Zinc in PDB 3ie1: Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna

The structure of Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna, PDB code: 3ie1 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 / 2.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.424, 148.165, 120.837, 90.00, 109.61, 90.00
R / Rfree (%)	23.1 / 29.1

The binding sites of Zinc atom in the Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna (pdb code 3ie1). 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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna, PDB code: 3ie1:
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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna


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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn452 b:58.5 occ:1.00 NE2 A:HIS400 2.2 51.5 1.0 OD2 A:ASP63 2.2 41.1 1.0 OD1 A:ASP162 2.4 35.0 1.0 NE2 A:HIS64 2.5 34.4 1.0 OP1 E:U1 2.8 73.3 1.0 CD2 A:HIS64 3.0 31.7 1.0 CG A:ASP63 3.1 39.6 1.0 CE1 A:HIS400 3.1 52.5 1.0 OD1 A:ASP63 3.1 41.0 1.0 CD2 A:HIS400 3.2 51.5 1.0 CG A:ASP162 3.2 37.1 1.0 ZN A:ZN453 3.3 60.0 1.0 OD2 A:ASP162 3.3 42.9 1.0 CE1 A:HIS64 3.7 33.6 1.0 P E:U1 3.8 71.6 1.0 OP2 E:U1 3.9 72.3 1.0 O5' E:U1 4.1 69.7 1.0 C5' E:U1 4.2 70.7 1.0 ND1 A:HIS400 4.2 52.0 1.0 CG A:HIS400 4.3 51.9 1.0 CG A:HIS64 4.3 33.3 1.0 NE2 A:HIS59 4.3 35.6 1.0 CE1 A:HIS59 4.5 34.8 1.0 CB A:ASP63 4.5 37.3 1.0 O A:VAL12 4.6 51.8 1.0 ND1 A:HIS64 4.6 32.6 1.0 CB A:ASP162 4.7 36.2 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna


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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn453 b:60.0 occ:1.00 NE2 A:HIS141 2.1 29.2 1.0 OD1 A:ASP162 2.2 35.0 1.0 ND1 A:HIS61 2.4 34.3 1.0 NE2 A:HIS59 2.5 35.6 1.0 O5' E:U1 2.9 69.7 1.0 CD2 A:HIS141 3.0 28.7 1.0 CE1 A:HIS141 3.1 30.0 1.0 ZN A:ZN452 3.3 58.5 1.0 CE1 A:HIS61 3.3 32.6 1.0 C5' E:U1 3.3 70.7 1.0 CG A:ASP162 3.3 37.1 1.0 CE1 A:HIS59 3.3 34.8 1.0 OP2 E:U1 3.4 72.3 1.0 CG A:HIS61 3.4 36.3 1.0 CD2 A:HIS59 3.5 35.2 1.0 P E:U1 3.6 71.6 1.0 CB A:HIS61 3.7 36.0 1.0 CB A:ASP162 3.9 36.2 1.0 OP1 E:U1 3.9 73.3 1.0 OD1 A:ASP63 3.9 41.0 1.0 ND1 A:HIS141 4.2 30.4 1.0 CG A:HIS141 4.2 29.0 1.0 OD2 A:ASP162 4.4 42.9 1.0 NE2 A:HIS64 4.4 34.4 1.0 NE2 A:HIS61 4.4 35.3 1.0 ND1 A:HIS59 4.4 35.8 1.0 CD2 A:HIS64 4.4 31.7 1.0 CD2 A:HIS61 4.5 35.0 1.0 CG A:HIS59 4.5 35.9 1.0 C4' E:U1 4.7 70.2 1.0 OD2 A:ASP63 4.8 41.1 1.0 CG A:ASP63 4.8 39.6 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna


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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn449 b:61.2 occ:1.00 NE2 B:HIS64 2.3 33.5 1.0 NE2 B:HIS400 2.4 32.7 1.0 OP1 F:U1 2.7 96.4 1.0 OD2 B:ASP63 2.8 52.0 1.0 CD2 B:HIS64 2.8 34.9 1.0 OD1 B:ASP162 2.9 46.2 1.0 ZN B:ZN450 3.1 65.8 1.0 OD1 B:ASP63 3.1 49.0 1.0 CD2 B:HIS400 3.3 33.0 1.0 OD2 B:ASP162 3.3 46.6 1.0 CG B:ASP63 3.3 48.7 1.0 CE1 B:HIS400 3.4 33.9 1.0 CG B:ASP162 3.4 45.1 1.0 P F:U1 3.5 96.9 1.0 O5' F:U1 3.5 97.2 1.0 CE1 B:HIS64 3.6 36.3 1.0 C5' F:U1 3.7 95.8 1.0 OP3 F:U1 3.8 97.3 1.0 CG B:HIS64 4.1 36.8 1.0 NE2 B:HIS59 4.2 38.9 1.0 CG B:HIS400 4.4 34.4 1.0 ND1 B:HIS400 4.4 31.7 1.0 CE1 B:HIS59 4.4 40.1 1.0 ND1 B:HIS64 4.5 36.0 1.0 CB B:ASP162 4.7 41.4 1.0 ND1 B:HIS61 4.8 42.0 1.0 CB B:ASP63 4.8 46.2 1.0 O B:VAL12 4.8 57.7 1.0 OP2 F:U1 4.9 97.1 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna


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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn450 b:65.8 occ:1.00 NE2 B:HIS59 2.4 38.9 1.0 ND1 B:HIS61 2.5 42.0 1.0 NE2 B:HIS141 2.5 43.2 1.0 O5' F:U1 2.6 97.2 1.0 OP1 F:U1 2.9 96.4 1.0 ZN B:ZN449 3.1 61.2 1.0 CD2 B:HIS141 3.1 42.1 1.0 OD1 B:ASP162 3.2 46.2 1.0 CE1 B:HIS61 3.3 42.2 1.0 CG B:ASP162 3.3 45.1 1.0 CD2 B:HIS59 3.3 40.8 1.0 P F:U1 3.4 96.9 1.0 CE1 B:HIS59 3.4 40.1 1.0 C5' F:U1 3.4 95.8 1.0 CG B:HIS61 3.5 42.2 1.0 CE1 B:HIS141 3.6 41.7 1.0 CB B:ASP162 3.7 41.4 1.0 OD2 B:ASP162 3.7 46.6 1.0 CB B:HIS61 3.8 45.2 1.0 CD2 B:HIS64 4.1 34.9 1.0 NE2 B:HIS64 4.1 33.5 1.0 OP2 F:U1 4.2 97.1 1.0 CG B:HIS141 4.3 43.0 1.0 OD1 B:ASP63 4.4 49.0 1.0 NE2 B:HIS61 4.4 43.0 1.0 CG B:HIS59 4.5 42.8 1.0 ND1 B:HIS59 4.5 41.5 1.0 CD2 B:HIS61 4.5 41.4 1.0 C4' F:U1 4.5 94.8 1.0 ND1 B:HIS141 4.5 40.3 1.0 OP3 F:U1 4.6 97.3 1.0 NE2 B:HIS400 5.0 32.7 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna


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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn442 b:0.5 occ:1.00 OD2 C:ASP63 2.6 62.5 1.0 OD1 C:ASP162 2.6 76.9 1.0 NE2 C:HIS400 2.7 72.5 1.0 OD1 C:ASP63 2.9 62.7 1.0 NE2 C:HIS64 2.9 59.1 1.0 CG C:ASP63 3.1 61.4 1.0 CE1 C:HIS400 3.1 73.8 1.0 CD2 C:HIS64 3.1 58.7 1.0 ZN C:ZN443 3.2 0.0 1.0 C5' G:U1 3.2 0.3 1.0 OP2 G:U1 3.3 0.4 1.0 O5' G:U1 3.5 0.8 1.0 ND1 C:HIS61 3.7 62.0 1.0 CG C:ASP162 3.8 77.0 1.0 CD2 C:HIS400 4.0 74.2 1.0 P G:U1 4.1 0.6 1.0 CE1 C:HIS64 4.2 59.3 1.0 OD2 C:ASP162 4.3 78.6 1.0 CB C:HIS61 4.4 62.6 1.0 ND1 C:HIS400 4.4 73.8 1.0 NE2 C:HIS59 4.4 74.9 1.0 CG C:HIS61 4.4 62.6 1.0 CG C:HIS64 4.5 57.7 1.0 CB C:ASP63 4.5 61.2 1.0 C4' G:U1 4.6 1.0 1.0 CE1 C:HIS61 4.7 64.7 1.0 CG C:HIS400 4.8 75.5 1.0 CE1 C:HIS59 4.9 75.2 1.0 NE2 C:HIS141 4.9 78.7 1.0 ND1 C:HIS64 4.9 58.8 1.0 CB C:ASP162 4.9 75.3 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna


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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn443 b:0.0 occ:1.00 NE2 C:HIS141 1.9 78.7 1.0 ND1 C:HIS61 1.9 62.0 1.0 CE1 C:HIS61 2.5 64.7 1.0 OD1 C:ASP162 2.6 76.9 1.0 NE2 C:HIS59 2.6 74.9 1.0 CD2 C:HIS141 2.7 78.5 1.0 CE1 C:HIS141 2.9 79.2 1.0 CG C:HIS61 3.2 62.6 1.0 ZN C:ZN442 3.2 0.5 1.0 CG C:ASP162 3.4 77.0 1.0 O5' G:U1 3.4 0.8 1.0 CD2 C:HIS59 3.5 73.4 1.0 CE1 C:HIS59 3.5 75.2 1.0 CB C:ASP162 3.5 75.3 1.0 NE2 C:HIS61 3.7 64.8 1.0 CB C:HIS61 3.8 62.6 1.0 CG C:HIS141 3.9 77.9 1.0 ND1 C:HIS141 3.9 78.7 1.0 CD2 C:HIS61 4.0 63.6 1.0 OP2 G:U1 4.1 0.4 1.0 C5' G:U1 4.2 0.3 1.0 P G:U1 4.2 0.6 1.0 CD2 C:HIS64 4.2 58.7 1.0 NE2 C:HIS64 4.3 59.1 1.0 OP3 G:U1 4.3 0.9 1.0 OD2 C:ASP162 4.5 78.6 1.0 CG C:HIS59 4.6 72.3 1.0 ND1 C:HIS59 4.6 75.1 1.0 OD1 C:ASP63 4.8 62.7 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna


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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn441 b:88.9 occ:1.00 OP2 H:U1 2.1 0.3 1.0 OD1 D:ASP162 2.2 72.7 1.0 OD2 D:ASP63 2.4 70.1 1.0 NE2 D:HIS64 2.4 64.3 1.0 NE2 D:HIS400 2.6 91.7 1.0 CD2 D:HIS64 2.7 63.5 1.0 OD1 D:ASP63 3.1 72.2 1.0 CG D:ASP63 3.1 70.1 1.0 CG D:ASP162 3.2 74.0 1.0 ZN D:ZN442 3.3 86.2 1.0 P H:U1 3.5 0.9 1.0 CD2 D:HIS400 3.6 92.4 1.0 CE1 D:HIS400 3.6 91.6 1.0 OD2 D:ASP162 3.7 74.5 1.0 CE1 D:HIS64 3.7 63.8 1.0 OP1 H:U1 3.8 0.8 1.0 CG D:HIS64 4.0 63.9 1.0 C5' H:U1 4.1 0.0 1.0 NE2 D:HIS59 4.2 68.3 1.0 ND1 D:HIS61 4.3 67.5 1.0 O5' H:U1 4.3 0.4 1.0 CE1 D:HIS59 4.4 67.7 1.0 ND1 D:HIS64 4.5 63.3 1.0 CB D:ASP162 4.5 73.1 1.0 CB D:ASP63 4.5 69.2 1.0 OP3 H:U1 4.6 0.3 1.0 CB D:HIS61 4.6 66.2 1.0 ND1 D:HIS400 4.7 91.8 1.0 CG D:HIS400 4.7 92.0 1.0 O D:ASP63 4.9 69.2 1.0 CG D:HIS61 4.9 66.9 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna


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 H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn442 b:86.2 occ:1.00 ND1 D:HIS61 1.8 67.5 1.0 NE2 D:HIS141 2.1 67.2 1.0 NE2 D:HIS59 2.4 68.3 1.0 CE1 D:HIS61 2.6 67.5 1.0 OD1 D:ASP162 2.7 72.7 1.0 CG D:HIS61 3.0 66.9 1.0 CD2 D:HIS141 3.0 66.8 1.0 OP1 H:U1 3.1 0.8 1.0 CE1 D:HIS141 3.1 67.7 1.0 CE1 D:HIS59 3.1 67.7 1.0 ZN D:ZN441 3.3 88.9 1.0 CD2 D:HIS59 3.4 68.0 1.0 CB D:HIS61 3.5 66.2 1.0 CG D:ASP162 3.6 74.0 1.0 OP2 H:U1 3.6 0.3 1.0 CB D:ASP162 3.7 73.1 1.0 P H:U1 3.7 0.9 1.0 NE2 D:HIS61 3.7 67.3 1.0 O5' H:U1 3.9 0.4 1.0 C5' H:U1 3.9 0.0 1.0 CD2 D:HIS61 3.9 65.9 1.0 CD2 D:HIS64 4.1 63.5 1.0 ND1 D:HIS59 4.2 67.7 1.0 ND1 D:HIS141 4.2 67.5 1.0 CG D:HIS141 4.2 66.0 1.0 NE2 D:HIS64 4.3 64.3 1.0 CG D:HIS59 4.3 67.6 1.0 OD1 D:ASP63 4.6 72.2 1.0 OD2 D:ASP162 4.7 74.5 1.0 CA D:HIS61 5.0 66.5 1.0 CD1 D:LEU142 5.0 62.8 1.0

H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui. Crystal Structure of H380A Mutant TTHA0252 From Thermus Thermophilus HB8 Complexed with Rna To Be Published.