Zinc in PDB 3idz: Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8

The structure of Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8, PDB code: 3idz was solved by H.Ishikawa, N.Nakagawa, S.Kuramitsu, S.Yokoyama, R.Masui, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.841, 147.197, 121.172, 90.00, 109.52, 90.00
R / Rfree (%)	24 / 27.8

The binding sites of Zinc atom in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 (pdb code 3idz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8, PDB code: 3idz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8


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 S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn455 b:67.6 occ:1.00 OD1 A:ASP162 2.0 35.5 1.0 OD2 A:ASP63 2.4 38.7 1.0 NE2 A:HIS64 2.5 34.5 1.0 NE2 A:HIS400 2.6 44.4 1.0 CD2 A:HIS64 2.8 32.1 1.0 CG A:ASP162 3.1 37.6 1.0 CG A:ASP63 3.3 39.0 1.0 CD2 A:HIS400 3.3 43.6 1.0 OD2 A:ASP162 3.5 40.6 1.0 OD1 A:ASP63 3.5 39.5 1.0 CE1 A:HIS400 3.6 44.0 1.0 ZN A:ZN456 3.7 72.0 1.0 O A:HOH494 3.8 60.6 1.0 O A:HOH492 3.8 33.7 1.0 CE1 A:HIS64 3.8 31.9 1.0 CG A:HIS64 4.2 33.5 1.0 NE2 A:HIS59 4.2 42.2 1.0 CB A:ASP162 4.4 35.8 1.0 CE1 A:HIS59 4.4 43.1 1.0 CG A:HIS400 4.6 44.1 1.0 ND1 A:HIS64 4.6 34.0 1.0 CB A:ASP63 4.6 37.5 1.0 CE1 A:HIS380 4.6 35.3 1.0 ND1 A:HIS400 4.7 44.7 1.0 O A:VAL12 4.7 43.0 1.0 O A:ASP63 4.9 34.7 1.0 NE2 A:HIS380 4.9 35.7 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8


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 S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn456 b:72.0 occ:1.00 ND1 A:HIS61 2.2 51.8 1.0 NE2 A:HIS59 2.4 42.2 1.0 NE2 A:HIS141 2.6 29.7 1.0 OD1 A:ASP162 3.0 35.5 1.0 CD2 A:HIS59 3.0 40.0 1.0 CE1 A:HIS61 3.1 49.5 1.0 CD2 A:HIS141 3.1 28.9 1.0 CG A:HIS61 3.2 49.5 1.0 CE1 A:HIS59 3.4 43.1 1.0 O A:HOH494 3.6 60.6 1.0 CB A:HIS61 3.6 44.3 1.0 ZN A:ZN455 3.7 67.6 1.0 CE1 A:HIS141 3.8 31.3 1.0 CG A:ASP162 3.9 37.6 1.0 CB A:ASP162 4.0 35.8 1.0 NE2 A:HIS61 4.2 52.0 1.0 CG A:HIS59 4.2 39.0 1.0 CD2 A:HIS61 4.3 50.1 1.0 ND1 A:HIS59 4.3 41.6 1.0 CG A:HIS141 4.4 24.8 1.0 OD1 A:ASP63 4.4 39.5 1.0 CD2 A:HIS64 4.5 32.1 1.0 CE1 A:HIS380 4.7 35.3 1.0 ND1 A:HIS141 4.7 30.2 1.0 NE2 A:HIS64 4.7 34.5 1.0 NE2 A:HIS380 4.9 35.7 1.0 CD1 A:LEU142 4.9 34.1 1.0 CA A:HIS61 5.0 41.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8


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 S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn457 b:72.5 occ:1.00 OD1 B:ASP162 2.4 47.9 1.0 NE2 B:HIS64 2.4 37.0 1.0 NE2 B:HIS400 2.4 22.6 1.0 OD2 B:ASP63 2.4 49.7 1.0 CD2 B:HIS64 2.8 35.2 1.0 CD2 B:HIS400 3.0 19.8 1.0 CG B:ASP162 3.2 43.4 1.0 CG B:ASP63 3.3 47.5 1.0 OD2 B:ASP162 3.3 39.2 1.0 OD1 B:ASP63 3.5 52.6 1.0 ZN B:ZN458 3.5 79.2 1.0 CE1 B:HIS400 3.5 22.0 1.0 CE1 B:HIS64 3.6 38.7 1.0 CG B:HIS64 4.1 36.0 1.0 NE2 B:HIS59 4.2 42.2 1.0 CG B:HIS400 4.2 27.7 1.0 ND1 B:HIS64 4.5 37.0 1.0 ND1 B:HIS400 4.5 24.3 1.0 CE1 B:HIS59 4.5 42.9 1.0 CB B:ASP162 4.5 38.6 1.0 O B:VAL12 4.6 56.1 1.0 CE1 B:HIS380 4.6 37.1 1.0 CB B:ASP63 4.7 44.4 1.0 OG B:SER15 4.8 44.1 1.0 O B:ASP63 4.9 39.9 1.0 O B:HOH465 4.9 25.8 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8


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 S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn458 b:79.2 occ:1.00 NE2 B:HIS59 2.2 42.2 1.0 NE2 B:HIS141 2.5 41.3 1.0 OD1 B:ASP162 2.7 47.9 1.0 CD2 B:HIS141 2.7 40.2 1.0 CD2 B:HIS59 2.8 41.9 1.0 ND1 B:HIS61 3.0 43.8 1.0 CE1 B:HIS59 3.3 42.9 1.0 CG B:ASP162 3.5 43.4 1.0 ZN B:ZN457 3.5 72.5 1.0 CB B:ASP162 3.7 38.6 1.0 CE1 B:HIS141 3.7 42.0 1.0 CB B:HIS61 3.8 42.6 1.0 CG B:HIS61 3.8 41.6 1.0 CD2 B:HIS64 4.0 35.2 1.0 CG B:HIS141 4.0 41.7 1.0 CE1 B:HIS61 4.1 44.0 1.0 CG B:HIS59 4.1 40.3 1.0 NE2 B:HIS64 4.2 37.0 1.0 ND1 B:HIS59 4.3 41.9 1.0 OD1 B:ASP63 4.4 52.6 1.0 ND1 B:HIS141 4.5 42.1 1.0 CE1 B:HIS380 4.5 37.1 1.0 OD2 B:ASP162 4.6 39.2 1.0 NE2 B:HIS380 4.8 38.6 1.0 CG B:HIS64 4.9 36.0 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8


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 S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn447 b:0.1 occ:1.00 OD2 C:ASP63 2.1 54.7 1.0 NE2 C:HIS400 2.3 50.2 1.0 OD1 C:ASP162 2.5 64.1 1.0 NE2 C:HIS64 2.7 56.1 1.0 CD2 C:HIS400 2.8 49.1 1.0 CD2 C:HIS64 2.9 54.4 1.0 CG C:ASP63 3.2 53.7 1.0 CG C:ASP162 3.4 64.2 1.0 CE1 C:HIS400 3.5 51.0 1.0 OD2 C:ASP162 3.6 65.3 1.0 OD1 C:ASP63 3.7 55.9 1.0 ZN C:ZN448 3.8 0.9 1.0 CE1 C:HIS64 4.0 55.8 1.0 CG C:HIS400 4.1 50.1 1.0 CG C:HIS64 4.3 53.5 1.0 ND1 C:HIS400 4.4 50.5 1.0 O C:ASP63 4.4 48.8 1.0 NE2 C:HIS59 4.4 56.8 1.0 CB C:ASP63 4.4 50.8 1.0 O C:VAL12 4.4 65.0 1.0 CE1 C:HIS380 4.5 91.1 1.0 OG C:SER15 4.7 42.5 1.0 ND1 C:HIS64 4.7 55.8 1.0 CE1 C:HIS59 4.8 55.2 1.0 CB C:ASP162 4.8 61.6 1.0 C C:ASP63 4.9 49.9 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8


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 S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn448 b:0.9 occ:1.00 NE2 C:HIS141 2.4 73.9 1.0 OD1 C:ASP162 2.4 64.1 1.0 ND1 C:HIS61 2.5 57.6 1.0 NE2 C:HIS59 2.7 56.8 1.0 CD2 C:HIS141 3.0 72.2 1.0 CD2 C:HIS59 3.2 55.2 1.0 CE1 C:HIS61 3.3 58.2 1.0 CG C:ASP162 3.4 64.2 1.0 CE1 C:HIS380 3.5 91.1 1.0 CE1 C:HIS141 3.5 73.8 1.0 CB C:ASP162 3.6 61.6 1.0 CG C:HIS61 3.6 55.4 1.0 CE1 C:HIS59 3.8 55.2 1.0 ZN C:ZN447 3.8 0.1 1.0 CB C:HIS61 4.0 53.6 1.0 CG C:HIS141 4.2 71.2 1.0 ND1 C:HIS380 4.2 90.8 1.0 NE2 C:HIS380 4.4 91.0 1.0 ND1 C:HIS141 4.4 72.7 1.0 CG C:HIS59 4.5 54.7 1.0 NE2 C:HIS61 4.5 58.1 1.0 OD2 C:ASP162 4.6 65.3 1.0 CD2 C:HIS64 4.6 54.4 1.0 CD2 C:HIS61 4.7 56.8 1.0 ND1 C:HIS59 4.7 56.1 1.0 OD1 C:ASP63 4.8 55.9 1.0 NE2 C:HIS64 4.8 56.1 1.0 OD2 C:ASP63 4.9 54.7 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8


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 S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn438 b:0.9 occ:1.00 NE2 D:HIS400 2.3 65.0 1.0 OD1 D:ASP162 2.5 67.8 1.0 OD2 D:ASP63 2.5 61.8 1.0 NE2 D:HIS64 2.9 55.5 1.0 CD2 D:HIS64 3.1 55.6 1.0 CD2 D:HIS400 3.2 66.6 1.0 CE1 D:HIS400 3.3 66.5 1.0 CG D:ASP63 3.4 60.8 1.0 CG D:ASP162 3.5 67.7 1.0 ZN D:ZN439 3.5 94.7 1.0 OD1 D:ASP63 3.5 60.3 1.0 OD2 D:ASP162 3.8 69.5 1.0 CE1 D:HIS64 4.2 54.9 1.0 CE1 D:HIS380 4.2 89.3 1.0 NE2 D:HIS59 4.3 66.0 1.0 CG D:HIS400 4.3 67.1 1.0 ND1 D:HIS400 4.4 67.0 1.0 CG D:HIS64 4.5 55.2 1.0 ND1 D:HIS61 4.6 70.1 1.0 NE2 D:HIS380 4.6 89.0 1.0 O D:VAL12 4.7 68.1 1.0 CE1 D:HIS59 4.8 65.4 1.0 CB D:ASP63 4.8 58.8 1.0 CB D:ASP162 4.8 64.4 1.0 O D:ASP63 4.9 57.2 1.0 ND1 D:HIS64 5.0 55.9 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8


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 S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn439 b:94.7 occ:1.00 ND1 D:HIS61 1.9 70.1 1.0 NE2 D:HIS141 2.2 74.9 1.0 NE2 D:HIS59 2.6 66.0 1.0 CE1 D:HIS61 2.7 69.6 1.0 OD1 D:ASP162 2.7 67.8 1.0 CD2 D:HIS141 2.9 73.5 1.0 CG D:HIS61 3.1 68.8 1.0 CE1 D:HIS141 3.3 74.6 1.0 CD2 D:HIS59 3.3 64.8 1.0 ZN D:ZN438 3.5 0.9 1.0 CE1 D:HIS59 3.5 65.4 1.0 CB D:HIS61 3.7 65.8 1.0 CG D:ASP162 3.7 67.7 1.0 NE2 D:HIS61 3.9 68.9 1.0 CE1 D:HIS380 4.0 89.3 1.0 CB D:ASP162 4.0 64.4 1.0 CG D:HIS141 4.1 73.0 1.0 CD2 D:HIS61 4.1 69.0 1.0 ND1 D:HIS141 4.2 75.1 1.0 NE2 D:HIS380 4.3 89.0 1.0 CG D:HIS59 4.4 63.9 1.0 CD2 D:HIS64 4.4 55.6 1.0 ND1 D:HIS59 4.5 65.1 1.0 OD1 D:ASP63 4.5 60.3 1.0 NE2 D:HIS64 4.6 55.5 1.0 OD2 D:ASP162 4.9 69.5 1.0

H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui. Crystal Structure of S378Q Mutant TTHA0252 From Thermus Thermophilus HB8 To Be Published.