Zinc in PDB 1f30: The Structural Basis For Dna Protection By E. Coli Dps Protein

The structure of The Structural Basis For Dna Protection By E. Coli Dps Protein, PDB code: 1f30 was solved by J.Luo, D.Liu, M.A.White, R.O.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 2.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	117.773, 140.780, 268.419, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.2

Pages:

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

Binding sites:

The binding sites of Zinc atom in the The Structural Basis For Dna Protection By E. Coli Dps Protein (pdb code 1f30). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the The Structural Basis For Dna Protection By E. Coli Dps Protein, PDB code: 1f30:
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 The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:33.5 occ:1.00 OE1 A:GLU82 1.8 38.5 1.0 NE2 B:HIS51 2.1 49.1 1.0 O B:HOH247 2.4 5.4 1.0 OD1 A:ASP78 2.5 30.9 1.0 OD2 A:ASP78 2.6 28.7 1.0 CD A:GLU82 2.9 39.3 1.0 CG A:ASP78 2.9 27.6 1.0 O B:HOH242 3.0 11.2 1.0 CE1 B:HIS51 3.0 50.1 1.0 O B:HOH252 3.1 11.5 1.0 CD2 B:HIS51 3.1 49.1 1.0 OE2 A:GLU82 3.4 42.3 1.0 NE2 B:HIS63 3.8 32.3 1.0 CE1 B:HIS63 3.8 31.8 1.0 OD2 B:ASP67 3.9 40.8 1.0 NZ B:LYS48 4.1 44.0 1.0 CG A:GLU82 4.1 37.7 1.0 ND1 B:HIS51 4.2 49.6 1.0 CG B:HIS51 4.3 49.7 1.0 CB A:ASP78 4.4 28.5 1.0 OD1 B:ASP67 4.6 43.8 1.0 CG B:ASP67 4.7 41.1 1.0 CD1 B:TRP52 4.9 46.8 1.0 NE1 B:TRP52 4.9 46.3 1.0 CD2 B:HIS63 5.0 33.6 1.0 ND1 B:HIS63 5.0 30.1 1.0

Zinc binding site 2 out of 12 in the The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:32.5 occ:1.00 OE1 B:GLU82 1.8 52.7 1.0 O A:HOH614 2.1 14.2 1.0 NE2 A:HIS51 2.1 35.6 1.0 OD1 B:ASP78 2.4 24.2 1.0 OD2 B:ASP78 2.6 21.3 1.0 CD B:GLU82 2.8 52.5 1.0 CG B:ASP78 2.8 24.0 1.0 CE1 A:HIS51 3.1 36.7 1.0 CD2 A:HIS51 3.2 37.1 1.0 OE2 B:GLU82 3.3 55.9 1.0 O A:HOH618 3.5 24.2 1.0 O A:HOH612 3.7 10.5 1.0 NE2 A:HIS63 3.8 30.4 1.0 CE1 A:HIS63 3.8 31.6 1.0 OD2 A:ASP67 4.0 38.7 1.0 CG B:GLU82 4.1 48.8 1.0 NZ A:LYS48 4.1 32.1 1.0 ND1 A:HIS51 4.2 37.9 1.0 CG A:HIS51 4.3 39.1 1.0 CB B:ASP78 4.4 26.1 1.0 OD1 A:ASP67 4.6 36.6 1.0 CG A:ASP67 4.7 36.1 1.0 CD1 A:TRP52 4.8 42.2 1.0 NE1 A:TRP52 4.8 41.1 1.0 ND1 A:HIS63 5.0 31.4 1.0 CD2 A:HIS63 5.0 30.9 1.0

Zinc binding site 3 out of 12 in the The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:31.2 occ:1.00 NE2 C:HIS51 2.1 37.5 1.0 O C:HOH645 2.4 11.0 1.0 O C:HOH651 3.0 33.5 1.0 CE1 C:HIS51 3.1 36.3 1.0 CD2 C:HIS51 3.1 37.3 1.0 NE2 C:HIS63 3.7 37.4 1.0 O C:HOH652 3.8 1.9 1.0 CE1 C:HIS63 3.8 37.5 1.0 OD2 C:ASP67 4.0 33.2 1.0 NZ C:LYS48 4.1 37.8 1.0 ND1 C:HIS51 4.2 36.2 1.0 CG C:HIS51 4.3 38.3 1.0 OD1 C:ASP67 4.6 31.0 1.0 CG C:ASP67 4.7 28.6 1.0 CD1 C:TRP52 4.8 44.4 1.0 NE1 C:TRP52 4.9 45.3 1.0 CD2 C:HIS63 4.9 37.6 1.0 ND1 C:HIS63 5.0 36.2 1.0

Zinc binding site 4 out of 12 in the The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:24.8 occ:1.00 NE2 D:HIS51 2.1 35.0 1.0 O D:HOH458 2.5 11.5 1.0 O D:HOH454 2.9 3.0 1.0 CE1 D:HIS51 3.0 35.6 1.0 CD2 D:HIS51 3.1 36.1 1.0 O D:HOH443 3.7 7.5 1.0 NE2 D:HIS63 3.7 33.2 1.0 CE1 D:HIS63 3.7 32.1 1.0 OD2 D:ASP67 3.9 25.9 1.0 NZ D:LYS48 4.0 32.8 1.0 ND1 D:HIS51 4.1 35.3 1.0 CG D:HIS51 4.2 35.6 1.0 OD1 D:ASP67 4.6 26.1 1.0 CG D:ASP67 4.7 24.2 1.0 CD1 D:TRP52 4.8 32.5 1.0 CD2 D:HIS63 4.9 32.4 1.0 ND1 D:HIS63 4.9 28.4 1.0 NE1 D:TRP52 4.9 32.0 1.0

Zinc binding site 5 out of 12 in the The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:29.7 occ:1.00 OE1 E:GLU82 1.8 40.0 1.0 NE2 F:HIS51 2.0 33.3 1.0 OD1 E:ASP78 2.4 29.2 1.0 OD2 E:ASP78 2.5 27.6 1.0 O F:HOH257 2.5 8.9 1.0 CG E:ASP78 2.8 28.9 1.0 CD E:GLU82 2.9 38.8 1.0 CE1 F:HIS51 3.0 33.0 1.0 CD2 F:HIS51 3.0 35.6 1.0 O F:HOH244 3.3 1.9 1.0 OE2 E:GLU82 3.4 42.4 1.0 OD2 F:ASP67 3.8 38.3 1.0 NE2 F:HIS63 3.8 26.7 1.0 CE1 F:HIS63 3.9 28.4 1.0 NZ F:LYS48 3.9 30.7 1.0 O F:HOH243 3.9 8.6 1.0 CG E:GLU82 4.1 36.1 1.0 ND1 F:HIS51 4.1 34.2 1.0 CG F:HIS51 4.2 36.2 1.0 CB E:ASP78 4.3 27.9 1.0 OD1 F:ASP67 4.6 34.5 1.0 CG F:ASP67 4.6 35.0 1.0 CD1 F:TRP52 4.8 43.6 1.0 NE1 F:TRP52 4.8 44.3 1.0

Zinc binding site 6 out of 12 in the The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:33.1 occ:1.00 OE1 F:GLU82 1.8 31.1 1.0 NE2 E:HIS51 2.1 27.7 1.0 O E:HOH657 2.3 12.8 1.0 OD1 F:ASP78 2.4 34.3 1.0 OD2 F:ASP78 2.5 32.1 1.0 CG F:ASP78 2.8 33.5 1.0 CD F:GLU82 2.9 31.2 1.0 CE1 E:HIS51 3.1 27.4 1.0 CD2 E:HIS51 3.1 29.8 1.0 O E:HOH660 3.2 1.9 1.0 OE2 F:GLU82 3.5 34.3 1.0 NE2 E:HIS63 3.9 33.6 1.0 CE1 E:HIS63 3.9 32.4 1.0 O E:HOH661 3.9 4.7 1.0 OD2 E:ASP67 3.9 33.5 1.0 NZ E:LYS48 3.9 31.7 1.0 CG F:GLU82 4.1 27.7 1.0 ND1 E:HIS51 4.2 30.3 1.0 CG E:HIS51 4.2 30.1 1.0 O F:HOH397 4.3 23.0 1.0 CB F:ASP78 4.4 33.2 1.0 OD1 E:ASP67 4.6 32.0 1.0 CD1 E:TRP52 4.7 40.9 1.0 CG E:ASP67 4.7 31.2 1.0 NE1 E:TRP52 4.7 42.2 1.0

Zinc binding site 7 out of 12 in the The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:78.0 occ:1.00 OE1 G:GLU82 1.9 89.0 1.0 NE2 H:HIS51 2.0 88.6 1.0 O H:HOH210 2.1 35.8 1.0 OD1 G:ASP78 2.7 67.2 1.0 OD2 G:ASP78 2.7 70.1 1.0 CE1 H:HIS51 2.9 88.5 1.0 CD G:GLU82 3.0 88.5 1.0 CG G:ASP78 3.0 69.4 1.0 CD2 H:HIS51 3.0 89.4 1.0 O G:HOH210 3.4 34.1 1.0 O H:HOH211 3.5 14.1 1.0 OE2 G:GLU82 3.5 89.6 1.0 NE2 H:HIS63 3.7 75.7 1.0 CE1 H:HIS63 3.8 76.5 1.0 OD2 H:ASP67 3.8 76.0 1.0 NZ H:LYS48 3.9 82.9 1.0 ND1 H:HIS51 4.1 88.8 1.0 CG H:HIS51 4.1 90.2 1.0 CG G:GLU82 4.2 87.2 1.0 OD1 H:ASP67 4.5 74.9 1.0 CB G:ASP78 4.5 70.0 1.0 CG H:ASP67 4.5 74.9 1.0 CD1 H:TRP52 4.8 94.2 1.0 CD2 H:HIS63 4.9 77.2 1.0 NE1 H:TRP52 4.9 95.3 1.0 ND1 H:HIS63 4.9 76.1 1.0

Zinc binding site 8 out of 12 in the The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn201 b:66.5 occ:1.00 OE1 H:GLU82 1.8 84.9 1.0 NE2 G:HIS51 2.0 72.5 1.0 OD1 H:ASP78 2.6 62.3 1.0 OD2 H:ASP78 2.6 59.1 1.0 CE1 G:HIS51 2.9 73.7 1.0 CD H:GLU82 2.9 84.1 1.0 CG H:ASP78 3.0 63.6 1.0 CD2 G:HIS51 3.0 74.7 1.0 O G:HOH203 3.3 34.4 1.0 OE2 H:GLU82 3.5 84.1 1.0 O G:HOH202 3.6 27.6 1.0 NE2 G:HIS63 3.7 57.8 1.0 CE1 G:HIS63 3.7 56.8 1.0 OD2 G:ASP67 3.8 69.5 1.0 NZ G:LYS48 4.0 79.0 1.0 ND1 G:HIS51 4.1 75.6 1.0 CG G:HIS51 4.1 77.1 1.0 CG H:GLU82 4.1 83.1 1.0 CB H:ASP78 4.5 66.5 1.0 OD1 G:ASP67 4.6 66.7 1.0 CG G:ASP67 4.6 66.8 1.0 CD1 G:TRP52 4.8 85.6 1.0 NE1 G:TRP52 4.8 86.6 1.0 ND1 G:HIS63 4.9 55.7 1.0 CD2 G:HIS63 4.9 58.5 1.0

Zinc binding site 9 out of 12 in the The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:48.3 occ:1.00 OE1 I:GLU82 1.8 55.5 1.0 NE2 J:HIS51 2.1 60.7 1.0 OD1 I:ASP78 2.5 52.8 1.0 OD2 I:ASP78 2.5 51.0 1.0 CG I:ASP78 2.8 51.0 1.0 CD I:GLU82 2.9 56.7 1.0 O J:HOH622 2.9 8.1 1.0 O J:HOH624 3.0 29.9 1.0 CE1 J:HIS51 3.0 60.8 1.0 CD2 J:HIS51 3.1 61.7 1.0 OE2 I:GLU82 3.4 56.2 1.0 O J:HOH625 3.8 35.1 1.0 NE2 J:HIS63 3.8 59.1 1.0 CE1 J:HIS63 3.8 56.4 1.0 OD2 J:ASP67 3.9 51.3 1.0 NZ J:LYS48 3.9 56.9 1.0 CG I:GLU82 4.1 56.8 1.0 ND1 J:HIS51 4.1 62.2 1.0 CG J:HIS51 4.2 61.9 1.0 CB I:ASP78 4.4 49.3 1.0 OD1 J:ASP67 4.5 53.4 1.0 CG J:ASP67 4.6 51.5 1.0 CD1 J:TRP52 4.7 65.1 1.0 NE1 J:TRP52 4.8 65.5 1.0 ND1 J:HIS63 5.0 55.9 1.0 CD2 J:HIS63 5.0 58.0 1.0

Zinc binding site 10 out of 12 in the The Structural Basis For Dna Protection By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Structural Basis For Dna Protection By E. Coli Dps Protein within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn201 b:62.9 occ:1.00 OE1 J:GLU82 1.9 78.1 1.0 NE2 I:HIS51 2.0 55.0 1.0 OD1 J:ASP78 2.5 46.9 1.0 OD2 J:ASP78 2.6 51.8 1.0 O I:HOH611 2.7 28.9 1.0 CG J:ASP78 2.8 51.0 1.0 O I:HOH608 2.9 17.1 1.0 CD J:GLU82 3.0 77.5 1.0 CE1 I:HIS51 3.0 55.9 1.0 CD2 I:HIS51 3.1 58.2 1.0 OE2 J:GLU82 3.5 77.3 1.0 OD2 I:ASP67 3.8 63.3 1.0 NE2 I:HIS63 3.8 66.6 1.0 CE1 I:HIS63 3.8 67.4 1.0 NZ I:LYS48 3.9 67.6 1.0 ND1 I:HIS51 4.1 57.0 1.0 CG J:GLU82 4.2 75.8 1.0 CG I:HIS51 4.2 59.1 1.0 CB J:ASP78 4.4 52.9 1.0 OD1 I:ASP67 4.4 64.1 1.0 CG I:ASP67 4.5 62.6 1.0 CD1 I:TRP52 4.8 74.2 1.0 NE1 I:TRP52 4.9 75.4 1.0 ND1 I:HIS63 5.0 66.5 1.0 CD2 I:HIS63 5.0 67.7 1.0

J.Luo, D.Liu, M.A.White, R.O.Fox. The Structural Basis For Dna Protection By E. Coli Dps Protein To Be Published.