Calcium in PDB 7wrr: X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes

All present enzymatic activity of X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes:
2.2.1.1;

The structure of X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes, PDB code: 7wrr was solved by S.Kamitori, A.Yoshihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.67 / 2.01
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	72.72, 88.84, 117.61, 72.56, 88.74, 73.74
R / Rfree (%)	19.8 / 22.8

The binding sites of Calcium atom in the X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes (pdb code 7wrr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes, PDB code: 7wrr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:38.9 occ:1.00 O3B A:TPP701 2.2 34.3 1.0 OD2 A:ASP159 2.2 31.1 1.0 O1A A:TPP701 2.2 46.6 1.0 O A:ILE191 2.3 38.1 1.0 O A:HOH835 2.4 24.1 1.0 OD1 A:ASN189 2.4 36.9 1.0 CG A:ASP159 3.2 31.1 1.0 CG A:ASN189 3.3 38.5 1.0 PA A:TPP701 3.4 43.6 1.0 PB A:TPP701 3.5 43.3 1.0 ND2 A:ASN189 3.5 37.0 1.0 C A:ILE191 3.6 39.0 1.0 O3A A:TPP701 3.7 43.5 1.0 CB A:ASP159 3.7 31.2 1.0 N A:ILE191 4.1 34.7 1.0 N A:ASP159 4.1 30.7 1.0 OD1 A:ASP159 4.2 28.7 1.0 O A:HOH801 4.3 30.9 1.0 O7 A:TPP701 4.3 42.6 1.0 O A:ASP187 4.4 28.6 1.0 O2B A:TPP701 4.4 42.2 1.0 CA A:ILE191 4.4 33.7 1.0 N A:SER192 4.5 34.2 1.0 O1B A:TPP701 4.5 46.6 1.0 CA A:ASP159 4.6 28.3 1.0 CA A:SER192 4.6 34.5 1.0 O2A A:TPP701 4.6 40.2 1.0 CB A:ASN189 4.7 36.1 1.0 N A:ASN189 4.8 33.2 1.0 N A:ARG190 4.8 29.3 1.0 CG2 A:THR197 4.9 36.5 1.0 CB A:ILE191 4.9 37.2 1.0 CB A:SER158 4.9 29.3 1.0 CB A:SER192 5.0 37.0 1.0 C A:ASN189 5.0 30.7 1.0

Calcium binding site 2 out of 4 in the X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:43.3 occ:1.00 O2A B:TPP802 2.1 46.9 1.0 OD2 B:ASP159 2.1 33.1 1.0 O3B B:TPP802 2.2 40.6 1.0 O B:ILE191 2.2 35.6 1.0 OD1 B:ASN189 2.4 36.1 1.0 CG B:ASP159 3.2 29.8 1.0 CG B:ASN189 3.3 39.2 1.0 PA B:TPP802 3.4 42.3 1.0 PB B:TPP802 3.4 45.0 1.0 C B:ILE191 3.5 34.8 1.0 ND2 B:ASN189 3.5 38.2 1.0 O3A B:TPP802 3.6 50.6 1.0 CB B:ASP159 3.8 27.8 1.0 N B:ILE191 4.0 36.1 1.0 OD1 B:ASP159 4.1 29.9 1.0 N B:ASP159 4.2 26.4 1.0 O7 B:TPP802 4.2 46.4 1.0 O1B B:TPP802 4.2 56.8 1.0 CA B:ILE191 4.3 34.9 1.0 O B:ASP187 4.4 35.2 1.0 N B:SER192 4.4 35.2 1.0 O2B B:TPP802 4.4 43.0 1.0 O1A B:TPP802 4.5 39.3 1.0 CA B:SER192 4.6 36.0 1.0 CA B:ASP159 4.6 27.0 1.0 CB B:ASN189 4.7 38.1 1.0 N B:ARG190 4.8 34.8 1.0 CB B:ILE191 4.8 38.2 1.0 CG2 B:THR197 4.8 42.6 1.0 N B:ASN189 4.9 35.6 1.0 CB B:SER158 4.9 29.5 1.0 C B:ASN189 5.0 33.6 1.0

Calcium binding site 3 out of 4 in the X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca702 b:52.8 occ:1.00 O2A C:TPP701 2.3 61.2 1.0 O3B C:TPP701 2.3 65.9 1.0 O C:ILE191 2.3 45.0 1.0 OD1 C:ASN189 2.4 58.4 1.0 OD2 C:ASP159 2.5 46.3 1.0 O C:HOH851 2.6 40.7 1.0 CG C:ASN189 3.2 48.0 1.0 CG C:ASP159 3.3 44.9 1.0 PA C:TPP701 3.5 59.2 1.0 ND2 C:ASN189 3.5 48.4 1.0 PB C:TPP701 3.5 64.8 1.0 C C:ILE191 3.5 45.2 1.0 O3A C:TPP701 3.7 67.7 1.0 CB C:ASP159 3.8 39.5 1.0 N C:ILE191 4.0 54.8 1.0 O C:HOH862 4.3 37.1 1.0 OD1 C:ASP159 4.3 48.0 1.0 O1B C:TPP701 4.3 53.9 1.0 N C:ASP159 4.3 41.7 1.0 CA C:ILE191 4.4 52.2 1.0 O C:ASP187 4.4 45.0 1.0 O7 C:TPP701 4.5 69.1 1.0 CB C:ASN189 4.5 45.1 1.0 N C:SER192 4.5 47.6 1.0 O1A C:TPP701 4.6 55.5 1.0 N C:ASN189 4.6 41.7 1.0 O2B C:TPP701 4.6 59.2 1.0 N C:ARG190 4.6 44.1 1.0 CA C:ASP159 4.8 46.8 1.0 CG2 C:THR197 4.8 51.5 1.0 CA C:SER192 4.8 44.6 1.0 CA C:ASN189 4.8 41.0 1.0 C C:ASN189 4.8 40.0 1.0

Calcium binding site 4 out of 4 in the X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Thermus Thermophilus HB8 Transketorase in Complex with Tpp and Mes within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca803 b:72.1 occ:1.00 O1A D:TPP802 2.4 69.7 1.0 O D:ILE191 2.5 43.5 1.0 OD1 D:ASN189 2.5 60.8 1.0 OD2 D:ASP159 2.7 51.9 1.0 O3B D:TPP802 3.0 77.4 1.0 O1B D:TPP802 3.2 67.3 1.0 CG D:ASN189 3.2 68.8 1.0 CG D:ASP159 3.3 54.4 1.0 ND2 D:ASN189 3.3 68.6 1.0 PB D:TPP802 3.5 69.1 1.0 PA D:TPP802 3.6 66.6 1.0 O3A D:TPP802 3.7 82.5 1.0 C D:ILE191 3.8 57.5 1.0 CB D:ASP159 3.8 52.8 1.0 N D:ASP159 3.9 46.6 1.0 OD1 D:ASP159 4.0 52.0 1.0 O D:ASP187 4.1 61.7 1.0 N D:ILE191 4.3 57.7 1.0 CB D:SER158 4.5 49.2 1.0 CA D:ASP159 4.5 51.4 1.0 O7 D:TPP802 4.6 85.1 1.0 CB D:ASN189 4.6 63.5 1.0 CA D:ILE191 4.6 61.6 1.0 O2A D:TPP802 4.7 66.3 1.0 N D:SER192 4.8 54.5 1.0 N D:ASN189 4.8 55.6 1.0 OD2 D:ASP187 4.9 61.8 1.0 CA D:SER158 4.9 45.3 1.0 C D:SER158 4.9 49.6 1.0 N D:ARG190 5.0 53.5 1.0 O2B D:TPP802 5.0 74.8 1.0

A.Yoshihara, Y.Takamatsu, S.Mochizuki, H.Yoshida, R.Masui, K.Izumori, S.Kamitori. Structural and Biochemical Characterizations of Thermus Thermophilus HB8 Transketolase Producing A Heptulose. Appl.Microbiol.Biotechnol. V. 107 233 2023.
ISSN: ESSN 1432-0614
PubMed: 36441206
DOI: 10.1007/S00253-022-12297-Z