Zinc in PDB 3iel: Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump

The structure of Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump, PDB code: 3iel was solved by H.Ishikawa, N.Nakagawa, S.Kuramitsu, S.Yokoyama, R.Masui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.238, 146.677, 120.349, 90.00, 110.11, 90.00
R / Rfree (%)	22.2 / 25.9

The binding sites of Zinc atom in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump (pdb code 3iel). 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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump, PDB code: 3iel:
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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn468 b:74.8 occ:1.00 OD1 A:ASP162 2.3 39.8 1.0 NE2 A:HIS400 2.4 37.7 1.0 OD2 A:ASP63 2.6 45.4 1.0 NE2 A:HIS64 3.1 36.3 1.0 CG A:ASP162 3.1 37.8 1.0 O A:HOH472 3.2 44.3 1.0 CE1 A:HIS400 3.3 36.7 1.0 OD2 A:ASP162 3.3 41.5 1.0 CD2 A:HIS400 3.3 35.7 1.0 CD2 A:HIS64 3.3 34.2 1.0 ZN A:ZN469 3.3 95.2 1.0 CG A:ASP63 3.4 41.1 1.0 OD1 A:ASP63 3.6 43.1 1.0 O A:HOH549 3.7 35.4 1.0 CE1 A:HIS64 4.2 36.9 1.0 NE2 A:HIS59 4.2 37.0 1.0 O A:VAL12 4.3 39.1 1.0 ND1 A:HIS400 4.3 35.9 1.0 CE1 A:HIS59 4.4 36.0 1.0 CG A:HIS400 4.4 36.0 1.0 CB A:ASP162 4.5 33.1 1.0 CE1 A:HIS380 4.5 29.8 1.0 CG A:HIS64 4.5 33.9 1.0 NE2 A:HIS380 4.7 32.7 1.0 CB A:ASP63 4.8 35.2 1.0 ND1 A:HIS64 4.9 35.9 1.0 OG A:SER15 4.9 32.7 1.0 O3' A:U5P465 5.0 53.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn469 b:95.2 occ:1.00 O A:HOH472 2.2 44.3 1.0 NE2 A:HIS141 2.5 27.7 1.0 ND1 A:HIS61 2.7 49.6 1.0 OD1 A:ASP162 2.9 39.8 1.0 NE2 A:HIS59 3.1 37.0 1.0 ZN A:ZN468 3.3 74.8 1.0 CE1 A:HIS141 3.3 27.9 1.0 CE1 A:HIS61 3.4 49.0 1.0 CD2 A:HIS141 3.5 25.8 1.0 CG A:HIS61 3.8 46.6 1.0 CE1 A:HIS59 3.8 36.0 1.0 CG A:ASP162 3.8 37.8 1.0 CD2 A:HIS59 4.0 35.9 1.0 CB A:HIS61 4.1 40.0 1.0 OD1 A:ASP63 4.2 43.1 1.0 CB A:ASP162 4.2 33.1 1.0 NE2 A:HIS380 4.3 32.7 1.0 ND1 A:HIS141 4.5 27.7 1.0 O3' A:U5P465 4.5 53.0 1.0 CE1 A:HIS380 4.5 29.8 1.0 O1 A:SO4448 4.6 0.9 1.0 CG A:HIS141 4.6 25.7 1.0 NE2 A:HIS61 4.6 50.6 1.0 OD2 A:ASP162 4.8 41.5 1.0 ND1 A:HIS59 4.8 37.4 1.0 CD2 A:HIS61 4.8 47.8 1.0 OD2 A:ASP63 4.8 45.4 1.0 CG A:HIS59 4.9 33.0 1.0 CG A:ASP63 4.9 41.1 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn458 b:70.8 occ:1.00 OD1 B:ASP162 2.3 40.8 1.0 NE2 B:HIS400 2.3 18.5 1.0 NE2 B:HIS64 2.8 43.6 1.0 OD2 B:ASP63 2.9 51.0 1.0 CD2 B:HIS64 3.0 43.0 1.0 O B:HOH462 3.1 44.8 1.0 CG B:ASP162 3.2 40.2 1.0 CD2 B:HIS400 3.2 17.4 1.0 CE1 B:HIS400 3.3 20.9 1.0 OD2 B:ASP162 3.3 41.8 1.0 CG B:ASP63 3.3 45.1 1.0 OD1 B:ASP63 3.3 50.5 1.0 ZN B:ZN459 3.7 84.8 1.0 CE1 B:HIS64 4.0 45.2 1.0 O B:VAL12 4.2 40.0 1.0 O B:HOH544 4.3 53.2 1.0 NE2 B:HIS59 4.3 46.1 1.0 CG B:HIS64 4.3 41.0 1.0 ND1 B:HIS400 4.4 23.8 1.0 CG B:HIS400 4.4 22.8 1.0 CE1 B:HIS59 4.4 45.4 1.0 CB B:ASP63 4.5 40.4 1.0 CB B:ASP162 4.6 31.5 1.0 OG B:SER15 4.7 33.4 1.0 O2' B:U5P456 4.7 60.0 1.0 ND1 B:HIS64 4.8 42.6 1.0 CE1 B:HIS380 4.9 24.0 1.0 NE2 B:HIS380 4.9 21.5 1.0 O B:ASP63 4.9 36.7 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn459 b:84.8 occ:1.00 NE2 B:HIS141 2.2 24.4 1.0 OD1 B:ASP162 2.7 40.8 1.0 O B:HOH462 2.7 44.8 1.0 ND1 B:HIS61 2.8 48.4 1.0 NE2 B:HIS59 2.8 46.1 1.0 CD2 B:HIS141 2.9 23.2 1.0 CE1 B:HIS141 3.2 25.2 1.0 CE1 B:HIS59 3.6 45.4 1.0 CD2 B:HIS59 3.6 44.6 1.0 CE1 B:HIS61 3.6 51.0 1.0 ZN B:ZN458 3.7 70.8 1.0 CG B:ASP162 3.7 40.2 1.0 CG B:HIS61 3.8 47.1 1.0 CB B:HIS61 4.1 41.0 1.0 CB B:ASP162 4.1 31.5 1.0 CG B:HIS141 4.1 26.2 1.0 ND1 B:HIS141 4.3 25.5 1.0 OD1 B:ASP63 4.4 50.5 1.0 O B:HOH500 4.5 42.1 1.0 NE2 B:HIS380 4.5 21.5 1.0 ND1 B:HIS59 4.6 45.1 1.0 OD2 B:ASP63 4.6 51.0 1.0 CG B:HIS59 4.6 42.8 1.0 OD2 B:ASP162 4.8 41.8 1.0 NE2 B:HIS61 4.8 52.8 1.0 CE1 B:HIS380 4.8 24.0 1.0 CD2 B:HIS61 4.9 49.7 1.0 CG B:ASP63 5.0 45.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn458 b:96.4 occ:1.00 OD2 C:ASP63 2.4 56.0 1.0 OD1 C:ASP162 2.4 46.0 1.0 NE2 C:HIS400 2.4 38.4 1.0 CE1 C:HIS400 3.2 38.7 1.0 NE2 C:HIS64 3.2 50.6 1.0 CG C:ASP63 3.3 50.8 1.0 O C:HOH479 3.3 67.5 1.0 CD2 C:HIS64 3.4 49.6 1.0 CG C:ASP162 3.4 46.0 1.0 ZN C:ZN459 3.4 97.5 1.0 OD1 C:ASP63 3.4 53.5 1.0 CD2 C:HIS400 3.5 38.2 1.0 OD2 C:ASP162 3.6 45.0 1.0 O C:HOH504 3.8 38.7 1.0 O2' C:U5P457 4.3 76.5 1.0 CE1 C:HIS380 4.3 48.0 1.0 ND1 C:HIS400 4.3 41.0 1.0 NE2 C:HIS59 4.4 51.7 1.0 CE1 C:HIS59 4.4 51.8 1.0 NE2 C:HIS380 4.4 45.9 1.0 CE1 C:HIS64 4.5 50.7 1.0 O C:VAL12 4.5 50.0 1.0 CG C:HIS400 4.6 40.3 1.0 CG C:HIS64 4.6 49.9 1.0 CB C:ASP63 4.7 47.1 1.0 CB C:ASP162 4.7 43.0 1.0 O C:HOH491 4.9 51.9 1.0 O3' C:U5P457 4.9 74.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn459 b:97.5 occ:1.00 NE2 C:HIS141 2.2 45.6 1.0 O C:HOH479 2.5 67.5 1.0 OD1 C:ASP162 2.7 46.0 1.0 ND1 C:HIS61 2.7 56.4 1.0 NE2 C:HIS59 2.9 51.7 1.0 CE1 C:HIS141 3.1 45.4 1.0 CD2 C:HIS141 3.2 46.6 1.0 CE1 C:HIS59 3.3 51.8 1.0 ZN C:ZN458 3.4 96.4 1.0 CE1 C:HIS61 3.5 56.9 1.0 CG C:HIS61 3.7 55.2 1.0 CG C:ASP162 3.7 46.0 1.0 CD2 C:HIS59 3.8 49.9 1.0 CB C:HIS61 4.0 52.1 1.0 CB C:ASP162 4.1 43.0 1.0 ND1 C:HIS141 4.2 46.1 1.0 OD1 C:ASP63 4.3 53.5 1.0 NE2 C:HIS380 4.3 45.9 1.0 CG C:HIS141 4.3 47.9 1.0 ND1 C:HIS59 4.3 52.9 1.0 CG C:HIS59 4.6 50.3 1.0 CE1 C:HIS380 4.6 48.0 1.0 NE2 C:HIS61 4.7 57.4 1.0 CD2 C:HIS61 4.8 57.0 1.0 OD2 C:ASP162 4.8 45.0 1.0 CD2 C:HIS64 4.9 49.6 1.0 OD2 C:ASP63 4.9 56.0 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn449 b:0.6 occ:1.00 OD1 D:ASP162 2.3 53.4 1.0 NE2 D:HIS400 2.6 62.8 1.0 OD2 D:ASP63 2.6 63.8 1.0 O D:HOH452 2.7 50.1 1.0 NE2 D:HIS64 2.8 64.2 1.0 CD2 D:HIS64 3.2 63.6 1.0 CG D:ASP162 3.2 50.2 1.0 ZN D:ZN450 3.3 0.0 1.0 CG D:ASP63 3.4 63.0 1.0 OD1 D:ASP63 3.4 63.8 1.0 OD2 D:ASP162 3.4 53.4 1.0 CD2 D:HIS400 3.5 62.0 1.0 CE1 D:HIS400 3.5 62.2 1.0 NE2 D:HIS380 4.0 59.2 1.0 CE1 D:HIS64 4.1 62.8 1.0 CE1 D:HIS380 4.1 59.3 1.0 O2' D:U5P448 4.2 94.7 1.0 NE2 D:HIS59 4.4 53.2 1.0 CG D:HIS64 4.5 62.7 1.0 CB D:ASP162 4.6 49.2 1.0 ND1 D:HIS400 4.6 61.6 1.0 CG D:HIS400 4.6 61.4 1.0 O D:VAL12 4.8 58.8 1.0 CE1 D:HIS59 4.8 52.5 1.0 CB D:ASP63 4.8 60.9 1.0 ND1 D:HIS64 4.9 63.2 1.0 O3' D:U5P448 4.9 95.1 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn450 b:0.0 occ:1.00 NE2 D:HIS141 2.2 50.8 1.0 ND1 D:HIS61 2.4 65.2 1.0 OD1 D:ASP162 2.6 53.4 1.0 NE2 D:HIS59 2.7 53.2 1.0 O D:HOH452 2.8 50.1 1.0 CD2 D:HIS141 3.0 49.8 1.0 CE1 D:HIS141 3.2 51.0 1.0 ZN D:ZN449 3.3 0.6 1.0 CE1 D:HIS61 3.4 64.2 1.0 CG D:HIS61 3.4 63.4 1.0 CD2 D:HIS59 3.4 51.7 1.0 CG D:ASP162 3.6 50.2 1.0 CB D:HIS61 3.6 60.0 1.0 CE1 D:HIS59 3.7 52.5 1.0 CB D:ASP162 4.0 49.2 1.0 CG D:HIS141 4.1 50.4 1.0 ND1 D:HIS141 4.2 51.3 1.0 CD2 D:HIS64 4.2 63.6 1.0 OD1 D:ASP63 4.3 63.8 1.0 NE2 D:HIS380 4.4 59.2 1.0 NE2 D:HIS64 4.4 64.2 1.0 NE2 D:HIS61 4.5 63.5 1.0 CD2 D:HIS61 4.5 63.5 1.0 CG D:HIS59 4.6 50.9 1.0 CE1 D:HIS380 4.6 59.3 1.0 ND1 D:HIS59 4.6 52.0 1.0 CD1 D:LEU142 4.7 53.1 1.0 OD2 D:ASP162 4.7 53.4 1.0

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