Zinc in PDB 5uk7: Escherichia Coli Hfq Bound to Dsdna

The structure of Escherichia Coli Hfq Bound to Dsdna, PDB code: 5uk7 was solved by J.Orans, A.R.Kovach, R.G.Brennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.69 / 3.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.749, 65.795, 81.996, 105.93, 92.28, 119.92
R / Rfree (%)	21.1 / 26

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Escherichia Coli Hfq Bound to Dsdna (pdb code 5uk7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Escherichia Coli Hfq Bound to Dsdna, PDB code: 5uk7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:24.0 occ:0.26 O A:HOH204 2.0 22.7 1.0 O I:HOH213 2.1 43.2 1.0 ND1 A:HIS57 2.5 23.5 1.0 CE1 A:HIS57 2.9 23.9 1.0 O I:HOH212 3.1 44.6 1.0 CG A:HIS57 3.8 25.9 1.0 CD1 A:TYR55 4.0 27.6 1.0 NE2 A:HIS57 4.2 25.4 1.0 CE1 A:TYR55 4.4 30.0 1.0 CB A:HIS57 4.4 23.6 1.0 CD2 A:HIS57 4.6 25.8 1.0 CD1 A:PHE42 4.7 44.8 1.0 CA I:HIS57 4.8 23.0 1.0 O I:LYS56 4.8 29.8 1.0 CB A:PHE42 4.9 42.7 1.0 CB I:LYS56 4.9 30.7 1.0 CG A:TYR55 4.9 29.3 1.0 C I:LYS56 4.9 28.0 1.0 N I:HIS57 4.9 25.3 1.0

Zinc binding site 2 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:34.0 occ:0.28 O B:HOH207 2.1 46.7 1.0 O A:HOH205 2.2 38.5 1.0 ND1 B:HIS57 2.7 24.4 1.0 CE1 B:HIS57 3.2 25.5 1.0 O A:HOH202 3.7 44.1 1.0 CG B:HIS57 4.0 26.2 1.0 CD1 B:PHE42 4.3 42.2 1.0 CD1 B:TYR55 4.4 28.0 1.0 NE2 B:HIS57 4.5 25.8 1.0 CB B:HIS57 4.6 25.8 1.0 CG B:PHE42 4.6 40.1 1.0 CB B:PHE42 4.7 38.5 1.0 CE1 B:TYR55 4.7 34.7 1.0 CD2 B:HIS57 4.9 26.0 1.0 CE1 B:PHE42 4.9 38.8 1.0

Zinc binding site 3 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:29.3 occ:0.27 O C:HOH206 2.1 31.8 1.0 O C:HOH207 2.1 25.8 1.0 O B:HOH208 2.3 32.2 1.0 ND1 C:HIS57 2.8 22.4 1.0 CE1 C:HIS57 3.4 22.0 1.0 O B:HOH204 3.6 34.9 1.0 CD2 C:PHE42 3.9 39.1 1.0 CG C:HIS57 4.1 23.3 1.0 CB C:PHE42 4.2 32.5 1.0 CG C:PHE42 4.3 36.7 1.0 CD1 C:TYR55 4.3 22.6 1.0 CB C:HIS57 4.6 19.6 1.0 CE2 C:PHE42 4.6 35.5 1.0 NE2 C:HIS57 4.6 20.9 1.0 CE1 C:TYR55 4.7 27.1 1.0 CD2 C:HIS57 5.0 22.8 1.0

Zinc binding site 4 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:33.5 occ:0.23 O D:HOH211 2.0 27.6 1.0 O D:HOH206 2.1 31.2 1.0 O D:HOH210 2.3 27.0 1.0 ND1 D:HIS57 2.4 27.9 1.0 CE1 D:HIS57 2.8 28.0 1.0 O D:HOH205 3.2 29.7 1.0 O L:HOH207 3.4 27.6 1.0 CG D:HIS57 3.7 24.2 1.0 CD1 D:TYR55 3.8 25.6 1.0 NE2 D:HIS57 4.1 24.3 1.0 CE1 D:TYR55 4.3 24.8 1.0 CB D:PHE42 4.4 26.8 1.0 CB D:HIS57 4.4 21.8 1.0 CD1 D:PHE42 4.5 39.0 1.0 CD2 D:HIS57 4.6 27.0 1.0 CG D:PHE42 4.6 35.9 1.0 CG D:TYR55 4.8 25.2 1.0 CB D:TYR55 4.9 26.8 1.0

Zinc binding site 5 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn101 b:33.9 occ:0.29 O E:HOH210 2.1 33.3 1.0 O E:HOH209 2.2 28.5 1.0 ND1 E:HIS57 2.5 27.7 1.0 CE1 E:HIS57 3.0 25.5 1.0 O D:HOH209 3.0 25.9 1.0 O E:HOH207 3.2 27.1 1.0 CG E:HIS57 3.7 25.8 1.0 CD1 E:TYR55 4.1 27.2 1.0 O D:HOH208 4.1 40.3 1.0 NE2 E:HIS57 4.2 23.4 1.0 CB E:PHE42 4.3 29.7 1.0 CD1 E:PHE42 4.3 38.5 1.0 CB E:HIS57 4.4 23.8 1.0 CG E:PHE42 4.5 37.2 1.0 CE1 E:TYR55 4.6 34.6 1.0 CD2 E:HIS57 4.6 26.9 1.0 CG E:TYR55 5.0 27.6 1.0

Zinc binding site 6 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:48.5 occ:0.36 O F:HOH207 2.2 42.2 1.0 O F:HOH210 2.4 32.5 1.0 O E:HOH208 3.0 25.6 1.0 ND1 F:HIS57 3.0 25.5 1.0 O F:HOH204 3.3 25.1 1.0 CE1 F:HIS57 3.5 26.5 1.0 O E:HOH204 3.7 44.5 1.0 CD2 F:PHE42 3.8 41.0 1.0 CB F:PHE42 4.1 34.1 1.0 CG F:PHE42 4.1 45.4 1.0 CG F:HIS57 4.2 30.1 1.0 CD1 F:TYR55 4.3 24.3 1.0 CE2 F:PHE42 4.5 39.5 1.0 CE1 F:TYR55 4.7 30.9 1.0 CB F:HIS57 4.8 31.5 1.0 NE2 F:HIS57 4.8 23.9 1.0

Zinc binding site 7 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn101 b:35.8 occ:0.35 O C:HOH208 2.1 33.9 1.0 O G:HOH208 2.1 33.0 1.0 O G:HOH207 2.1 36.7 1.0 ND1 G:HIS57 3.2 27.9 1.0 O G:HOH202 3.5 27.8 1.0 CE1 G:HIS57 3.6 26.9 1.0 O C:HOH205 3.8 44.6 1.0 CD1 G:PHE42 3.8 32.8 1.0 CG G:PHE42 4.2 35.4 1.0 CB G:PHE42 4.3 30.4 1.0 CG G:HIS57 4.4 24.1 1.0 CE1 G:PHE42 4.5 32.5 1.0 CD1 G:TYR55 4.7 24.8 1.0 CB G:HIS57 4.9 22.1 1.0 NE2 G:HIS57 4.9 21.4 1.0 CE1 G:TYR55 5.0 31.8 1.0

Zinc binding site 8 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn101 b:32.6 occ:0.24 O H:HOH209 2.1 30.4 1.0 ND1 H:HIS57 2.2 27.7 1.0 O H:HOH212 2.4 33.2 1.0 O H:HOH211 2.5 30.4 1.0 CE1 H:HIS57 2.6 26.0 1.0 O H:HOH207 3.3 31.4 1.0 CG H:HIS57 3.6 27.9 1.0 CD1 H:TYR55 3.8 25.5 1.0 NE2 H:HIS57 3.9 22.5 1.0 CE1 H:TYR55 4.3 31.7 1.0 CB H:HIS57 4.3 23.8 1.0 CD2 H:HIS57 4.3 26.2 1.0 O G:HOH205 4.5 39.7 1.0 CG H:TYR55 4.6 25.5 1.0 O G:LYS56 4.7 28.0 1.0 CA G:HIS57 4.7 24.6 1.0 CD1 H:PHE42 4.8 35.3 1.0 C G:LYS56 4.8 27.2 1.0 CB H:PHE42 4.8 28.6 1.0 CB H:TYR55 4.9 26.3 1.0 N G:HIS57 4.9 29.2 1.0 CB G:LYS56 4.9 30.3 1.0

Zinc binding site 9 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn101 b:45.1 occ:0.38 O I:HOH210 2.1 35.2 1.0 O I:HOH214 2.2 35.1 1.0 O H:HOH210 2.5 28.6 1.0 ND1 I:HIS57 3.1 26.2 1.0 O I:HOH206 3.1 28.0 1.0 CE1 I:HIS57 3.5 26.3 1.0 CD2 I:PHE42 4.0 41.0 1.0 CB I:PHE42 4.0 36.3 1.0 CG I:PHE42 4.0 37.5 1.0 CD1 I:TYR55 4.1 25.7 1.0 CG I:HIS57 4.3 26.9 1.0 CE1 I:TYR55 4.4 32.4 1.0 CE2 I:PHE42 4.7 43.5 1.0 O I:PHE42 4.7 27.3 1.0 NE2 I:HIS57 4.8 24.8 1.0 CD1 I:PHE42 4.8 38.3 1.0 CB I:HIS57 4.9 23.8 1.0

Zinc binding site 10 out of 12 in the Escherichia Coli Hfq Bound to Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Escherichia Coli Hfq Bound to Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:34.3 occ:0.28 O J:HOH208 2.1 26.3 1.0 O F:HOH211 2.3 33.5 1.0 ND1 J:HIS57 2.5 29.3 1.0 CE1 J:HIS57 2.7 26.1 1.0 O F:HOH209 3.1 27.9 1.0 CG J:HIS57 3.8 33.2 1.0 CD1 J:TYR55 3.8 22.1 1.0 NE2 J:HIS57 4.0 23.4 1.0 CE1 J:TYR55 4.2 26.9 1.0 O F:LYS56 4.5 29.9 1.0 CD2 J:HIS57 4.5 33.1 1.0 CA F:HIS57 4.6 29.0 1.0 CB J:HIS57 4.6 27.9 1.0 C F:LYS56 4.6 29.1 1.0 CB F:LYS56 4.7 27.8 1.0 N F:HIS57 4.7 28.0 1.0 CG J:TYR55 4.7 25.4 1.0 CD1 J:PHE42 4.9 34.7 1.0 CB J:TYR55 5.0 26.6 1.0

J.Orans, A.R.Kovach, K.E.Hoff, R.G.Brennan. Crystal Structure of Escherichia Coli Hfq Dna Complex Reveals Multifunctional Nucleic Acid Binding Site To Be Published.