Zinc in PDB 2dkf: Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily

The structure of Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily, PDB code: 2dkf was solved by I.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)	19.99 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.220, 147.100, 121.230, 90.00, 109.25, 90.00
R / Rfree (%)	24.2 / 28.5

The binding sites of Zinc atom in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily (pdb code 2dkf). 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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily, PDB code: 2dkf:
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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily


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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn432 b:20.0 occ:0.50 OD1 A:ASP162 2.0 34.2 1.0 NE2 A:HIS400 2.3 43.6 1.0 OD2 A:ASP63 2.3 45.9 1.0 NE2 A:HIS64 2.3 31.4 1.0 CG A:ASP162 2.8 33.5 1.0 CD2 A:HIS64 2.9 31.4 1.0 OD2 A:ASP162 3.0 37.6 1.0 CE1 A:HIS400 3.2 44.6 1.0 CD2 A:HIS400 3.3 44.7 1.0 CG A:ASP63 3.4 45.1 1.0 CE1 A:HIS64 3.5 32.6 1.0 ZN A:ZN433 3.5 37.2 0.5 OD1 A:ASP63 3.9 47.0 1.0 NE2 A:HIS59 4.1 35.0 1.0 CG A:HIS64 4.2 32.8 1.0 CB A:ASP162 4.3 32.1 1.0 NE2 A:HIS380 4.3 39.0 1.0 ND1 A:HIS400 4.3 45.4 1.0 CE1 A:HIS59 4.4 34.9 1.0 ND1 A:HIS64 4.4 32.8 1.0 CG A:HIS400 4.4 45.0 1.0 O A:VAL12 4.6 47.6 1.0 CB A:ASP63 4.7 41.7 1.0 CE1 A:HIS380 4.8 37.4 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily


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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn433 b:37.2 occ:0.50 CE1 A:HIS141 2.1 23.6 1.0 ND1 A:HIS61 2.4 43.9 1.0 NE2 A:HIS59 2.5 35.0 1.0 OD1 A:ASP162 2.6 34.2 1.0 ND1 A:HIS141 3.1 22.9 1.0 NE2 A:HIS141 3.1 23.6 1.0 CD2 A:HIS59 3.1 35.2 1.0 CE1 A:HIS61 3.2 43.7 1.0 CG A:ASP162 3.4 33.5 1.0 CG A:HIS61 3.5 42.1 1.0 ZN A:ZN432 3.5 20.0 0.5 CE1 A:HIS59 3.6 34.9 1.0 CB A:ASP162 3.8 32.1 1.0 CB A:HIS61 3.9 39.7 1.0 CG A:HIS141 4.2 23.7 1.0 CD2 A:HIS141 4.3 24.0 1.0 NE2 A:HIS64 4.3 31.4 1.0 CG A:HIS59 4.3 32.9 1.0 NE2 A:HIS61 4.3 44.4 1.0 CD2 A:HIS64 4.3 31.4 1.0 OD2 A:ASP162 4.4 37.6 1.0 NE2 A:HIS380 4.5 39.0 1.0 CD2 A:HIS61 4.5 43.3 1.0 ND1 A:HIS59 4.5 34.2 1.0 CE1 A:HIS380 4.6 37.4 1.0 OD1 A:ASP63 4.8 47.0 1.0 OD2 A:ASP63 4.8 45.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily


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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn432 b:28.7 occ:0.50 NE2 B:HIS64 2.2 28.1 1.0 NE2 B:HIS400 2.4 37.2 1.0 OD2 B:ASP63 2.7 47.0 1.0 OD2 B:ASP162 2.8 37.4 1.0 CD2 B:HIS400 3.1 36.8 1.0 CD2 B:HIS64 3.1 31.3 1.0 CE1 B:HIS64 3.2 30.1 1.0 OD1 B:ASP162 3.2 37.2 1.0 ZN B:ZN433 3.3 43.0 0.5 CG B:ASP162 3.3 37.9 1.0 CE1 B:HIS400 3.6 35.9 1.0 CG B:ASP63 3.8 44.8 1.0 NE2 B:HIS59 4.1 39.4 1.0 CE1 B:HIS59 4.3 40.0 1.0 CG B:HIS64 4.3 33.2 1.0 ND1 B:HIS64 4.3 29.3 1.0 CG B:HIS400 4.4 37.5 1.0 OG B:SER15 4.4 45.4 1.0 ND1 B:HIS400 4.6 36.0 1.0 CB B:ASP63 4.6 43.1 1.0 OD1 B:ASP63 4.6 44.6 1.0 NE2 B:HIS380 4.6 33.7 1.0 CB B:ASP162 4.8 35.8 1.0 O B:VAL12 4.8 48.0 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily


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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn433 b:43.0 occ:0.50 CE1 B:HIS141 2.2 34.8 1.0 NE2 B:HIS59 2.3 39.4 1.0 ND1 B:HIS61 2.7 42.7 1.0 ND1 B:HIS141 3.0 33.2 1.0 CD2 B:HIS59 3.1 40.5 1.0 CG B:ASP162 3.1 37.9 1.0 ZN B:ZN432 3.3 28.7 0.5 OD2 B:ASP162 3.3 37.4 1.0 NE2 B:HIS141 3.3 34.3 1.0 CE1 B:HIS59 3.3 40.0 1.0 OD1 B:ASP162 3.4 37.2 1.0 CB B:ASP162 3.6 35.8 1.0 CE1 B:HIS61 3.6 43.0 1.0 CG B:HIS61 3.7 43.0 1.0 CB B:HIS61 4.0 43.4 1.0 NE2 B:HIS64 4.0 28.1 1.0 CG B:HIS141 4.2 33.4 1.0 NE2 B:HIS380 4.2 33.7 1.0 CG B:HIS59 4.3 40.6 1.0 CD2 B:HIS141 4.3 33.4 1.0 ND1 B:HIS59 4.3 39.2 1.0 CD2 B:HIS64 4.4 31.3 1.0 CE1 B:HIS380 4.6 32.3 1.0 NE2 B:HIS61 4.8 42.7 1.0 CD2 B:HIS61 4.9 43.2 1.0 CE1 B:HIS64 4.9 30.1 1.0 OD2 B:ASP63 5.0 47.0 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily


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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn432 b:48.0 occ:0.50 ND1 C:HIS61 2.1 67.9 1.0 NE2 C:HIS59 2.5 59.5 1.0 CE1 C:HIS141 2.5 49.1 1.0 OD1 C:ASP162 2.7 62.9 1.0 NE2 C:HIS141 2.7 49.5 1.0 CE1 C:HIS61 2.8 67.6 1.0 CE1 C:HIS59 3.3 59.9 1.0 CD2 C:HIS59 3.3 59.5 1.0 ZN C:ZN433 3.4 44.6 0.5 CG C:HIS61 3.4 67.4 1.0 O C:HOH447 3.6 57.9 1.0 ND1 C:HIS141 3.7 49.8 1.0 CG C:ASP162 3.8 63.2 1.0 CB C:HIS61 4.0 66.2 1.0 CD2 C:HIS141 4.0 49.3 1.0 NE2 C:HIS61 4.0 67.7 1.0 NE2 C:HIS380 4.1 89.1 1.0 OD1 C:ASP63 4.1 64.9 1.0 CB C:ASP162 4.1 62.0 1.0 CE1 C:HIS380 4.1 88.9 1.0 CD2 C:HIS61 4.3 67.3 1.0 ND1 C:HIS59 4.3 59.7 1.0 CD2 C:HIS64 4.4 56.9 1.0 CG C:HIS59 4.4 59.0 1.0 NE2 C:HIS64 4.4 56.4 1.0 CG C:HIS141 4.5 49.5 1.0 OD2 C:ASP162 4.9 64.0 1.0 CG C:ASP63 4.9 64.4 1.0 OD2 C:ASP63 5.0 63.7 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily


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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn433 b:44.6 occ:0.50 OD1 C:ASP162 2.2 62.9 1.0 OD2 C:ASP63 2.2 63.7 1.0 NE2 C:HIS64 2.3 56.4 1.0 NE2 C:HIS400 2.3 69.8 1.0 CD2 C:HIS64 2.7 56.9 1.0 CG C:ASP63 3.0 64.4 1.0 OD1 C:ASP63 3.0 64.9 1.0 O C:HOH447 3.2 57.9 1.0 CG C:ASP162 3.2 63.2 1.0 CE1 C:HIS400 3.2 69.6 1.0 CD2 C:HIS400 3.3 69.9 1.0 ZN C:ZN432 3.4 48.0 0.5 OD2 C:ASP162 3.5 64.0 1.0 CE1 C:HIS64 3.6 57.4 1.0 NE2 C:HIS59 4.0 59.5 1.0 CG C:HIS64 4.1 57.6 1.0 CE1 C:HIS59 4.2 59.9 1.0 NE2 C:HIS380 4.2 89.1 1.0 ND1 C:HIS400 4.3 70.0 1.0 ND1 C:HIS64 4.4 57.4 1.0 CB C:ASP63 4.4 64.0 1.0 CG C:HIS400 4.4 69.9 1.0 CB C:ASP162 4.5 62.0 1.0 O C:ASP63 4.7 62.8 1.0 CE1 C:HIS380 4.8 88.9 1.0 ND1 C:HIS61 4.8 67.9 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily


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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn432 b:59.9 occ:0.50 NE2 D:HIS400 2.1 68.4 1.0 OD1 D:ASP162 2.4 64.6 1.0 NE2 D:HIS64 2.4 54.8 1.0 OD1 D:ASP63 2.9 61.3 1.0 CE1 D:HIS400 3.0 68.1 1.0 CD2 D:HIS400 3.2 69.4 1.0 CD2 D:HIS64 3.2 54.5 1.0 OD2 D:ASP63 3.2 61.3 1.0 CG D:ASP162 3.2 65.8 1.0 OD2 D:ASP162 3.4 66.8 1.0 CG D:ASP63 3.5 61.2 1.0 ZN D:ZN433 3.5 74.0 0.5 CE1 D:HIS64 3.6 54.9 1.0 ND1 D:HIS400 4.2 69.1 1.0 NE2 D:HIS59 4.2 58.1 1.0 CG D:HIS400 4.3 69.8 1.0 NE2 D:HIS380 4.3 0.7 1.0 CG D:HIS64 4.4 54.7 1.0 CE1 D:HIS59 4.4 57.5 1.0 ND1 D:HIS64 4.6 55.1 1.0 CE1 D:HIS380 4.6 0.7 1.0 CB D:ASP162 4.6 65.7 1.0 OG D:SER15 4.8 52.1 1.0 ND1 D:HIS61 4.8 63.3 1.0 CB D:ASP63 5.0 59.9 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily


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, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn433 b:74.0 occ:0.50 ND1 D:HIS61 2.0 63.3 1.0 OD1 D:ASP162 2.4 64.6 1.0 CE1 D:HIS141 2.5 66.1 1.0 CE1 D:HIS61 2.8 64.1 1.0 NE2 D:HIS59 2.9 58.1 1.0 CG D:HIS61 3.1 63.1 1.0 NE2 D:HIS141 3.1 66.2 1.0 ND1 D:HIS141 3.4 65.4 1.0 CD2 D:HIS59 3.4 57.6 1.0 CG D:ASP162 3.5 65.8 1.0 CE1 D:HIS59 3.5 57.5 1.0 ZN D:ZN432 3.5 59.9 0.5 CB D:HIS61 3.6 62.2 1.0 CB D:ASP162 3.9 65.7 1.0 NE2 D:HIS61 4.0 64.2 1.0 CD2 D:HIS61 4.1 63.6 1.0 CE1 D:HIS380 4.2 0.7 1.0 CD2 D:HIS141 4.3 65.5 1.0 CG D:HIS59 4.3 57.6 1.0 ND1 D:HIS59 4.3 58.4 1.0 CG D:HIS141 4.4 64.9 1.0 NE2 D:HIS64 4.4 54.8 1.0 NE2 D:HIS380 4.5 0.7 1.0 CD2 D:HIS64 4.5 54.5 1.0 OD1 D:ASP63 4.6 61.3 1.0 OD2 D:ASP162 4.6 66.8 1.0

H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui. Crystal Structure of TTHA0252 From Thermus Thermophilus HB8, A Rna Degradation Protein of the Metallo-Beta-Lactamase Superfamily J.Biochem.(Tokyo) V. 140 535 2006.
ISSN: ISSN 0021-924X
PubMed: 16945939
DOI: 10.1093/JB/MVJ183