Zinc in PDB 7r7j: Crystal Structure of Radd with Adp

All present enzymatic activity of Crystal Structure of Radd with Adp:
3.6.4.12;

The structure of Crystal Structure of Radd with Adp, PDB code: 7r7j was solved by M.A.Osorio Garcia, K.A.Satyshur, J.L.Keck, M.M.Cox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.65 / 2.03
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.415, 74.449, 109.4, 84.66, 80.03, 82.77
R / Rfree (%)	23.6 / 26.9

The structure of Crystal Structure of Radd with Adp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Radd with Adp (pdb code 7r7j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Radd with Adp, PDB code: 7r7j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Radd with Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Radd with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:24.6 occ:1.00 SG A:CYS425 2.3 20.9 1.0 SG A:CYS411 2.4 21.5 1.0 SG A:CYS387 2.4 18.7 1.0 SG A:CYS384 2.5 25.5 1.0 HB3 A:CYS411 3.0 33.4 1.0 HB3 A:CYS425 3.0 39.5 1.0 CB A:CYS411 3.1 27.3 1.0 CB A:CYS425 3.1 32.4 1.0 HB2 A:CYS384 3.1 35.1 1.0 HB2 A:CYS425 3.1 39.5 1.0 HB2 A:CYS411 3.1 33.4 1.0 HB3 A:CYS384 3.1 35.1 1.0 H A:CYS387 3.1 31.9 1.0 CB A:CYS384 3.1 28.8 1.0 HB3 A:CYS387 3.3 37.4 1.0 CB A:CYS387 3.5 30.7 1.0 HB3 A:ALA386 3.6 29.0 1.0 HB3 A:PHE427 3.7 28.7 1.0 N A:CYS387 3.9 26.1 1.0 HB3 A:PHE389 3.9 30.4 1.0 H A:PHE389 4.2 27.6 1.0 HB2 A:PHE427 4.2 28.7 1.0 CA A:CYS387 4.2 27.4 1.0 HB2 A:CYS387 4.3 37.4 1.0 H A:GLY413 4.3 29.0 1.0 HD21 A:ASN391 4.3 34.9 1.0 H A:PHE427 4.4 33.3 1.0 CB A:PHE427 4.4 23.4 1.0 H A:ALA386 4.5 28.7 1.0 CA A:CYS411 4.5 26.3 1.0 CA A:CYS425 4.5 29.5 1.0 CB A:ALA386 4.5 23.7 1.0 H A:GLY388 4.6 30.8 1.0 HA3 A:GLY413 4.6 34.0 1.0 CA A:CYS384 4.6 21.2 1.0 HB2 A:PHE389 4.6 30.4 1.0 CB A:PHE389 4.7 24.9 1.0 HA A:CYS425 4.8 35.9 1.0 C A:CYS387 4.8 33.9 1.0 HE2 A:PHE415 4.8 64.3 1.0 HA A:CYS411 4.9 32.1 1.0 N A:GLY388 4.9 25.2 1.0 C A:ALA386 4.9 27.1 1.0 HB1 A:ALA386 4.9 29.0 1.0 HA A:CYS384 4.9 26.1 1.0 N A:PHE389 4.9 22.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Radd with Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Radd with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:44.6 occ:1.00 SG A:CYS434 2.3 39.7 1.0 SG A:CYS437 2.3 42.8 1.0 SG A:CYS448 2.4 46.0 1.0 SG A:CYS451 2.4 50.9 1.0 HB3 A:CYS451 2.9 53.1 1.0 H A:CYS437 2.9 61.6 1.0 HB3 A:CYS434 3.1 57.5 1.0 CB A:CYS434 3.1 47.4 1.0 HB2 A:CYS434 3.1 57.5 1.0 HB3 A:CYS437 3.1 66.7 1.0 CB A:CYS448 3.2 48.2 1.0 HB3 A:CYS448 3.2 58.4 1.0 HB2 A:CYS448 3.2 58.4 1.0 CB A:CYS451 3.2 43.8 1.0 H A:CYS451 3.2 66.3 1.0 CB A:CYS437 3.3 55.1 1.0 N A:CYS437 3.7 50.9 1.0 N A:CYS451 3.8 54.8 1.0 HB A:THR453 4.0 73.9 1.0 HB2 A:CYS451 4.0 53.1 1.0 CA A:CYS437 4.0 47.5 1.0 HB2 A:GLU450 4.0 61.1 1.0 HB3 A:ALA439 4.0 55.2 1.0 H A:ALA439 4.0 63.1 1.0 CA A:CYS451 4.1 55.3 1.0 HB2 A:CYS437 4.1 66.7 1.0 H A:THR453 4.1 66.8 1.0 H A:GLN436 4.3 62.0 1.0 H A:ASN438 4.4 66.3 1.0 H A:GLU450 4.4 59.9 1.0 HD21 A:ASN441 4.5 50.5 1.0 H A:ASP452 4.5 63.1 1.0 CA A:CYS434 4.6 47.4 1.0 C A:CYS437 4.6 50.5 1.0 C A:CYS451 4.7 56.3 1.0 CA A:CYS448 4.7 47.9 1.0 CB A:GLN436 4.7 54.9 1.0 N A:ASN438 4.7 54.8 1.0 HB2 A:ALA439 4.7 55.2 1.0 HG1 A:THR453 4.7 72.9 1.0 C A:GLN436 4.8 56.9 1.0 CB A:ALA439 4.8 45.5 1.0 CB A:THR453 4.8 61.1 1.0 N A:ASP452 4.8 52.1 1.0 HA A:CYS437 4.8 57.6 1.0 C A:GLU450 4.8 52.0 1.0 N A:ALA439 4.9 52.1 1.0 OG1 A:THR453 4.9 60.3 1.0 HA A:CYS451 4.9 66.9 1.0 HA A:CYS434 4.9 57.5 1.0 CB A:GLU450 4.9 50.5 1.0 HA A:CYS448 5.0 58.1 1.0 N A:THR453 5.0 55.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Radd with Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Radd with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:29.5 occ:1.00 SG B:CYS411 2.3 27.9 1.0 SG B:CYS425 2.3 17.9 1.0 SG B:CYS387 2.4 25.0 1.0 SG B:CYS384 2.5 27.4 1.0 HB3 B:CYS411 3.1 37.8 1.0 CB B:CYS411 3.1 31.0 1.0 HB3 B:CYS384 3.1 31.6 1.0 HB2 B:CYS384 3.1 31.6 1.0 H B:CYS387 3.1 51.9 1.0 CB B:CYS384 3.1 25.8 1.0 HB2 B:CYS411 3.1 37.8 1.0 HB3 B:CYS425 3.2 46.6 1.0 CB B:CYS425 3.2 38.4 1.0 HB2 B:CYS425 3.2 46.6 1.0 HB3 B:CYS387 3.4 52.6 1.0 CB B:CYS387 3.5 43.3 1.0 HB3 B:ALA386 3.7 42.0 1.0 HB3 B:PHE389 3.7 36.5 1.0 HB3 B:PHE427 3.8 37.2 1.0 N B:CYS387 3.9 42.8 1.0 H B:PHE389 4.0 40.8 1.0 CA B:CYS387 4.3 47.0 1.0 H B:GLY413 4.3 32.5 1.0 HB2 B:CYS387 4.3 52.6 1.0 HB2 B:PHE427 4.3 37.2 1.0 HD21 B:ASN391 4.4 45.0 1.0 H B:GLY388 4.4 42.9 1.0 H B:PHE427 4.5 35.3 1.0 H B:ALA386 4.5 40.1 1.0 CB B:PHE427 4.5 30.6 1.0 CA B:CYS411 4.6 24.3 1.0 CB B:PHE389 4.6 30.0 1.0 HB2 B:PHE389 4.6 36.5 1.0 HA3 B:GLY413 4.6 34.1 1.0 CA B:CYS384 4.6 28.3 1.0 CB B:ALA386 4.7 34.5 1.0 CA B:CYS425 4.7 33.0 1.0 N B:PHE389 4.8 33.5 1.0 N B:GLY388 4.8 35.2 1.0 C B:CYS387 4.8 38.7 1.0 HA B:CYS411 4.9 29.7 1.0 C B:ALA386 5.0 40.9 1.0 HA B:CYS384 5.0 34.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Radd with Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Radd with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:57.2 occ:1.00 SG B:CYS434 2.1 52.1 1.0 SG B:CYS448 2.3 49.8 1.0 SG B:CYS437 2.4 61.1 1.0 SG B:CYS451 2.4 51.5 1.0 HB3 B:CYS434 2.9 66.6 1.0 CB B:CYS434 2.9 55.0 1.0 HB2 B:CYS434 3.0 66.6 1.0 H B:CYS437 3.0 74.8 1.0 HB2 B:CYS448 3.1 56.5 1.0 CB B:CYS448 3.2 46.6 1.0 HB3 B:CYS448 3.3 56.5 1.0 HB3 B:CYS437 3.3 67.4 1.0 H B:CYS451 3.3 65.7 1.0 CB B:CYS437 3.4 55.7 1.0 HB2 B:GLU450 3.8 73.6 1.0 N B:CYS437 3.8 61.8 1.0 CB B:CYS451 3.8 58.8 1.0 HB3 B:CYS451 3.8 71.1 1.0 HB2 B:GLN436 3.9 80.7 1.0 HB3 B:ALA439 3.9 58.4 1.0 HG1 B:THR453 3.9 66.0 1.0 H B:ALA439 4.0 58.2 1.0 N B:CYS451 4.1 54.3 1.0 CA B:CYS437 4.1 60.4 1.0 HB B:THR453 4.1 59.2 1.0 HB2 B:CYS437 4.2 67.4 1.0 H B:GLN436 4.3 79.7 1.0 OG1 B:THR453 4.4 54.6 1.0 H B:THR453 4.4 55.7 1.0 HD21 B:ASN441 4.4 53.6 1.0 CA B:CYS434 4.4 54.3 1.0 H B:GLU450 4.5 73.5 1.0 CA B:CYS451 4.5 58.0 1.0 H B:ASN438 4.5 67.1 1.0 HB2 B:CYS451 4.5 71.1 1.0 HB2 B:ALA439 4.6 58.4 1.0 CA B:CYS448 4.6 46.0 1.0 C B:CYS437 4.6 55.5 1.0 CB B:ALA439 4.7 48.2 1.0 CB B:GLU450 4.7 60.9 1.0 HA B:CYS434 4.7 65.7 1.0 CB B:THR453 4.7 48.8 1.0 N B:ASN438 4.8 55.4 1.0 CB B:GLN436 4.8 66.8 1.0 N B:ALA439 4.8 48.0 1.0 HA B:CYS448 4.9 55.8 1.0 C B:GLN436 4.9 66.6 1.0 C B:CYS434 5.0 59.7 1.0 HD21 B:LEU455 5.0 54.8 1.0 HA B:CYS437 5.0 73.0 1.0

M.A.Osorio Garcia, K.A.Satyshur, M.M.Cox, J.L.Keck. X-Ray Crystal Structure of the Escherichia Coli Radd Dna Repair Protein Bound to Adp Reveals A Novel Zinc Ribbon Domain. Plos One V. 17 66031 2022.
ISSN: ESSN 1932-6203
PubMed: 35482735
DOI: 10.1371/JOURNAL.PONE.0266031