Zinc in PDB 3iem: Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna Analog

The structure of Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna Analog, PDB code: 3iem was solved by H.Ishikawa, N.Nakagawa, S.Kuramitus, 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 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.694, 146.441, 119.975, 90.00, 110.37, 90.00
R / Rfree (%)	21.3 / 25.7

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


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 Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn448 b:56.7 occ:1.00 OD1 A:ASP162 2.3 22.4 1.0 OD2 A:ASP63 2.3 29.1 1.0 NE2 A:HIS400 2.4 29.8 1.0 S1P G:SSU3 2.8 77.4 1.0 NE2 A:HIS64 2.8 25.0 1.0 CD2 A:HIS64 3.0 22.2 1.0 CG A:ASP63 3.1 25.8 1.0 CD2 A:HIS400 3.1 29.1 1.0 OD1 A:ASP63 3.2 26.4 1.0 CG A:ASP162 3.4 24.6 1.0 ZN A:ZN449 3.5 73.4 1.0 CE1 A:HIS400 3.5 29.9 1.0 O A:HOH469 3.7 30.7 1.0 OD2 A:ASP162 3.8 27.2 1.0 CE1 A:HIS64 4.1 24.8 1.0 NE2 A:HIS59 4.1 24.8 1.0 CG A:HIS64 4.3 24.3 1.0 CG A:HIS400 4.4 30.0 1.0 CE1 A:HIS59 4.4 24.7 1.0 CB A:ASP63 4.5 24.3 1.0 ND1 A:HIS400 4.5 29.5 1.0 O A:VAL12 4.7 25.3 1.0 CB A:ASP162 4.7 19.4 1.0 P G:SSU3 4.7 78.1 1.0 ND1 A:HIS64 4.8 25.2 1.0 O A:ASP63 4.8 23.7 1.0 CE1 A:HIS380 4.8 20.9 1.0 O2' G:SSU2 4.9 65.2 1.0 OG A:SER15 5.0 24.9 1.0

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


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 Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn449 b:73.4 occ:1.00 NE2 A:HIS141 2.4 13.7 1.0 ND1 A:HIS61 2.5 29.1 1.0 NE2 A:HIS59 2.6 24.8 1.0 OD1 A:ASP162 2.8 22.4 1.0 S1P G:SSU3 3.1 77.4 1.0 CD2 A:HIS141 3.1 13.1 1.0 CD2 A:HIS59 3.3 25.2 1.0 CE1 A:HIS61 3.4 25.1 1.0 CE1 A:HIS141 3.4 12.0 1.0 CE1 A:HIS59 3.5 24.7 1.0 ZN A:ZN448 3.5 56.7 1.0 CG A:HIS61 3.5 27.0 1.0 CG A:ASP162 3.8 24.6 1.0 CB A:HIS61 3.8 26.1 1.0 OP2 G:SSU3 3.9 78.4 1.0 P G:SSU3 4.0 78.1 1.0 CB A:ASP162 4.0 19.4 1.0 O5' G:SSU3 4.3 77.9 1.0 CG A:HIS141 4.3 12.3 1.0 OD1 A:ASP63 4.3 26.4 1.0 CG A:HIS59 4.4 23.8 1.0 ND1 A:HIS141 4.4 12.4 1.0 ND1 A:HIS59 4.4 25.6 1.0 NE2 A:HIS61 4.5 25.8 1.0 CE1 A:HIS380 4.6 20.9 1.0 CD2 A:HIS61 4.6 27.3 1.0 NE2 A:HIS380 4.7 21.7 1.0 CD2 A:HIS64 4.8 22.2 1.0 NE2 A:HIS64 4.9 25.0 1.0 OD2 A:ASP162 5.0 27.2 1.0

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


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 Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn451 b:56.6 occ:1.00 OD1 B:ASP162 2.4 28.4 1.0 OD2 B:ASP63 2.4 28.7 1.0 NE2 B:HIS400 2.5 17.4 1.0 NE2 B:HIS64 2.7 29.7 1.0 CD2 B:HIS64 2.9 27.5 1.0 O5' K:SSU1 3.0 90.5 1.0 OD1 B:ASP63 3.0 26.5 1.0 CG B:ASP63 3.0 25.5 1.0 CD2 B:HIS400 3.3 15.4 1.0 CG B:ASP162 3.3 28.2 1.0 ZN B:ZN452 3.5 64.1 1.0 CE1 B:HIS400 3.5 14.6 1.0 OD2 B:ASP162 3.5 28.6 1.0 O B:HOH487 3.9 24.9 1.0 CE1 B:HIS64 3.9 31.3 1.0 C5' K:SSU1 4.1 93.1 1.0 NE2 B:HIS59 4.2 31.1 1.0 CG B:HIS64 4.3 27.6 1.0 CE1 B:HIS59 4.4 32.5 1.0 CG B:HIS400 4.5 18.3 1.0 CB B:ASP63 4.5 24.7 1.0 ND1 B:HIS400 4.5 17.8 1.0 CB B:ASP162 4.7 24.9 1.0 ND1 B:HIS64 4.7 27.9 1.0 S1P K:SSU2 4.8 97.5 1.0 O B:VAL12 4.9 30.9 1.0 O B:ASP63 4.9 26.0 1.0 OG B:SER15 4.9 26.7 1.0 CE1 B:HIS380 4.9 19.6 1.0

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


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 Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn452 b:64.1 occ:1.00 NE2 B:HIS141 2.2 22.8 1.0 ND1 B:HIS61 2.5 27.7 1.0 OD1 B:ASP162 2.7 28.4 1.0 NE2 B:HIS59 2.8 31.1 1.0 CD2 B:HIS141 3.0 21.1 1.0 CE1 B:HIS141 3.2 20.9 1.0 O5' K:SSU1 3.2 90.5 1.0 CE1 B:HIS61 3.4 25.0 1.0 ZN B:ZN451 3.5 56.6 1.0 CG B:HIS61 3.5 24.3 1.0 CE1 B:HIS59 3.5 32.5 1.0 CD2 B:HIS59 3.7 29.8 1.0 CB B:HIS61 3.7 23.3 1.0 CG B:ASP162 3.8 28.2 1.0 CG B:HIS141 4.1 23.1 1.0 CB B:ASP162 4.1 24.9 1.0 ND1 B:HIS141 4.2 22.7 1.0 OD1 B:ASP63 4.3 26.5 1.0 C5' K:SSU1 4.5 93.1 1.0 NE2 B:HIS61 4.5 28.8 1.0 ND1 B:HIS59 4.5 33.1 1.0 NE2 B:HIS380 4.5 19.6 1.0 CD2 B:HIS61 4.6 27.3 1.0 CG B:HIS59 4.7 29.8 1.0 OP2 K:SSU2 4.7 94.3 1.0 CE1 B:HIS380 4.7 19.6 1.0 CD2 B:HIS64 4.8 27.5 1.0 NE2 B:HIS64 4.8 29.7 1.0 OD2 B:ASP162 4.9 28.6 1.0

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


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 Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn444 b:75.2 occ:1.00 OD2 C:ASP63 2.1 48.0 1.0 OD1 C:ASP162 2.4 50.6 1.0 NE2 C:HIS400 2.7 37.9 1.0 NE2 C:HIS64 2.8 42.4 1.0 CG C:ASP63 3.0 46.2 1.0 CD2 C:HIS64 3.1 41.2 1.0 OD1 C:ASP63 3.2 50.6 1.0 ZN C:ZN445 3.2 81.2 1.0 CE1 C:HIS400 3.5 39.9 1.0 CG C:ASP162 3.5 49.8 1.0 CD2 C:HIS400 3.7 40.3 1.0 OD2 C:ASP162 4.0 50.8 1.0 CE1 C:HIS64 4.0 40.5 1.0 NE2 C:HIS59 4.1 46.7 1.0 CB C:ASP63 4.4 43.0 1.0 NE2 C:HIS380 4.4 56.2 1.0 CG C:HIS64 4.4 39.9 1.0 CE1 C:HIS380 4.6 56.2 1.0 OP2 P:SSU2 4.6 0.4 1.0 ND1 C:HIS400 4.7 40.9 1.0 CE1 C:HIS59 4.7 48.1 1.0 CB C:ASP162 4.8 47.8 1.0 CG C:HIS400 4.8 41.9 1.0 ND1 C:HIS64 4.8 41.1 1.0 C3' P:SSU1 4.9 0.8 1.0

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


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 Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn445 b:81.2 occ:1.00 NE2 C:HIS141 2.3 52.1 1.0 ND1 C:HIS61 2.5 45.6 1.0 CD2 C:HIS141 2.9 52.5 1.0 OD1 C:ASP162 2.9 50.6 1.0 NE2 C:HIS59 2.9 46.7 1.0 ZN C:ZN444 3.2 75.2 1.0 CD2 C:HIS59 3.4 46.4 1.0 CG C:HIS61 3.4 45.2 1.0 CE1 C:HIS61 3.4 45.5 1.0 CE1 C:HIS141 3.5 51.8 1.0 CB C:HIS61 3.6 44.9 1.0 OP2 P:SSU2 3.7 0.4 1.0 CG C:ASP162 3.9 49.8 1.0 CE1 C:HIS59 3.9 48.1 1.0 CB C:ASP162 4.1 47.8 1.0 CG C:HIS141 4.1 52.5 1.0 NE2 C:HIS380 4.2 56.2 1.0 OD1 C:ASP63 4.3 50.6 1.0 ND1 C:HIS141 4.4 51.7 1.0 CG C:HIS59 4.5 46.4 1.0 NE2 C:HIS61 4.6 46.0 1.0 CD2 C:HIS61 4.6 44.3 1.0 NE2 C:HIS64 4.7 42.4 1.0 CD2 C:HIS64 4.7 41.2 1.0 ND1 C:HIS59 4.7 48.1 1.0 CE1 C:HIS380 4.8 56.2 1.0 OD2 C:ASP63 4.8 48.0 1.0

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


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 Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn443 b:70.8 occ:1.00 OD1 D:ASP162 2.2 45.9 1.0 NE2 D:HIS64 2.3 42.2 1.0 S1P I:SSU3 2.6 1.0 1.0 OD2 D:ASP63 2.7 45.1 1.0 NE2 D:HIS400 2.7 41.2 1.0 CD2 D:HIS64 2.7 40.1 1.0 OD1 D:ASP63 3.0 46.2 1.0 CG D:ASP162 3.1 44.4 1.0 CG D:ASP63 3.2 43.9 1.0 ZN D:ZN444 3.3 69.9 1.0 OD2 D:ASP162 3.4 46.0 1.0 CD2 D:HIS400 3.5 41.6 1.0 CE1 D:HIS64 3.6 41.1 1.0 CE1 D:HIS400 3.7 41.8 1.0 NE2 D:HIS59 4.0 34.3 1.0 CG D:HIS64 4.1 42.3 1.0 P I:SSU3 4.2 0.6 1.0 CE1 D:HIS59 4.3 34.0 1.0 ND1 D:HIS64 4.4 41.6 1.0 CB D:ASP162 4.5 39.4 1.0 OP2 I:SSU3 4.5 0.1 1.0 O5' I:SSU3 4.6 0.6 1.0 NE2 D:HIS380 4.6 43.4 1.0 CB D:ASP63 4.7 42.4 1.0 CG D:HIS400 4.7 42.4 1.0 CE1 D:HIS380 4.8 44.7 1.0 ND1 D:HIS400 4.8 43.2 1.0 O2' I:SSU2 4.9 1.0 1.0 OG D:SER15 4.9 38.9 1.0

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


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 Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn444 b:69.9 occ:1.00 NE2 D:HIS141 2.3 38.5 1.0 NE2 D:HIS59 2.4 34.3 1.0 OD1 D:ASP162 2.5 45.9 1.0 ND1 D:HIS61 2.6 39.9 1.0 OP2 I:SSU3 3.0 0.1 1.0 CD2 D:HIS141 3.1 39.8 1.0 CD2 D:HIS59 3.1 33.7 1.0 CE1 D:HIS141 3.3 40.0 1.0 ZN D:ZN443 3.3 70.8 1.0 CE1 D:HIS59 3.4 34.0 1.0 CG D:HIS61 3.5 40.2 1.0 S1P I:SSU3 3.5 1.0 1.0 CG D:ASP162 3.6 44.4 1.0 CE1 D:HIS61 3.6 39.2 1.0 CB D:HIS61 3.6 40.6 1.0 P I:SSU3 3.8 0.6 1.0 CB D:ASP162 3.9 39.4 1.0 CG D:HIS141 4.2 40.0 1.0 ND1 D:HIS141 4.3 42.4 1.0 OD1 D:ASP63 4.3 46.2 1.0 CG D:HIS59 4.3 33.6 1.0 CD2 D:HIS64 4.3 40.1 1.0 ND1 D:HIS59 4.4 33.7 1.0 NE2 D:HIS64 4.5 42.2 1.0 NE2 D:HIS380 4.6 43.4 1.0 CD2 D:HIS61 4.7 38.4 1.0 NE2 D:HIS61 4.7 38.6 1.0 OD2 D:ASP162 4.7 46.0 1.0 O5' I:SSU3 4.7 0.6 1.0 CE1 D:HIS380 4.8 44.7 1.0 CD1 D:LEU142 4.9 33.5 1.0

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