Zinc in PDB 6iz2: Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1

The structure of Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1, PDB code: 6iz2 was solved by M.-K.Kim, J.Zhang, L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.02 / 2.07
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.843, 109.012, 55.894, 90.00, 89.99, 90.00
R / Rfree (%)	18.2 / 22.4

The binding sites of Zinc atom in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1 (pdb code 6iz2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1, PDB code: 6iz2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1


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 Dinb/Yfit Protein DR0053 From D. Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:76.9 occ:1.00 NE2 A:HIS39 2.5 29.7 1.0 O A:HOH348 2.6 46.6 1.0 O A:HOH351 2.9 48.6 1.0 CD2 A:HIS39 3.3 23.6 1.0 O A:HOH373 3.3 46.7 1.0 CE1 A:HIS39 3.5 29.3 1.0 CG A:HIS39 4.5 25.6 1.0 ND1 A:HIS39 4.6 26.7 1.0 O A:ALA37 4.8 23.9 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1


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 Dinb/Yfit Protein DR0053 From D. Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:43.8 occ:1.00 O A:HOH303 2.0 32.4 1.0 NE2 A:HIS136 2.1 24.5 1.0 O A:HOH359 2.2 31.9 1.0 OE1 A:GLU52 2.3 20.2 1.0 OE2 A:GLU52 2.6 29.0 1.0 CD A:GLU52 2.8 29.6 1.0 CE1 A:HIS136 3.0 24.9 1.0 CD2 A:HIS136 3.1 17.2 1.0 OD1 A:ASN132 3.6 25.0 1.0 NH2 A:ARG44 3.7 23.1 1.0 ND2 A:ASN132 3.8 23.4 1.0 CG A:ASN132 4.1 26.5 1.0 ND1 A:HIS136 4.2 19.0 1.0 CG A:HIS136 4.3 15.8 1.0 CG A:GLU52 4.3 31.4 1.0 CZ A:ARG44 4.7 34.1 1.0 O A:HOH354 4.8 23.9 1.0 NH1 A:ARG44 4.9 27.9 1.0 O A:HOH381 5.0 45.6 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1


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 Dinb/Yfit Protein DR0053 From D. Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:79.9 occ:1.00 NE2 A:HIS19 2.2 45.9 1.0 O A:HOH370 2.3 39.1 1.0 NE2 A:HIS15 2.5 39.4 1.0 CE1 A:HIS15 2.7 39.4 1.0 CE1 A:HIS19 2.9 42.0 1.0 CD2 A:HIS19 3.2 51.8 1.0 O A:HOH374 3.4 51.8 1.0 O A:HOH365 3.6 48.6 1.0 CD2 A:HIS15 3.6 42.9 1.0 ND1 A:HIS15 3.7 46.5 1.0 ND1 A:HIS19 4.1 49.6 1.0 CG A:HIS15 4.2 35.6 1.0 CG A:HIS19 4.2 36.8 1.0 O A:HOH364 4.3 40.7 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1


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 Dinb/Yfit Protein DR0053 From D. Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:48.3 occ:1.00 ND1 A:HIS38 2.2 24.4 1.0 O A:HOH368 2.3 37.0 1.0 O A:HOH378 2.4 37.7 1.0 O A:HOH375 2.6 49.4 1.0 O A:HOH371 2.6 42.1 1.0 CG A:HIS38 3.2 21.4 1.0 CE1 A:HIS38 3.2 23.6 1.0 CB A:HIS38 3.4 16.5 1.0 CA A:HIS38 3.7 24.3 1.0 NE2 A:HIS38 4.3 27.9 1.0 CD2 A:HIS38 4.3 22.3 1.0 CD2 A:LEU147 4.5 19.1 1.0 N A:HIS39 4.7 16.8 1.0 N A:HIS38 4.7 24.5 1.0 C A:HIS38 4.7 23.2 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:83.7 occ:1.00 NE2 B:HIS19 2.2 42.6 1.0 CE1 B:HIS15 2.3 34.3 1.0 NE2 B:HIS15 2.9 42.2 1.0 CE1 B:HIS19 3.2 41.6 1.0 CD2 B:HIS19 3.2 46.5 1.0 ND1 B:HIS15 3.3 36.4 1.0 CD2 B:HIS15 4.0 43.5 1.0 CG B:HIS15 4.2 35.4 1.0 ND1 B:HIS19 4.3 43.8 1.0 CG B:HIS19 4.3 35.4 1.0 O B:HOH483 5.0 44.1 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:50.0 occ:1.00 O B:HOH471 2.1 42.9 1.0 ND1 B:HIS38 2.2 22.8 1.0 O B:HOH481 2.5 32.4 1.0 O B:HOH480 2.8 41.4 1.0 CE1 B:HIS38 3.2 22.4 1.0 CG B:HIS38 3.2 21.9 1.0 O B:HOH469 3.4 45.7 1.0 CB B:HIS38 3.5 13.7 1.0 CA B:HIS38 3.8 24.0 1.0 NE2 B:HIS38 4.3 23.9 1.0 CD2 B:HIS38 4.3 20.8 1.0 CD2 B:LEU147 4.4 20.2 1.0 N B:HIS39 4.7 19.2 1.0 N B:HIS38 4.7 22.0 1.0 C B:HIS38 4.8 22.2 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:74.6 occ:1.00 O B:HOH485 2.4 58.8 1.0 NE2 B:HIS39 2.5 35.2 1.0 O B:HOH435 2.8 51.7 1.0 O B:HOH477 3.0 48.2 1.0 CD2 B:HIS39 3.4 27.4 1.0 O B:HOH476 3.4 47.6 1.0 CE1 B:HIS39 3.6 31.0 1.0 CG B:HIS39 4.6 29.7 1.0 ND1 B:HIS39 4.6 29.6 1.0 O B:ALA37 4.8 24.7 1.0 O B:HOH469 4.9 45.7 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:0.8 occ:1.00 O B:HOH432 2.7 44.7 1.0 SG B:CYS51 3.1 45.1 1.0 O B:HOH437 3.3 36.0 1.0 O B:HOH493 3.6 51.9 1.0 CB B:CYS51 3.9 25.0 1.0 O B:CYS51 4.2 25.4 1.0 C B:CYS51 4.2 18.9 1.0 O B:HOH495 4.3 55.6 1.0 N B:GLU52 4.4 19.1 1.0 CA B:GLU52 4.7 20.4 1.0 CA B:CYS51 4.7 19.6 1.0 CD2 B:LEU80 4.7 48.2 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Dinb/Yfit Protein DR0053 From D. Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn306 b:43.2 occ:1.00 O B:HOH407 2.0 29.4 1.0 NE2 B:HIS136 2.1 24.8 1.0 O B:HOH453 2.2 34.9 1.0 OE2 B:GLU52 2.3 23.4 1.0 OE1 B:GLU52 2.7 28.5 1.0 CD B:GLU52 2.9 29.7 1.0 CE1 B:HIS136 2.9 30.3 1.0 CD2 B:HIS136 3.2 19.8 1.0 OD1 B:ASN132 3.6 22.8 1.0 NH2 B:ARG44 3.7 26.9 1.0 ND2 B:ASN132 3.8 24.6 1.0 ND1 B:HIS136 4.1 19.6 1.0 CG B:ASN132 4.1 26.1 1.0 O B:HOH473 4.2 52.4 1.0 CG B:HIS136 4.3 16.2 1.0 CG B:GLU52 4.4 34.0 1.0 CZ B:ARG44 4.7 40.8 1.0 O B:HOH464 4.8 27.2 1.0

J.Zhang, L.Zhao, H.S.Seo, J.H.Jung, J.I.Choi, M.K.Kim, S.Lim. Crystal Structure of the Highly Radiation-Inducible Dinb/Yfit Superfamily Protein DR0053 From Deinococcus Radiodurans R1. Biochem.Biophys.Res.Commun. V. 513 354 2019.
ISSN: ESSN 1090-2104
PubMed: 30961930
DOI: 10.1016/J.BBRC.2019.03.209