GLU111 2.7 51.7 1.0 OE2 B:GLU111 2.9 54.0 1.0 CD2 B:HIS77 3.0 45.4 1.0 CE1 B:HIS77 3.1 48.0 1.0 CB B:CYS88 3.3 54.2 1.0 CD2 B:HIS96 3.4 79.8 1.0 ND1 B:HIS89 3.8 90.6 1.0 ND1 B:HIS96 3.9 84.5 1.0 CA B:CYS88 3.9 51.5 1.0 CG B:GLU111 4.2 51.1 1.0 N B:HIS89 4.2 67.5 1.0 ND1 B:HIS77 4.2 47.6 1.0 CG B:HIS77 4.2 45.2 1.0 CG B:HIS96 4.2 83.2 1.0 CE1 B:HIS89 4.3 90.5 1.0 C B:CYS88 4.4 57.2 1.0 CB B:SER98 4.5 69.9 1.0 OG B:SER98 4.6 69.8 1.0 O B:LEU90 4.8 80.5 1.0 N B:LEU90 4.9 76.8 1.0

Zinc binding site 4 out of 8 in the Zinc Uptake Regulator Complexed with Zinc and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc Uptake Regulator Complexed with Zinc and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:67.8 occ:1.00 SG B:CYS146 2.3 76.2 1.0 SG B:CYS143 2.3 66.9 1.0 SG B:CYS106 2.3 72.8 1.0 SG B:CYS103 2.3 58.5 1.0 CB B:CYS146 3.3 76.9 1.0 CB B:CYS103 3.3 57.1 1.0 CB B:CYS106 3.3 71.6 1.0 CB B:CYS143 3.4 63.7 1.0 N B:CYS143 3.8 59.9 1.0 N B:CYS146 3.9 72.5 1.0 N B:CYS106 3.9 73.0 1.0 CA B:CYS143 4.1 62.5 1.0 CA B:CYS146 4.2 74.8 1.0 CA B:CYS106 4.2 73.2 1.0 C B:CYS143 4.6 61.2 1.0 O B:CYS143 4.7 54.5 1.0 CA B:CYS103 4.8 59.3 1.0 CB B:ARG105 4.8 85.2 1.0 CB B:ALA145 4.9 66.8 1.0 C B:CYS106 4.9 75.2 1.0 C B:LEU142 4.9 59.0 1.0 C B:ALA145 5.0 69.9 1.0

Zinc binding site 5 out of 8 in the Zinc Uptake Regulator Complexed with Zinc and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc Uptake Regulator Complexed with Zinc and Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:45.6 occ:1.00 SG C:CYS106 2.3 44.5 1.0 SG C:CYS146 2.3 49.4 1.0 SG C:CYS143 2.3 55.2 1.0 SG C:CYS103 2.3 45.0 1.0 CB C:CYS106 3.2 46.4 1.0 CB C:CYS103 3.3 44.2 1.0 CB C:CYS146 3.4 50.3 1.0 CB C:CYS143 3.6 51.2 1.0 N C:CYS106 3.7 48.5 1.0 CA C:CYS106 4.0 47.0 1.0 N C:CYS143 4.1 51.5 1.0 N C:CYS146 4.2 52.1 1.0 CA C:CYS143 4.3 51.2 1.0 CA C:CYS146 4.4 50.9 1.0 CB C:ARG105 4.7 54.1 1.0 CA C:CYS103 4.7 44.6 1.0 C C:CYS106 4.8 47.8 1.0 C C:ARG105 4.8 51.1 1.0 CB C:ALA108 4.9 46.8 1.0 C C:CYS143 4.9 50.9 1.0 O C:CYS143 4.9 49.9 1.0 N C:GLY107 5.0 48.6 1.0

Zinc binding site 6 out of 8 in the Zinc Uptake Regulator Complexed with Zinc and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zinc Uptake Regulator Complexed with Zinc and Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:56.5 occ:1.00 OE1 C:GLU111 2.0 48.2 1.0 NE2 C:HIS77 2.1 65.2 1.0 NE2 C:HIS96 2.1 72.8 1.0 SG C:CYS88 2.3 62.9 1.0 CD C:GLU111 2.8 50.5 1.0 OE2 C:GLU111 2.8 51.2 1.0 CE1 C:HIS96 2.9 74.6 1.0 CD2 C:HIS77 2.9 62.2 1.0 CE1 C:HIS77 3.2 63.6 1.0 CD2 C:HIS96 3.2 74.5 1.0 CB C:CYS88 3.4 64.8 1.0 N C:HIS89 3.8 90.3 1.0 CA C:CYS88 3.8 67.4 1.0 ND1 C:HIS96 4.1 75.8 1.0 CG C:HIS77 4.1 60.4 1.0 CG C:GLU111 4.2 51.1 1.0 ND1 C:HIS77 4.2 62.8 1.0 CG C:HIS96 4.3 78.8 1.0 C C:CYS88 4.3 75.8 1.0 CB C:SER98 4.5 65.5 1.0 CB C:HIS89 4.7 0.5 1.0 CA C:HIS89 4.8 0.6 1.0 O C:LEU90 4.9 0.5 1.0

Zinc binding site 7 out of 8 in the Zinc Uptake Regulator Complexed with Zinc and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zinc Uptake Regulator Complexed with Zinc and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:99.5 occ:1.00 SG D:CYS106 2.3 0.9 1.0 SG D:CYS103 2.3 88.1 1.0 SG D:CYS146 2.3 0.0 1.0 SG D:CYS143 2.3 96.1 1.0 CB D:CYS103 3.3 89.9 1.0 CB D:CYS146 3.3 0.4 1.0 CB D:CYS106 3.4 98.0 1.0 CB D:CYS143 3.5 95.3 1.0 N D:CYS143 3.8 94.1 1.0 N D:CYS146 4.0 0.1 1.0 CA D:CYS143 4.1 95.6 1.0 N D:CYS106 4.2 95.0 1.0 CA D:CYS146 4.2 0.8 1.0 CA D:CYS106 4.3 98.9 1.0 O D:CYS143 4.3 100.0 1.0 C D:CYS143 4.4 97.8 1.0 CA D:CYS103 4.7 86.8 1.0 C D:CYS106 4.8 99.9 1.0 C D:LEU142 5.0 91.8 1.0

Zinc binding site 8 out of 8 in the Zinc Uptake Regulator Complexed with Zinc and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zinc Uptake Regulator Complexed with Zinc and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:59.2 occ:1.00 OE1 D:GLU111 2.0 56.9 1.0 NE2 D:HIS96 2.1 72.5 1.0 NE2 D:HIS77 2.1 58.1 1.0 SG D:CYS88 2.3 57.0 1.0 CD D:GLU111 2.6 57.4 1.0 OE2 D:GLU111 2.6 57.6 1.0 CE1 D:HIS96 2.8 76.5 1.0 CD2 D:HIS77 2.9 53.6 1.0 CE1 D:HIS77 3.2 56.1 1.0 CD2 D:HIS96 3.3 77.1 1.0 CB D:CYS88 3.3 58.1 1.0 CA D:CYS88 4.0 57.7 1.0 ND1 D:HIS96 4.0 77.5 1.0 CG D:GLU111 4.1 61.2 1.0 CG D:HIS77 4.1 53.1 1.0 CB D:LEU90 4.2 77.4 1.0 ND1 D:HIS77 4.2 55.0 1.0 CG D:HIS96 4.3 82.7 1.0 N D:LEU90 4.5 72.9 1.0 CD1 D:LEU90 4.5 80.5 1.0 N D:HIS89 4.5 65.1 1.0 C D:CYS88 4.5 59.8 1.0 OG D:SER98 4.6 84.0 1.0 CG D:LEU90 4.6 80.0 1.0 CB D:SER98 4.7 82.8 1.0 CA D:LEU90 4.8 74.9 1.0 C D:LEU90 4.9 74.6 1.0

B.A.Gilston, S.Wang, M.D.Marcus, M.A.Canalizo-Hernandez, E.P.Swindell, Y.Xue, A.Mondragon, T.V.O'halloran. Structural and Mechanistic Basis of Zinc Regulation Across the E. Coli Zur Regulon. Plos Biol. V. 12 01987 2014.
ISSN: ISSN 1544-9173
PubMed: 25369000
DOI: 10.1371/JOURNAL.PBIO.1001987