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Calcium in PDB 7wrt: X-Ray Structure Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate

Enzymatic activity of X-Ray Structure Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate

All present enzymatic activity of X-Ray Structure Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate:
2.2.1.1;

Protein crystallography data

The structure of X-Ray Structure Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate, PDB code: 7wrt 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) 41.86 / 2.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.68, 88.86, 117.37, 72.31, 88.7, 73.46
R / Rfree (%) 20.2 / 25.4

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate (pdb code 7wrt). 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 Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate, PDB code: 7wrt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7wrt

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Calcium binding site 1 out of 4 in the X-Ray Structure Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate


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 Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:59.8
occ:1.00
 O2A A:TPP701 2.2 100.8 1.0
OD2 A:ASP159 2.2 38.9 1.0
O A:ILE191 2.4 44.6 1.0
O A:HOH817 2.4 37.4 1.0
OD1 A:ASN189 2.6 51.8 1.0
O2B A:TPP701 2.7 81.8 1.0
CG A:ASP159 3.1 44.4 1.0
O3B A:TPP701 3.4 88.0 1.0
PA A:TPP701 3.4 75.3 1.0
PB A:TPP701 3.4 73.8 1.0
CG A:ASN189 3.5 50.0 1.0
C A:ILE191 3.6 48.8 1.0
ND2 A:ASN189 3.6 56.5 1.0
CB A:ASP159 3.7 40.6 1.0
O3A A:TPP701 3.7 85.0 1.0
OD1 A:ASP159 4.0 42.2 1.0
N A:ILE191 4.1 49.0 1.0
N A:ASP159 4.1 42.9 1.0
O A:ASP187 4.4 40.0 1.0
CA A:ILE191 4.4 47.2 1.0
O1A A:TPP701 4.5 87.8 1.0
O7 A:TPP701 4.5 83.1 1.0
N A:SER192 4.5 48.4 1.0
CA A:ASP159 4.5 39.3 1.0
CA A:SER192 4.7 51.7 1.0
CG2 A:THR197 4.7 49.0 1.0
N A:ARG190 4.7 41.5 1.0
N A:ASN189 4.8 46.6 1.0
CB A:ASN189 4.8 43.0 1.0
O1B A:TPP701 4.9 65.3 1.0
CB A:SER158 5.0 38.0 1.0
CB A:ILE191 5.0 50.5 1.0

Calcium binding site 2 out of 4 in 7wrt

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Calcium binding site 2 out of 4 in the X-Ray Structure Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate


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 Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:59.0
occ:1.00
 O B:ILE191 2.2 45.9 1.0
O1A B:TPP802 2.2 85.5 1.0
OD2 B:ASP159 2.4 43.9 1.0
O B:HOH903 2.5 41.7 1.0
OD1 B:ASN189 2.6 56.7 1.0
O3B B:TPP802 3.0 86.4 1.0
CG B:ASP159 3.1 40.0 1.0
O1B B:TPP802 3.2 82.0 1.0
CG B:ASN189 3.4 48.8 1.0
C B:ILE191 3.4 51.4 1.0
PA B:TPP802 3.5 77.0 1.0
PB B:TPP802 3.5 74.9 1.0
ND2 B:ASN189 3.7 50.4 1.0
O3A B:TPP802 3.7 92.4 1.0
CB B:ASP159 3.7 41.4 1.0
OD1 B:ASP159 4.0 41.7 1.0
N B:ILE191 4.1 55.6 1.0
O7 B:TPP802 4.2 85.3 1.0
O B:ASP187 4.2 50.4 1.0
N B:ASP159 4.3 41.7 1.0
CA B:ILE191 4.3 52.9 1.0
N B:SER192 4.4 53.6 1.0
CA B:SER192 4.5 54.9 1.0
CA B:ASP159 4.6 42.2 1.0
CG2 B:THR197 4.7 63.4 1.0
CB B:ASN189 4.7 47.3 1.0
O2A B:TPP802 4.7 74.8 1.0
N B:ASN189 4.8 47.1 1.0
CB B:ILE191 4.9 58.0 1.0
CB B:SER158 4.9 41.8 1.0
N B:ARG190 4.9 47.3 1.0
C B:ASN189 4.9 44.0 1.0
O2B B:TPP802 5.0 82.3 1.0

Calcium binding site 3 out of 4 in 7wrt

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Calcium binding site 3 out of 4 in the X-Ray Structure Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate


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 Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:73.4
occ:1.00
 O2A C:TPP701 2.3 118.1 1.0
O C:ILE191 2.4 56.9 1.0
OD2 C:ASP159 2.8 56.4 1.0
OD1 C:ASN189 2.8 63.5 1.0
O3B C:TPP701 3.2 106.8 1.0
CG C:ASP159 3.3 54.5 1.0
CG C:ASN189 3.4 66.4 1.0
ND2 C:ASN189 3.5 68.1 1.0
O1B C:TPP701 3.5 77.5 1.0
C C:ILE191 3.6 65.9 1.0
PA C:TPP701 3.6 107.2 1.0
PB C:TPP701 3.8 101.8 1.0
N C:ILE191 3.8 67.0 1.0
CB C:ASP159 3.9 51.8 1.0
O3A C:TPP701 4.0 116.2 1.0
OD1 C:ASP159 4.0 56.6 1.0
CA C:ILE191 4.3 71.2 1.0
N C:ASP159 4.3 45.4 1.0
O C:ASP187 4.3 53.2 1.0
N C:ARG190 4.4 62.0 1.0
O7 C:TPP701 4.4 115.4 1.0
N C:ASN189 4.6 52.0 1.0
CB C:ASN189 4.6 62.3 1.0
N C:SER192 4.7 66.7 1.0
C C:ASN189 4.7 53.6 1.0
CG2 C:THR197 4.7 74.8 1.0
CA C:ASP159 4.8 55.2 1.0
CA C:ASN189 4.8 56.9 1.0
O1A C:TPP701 4.8 95.2 1.0
CB C:ILE191 4.9 76.2 1.0
C C:ARG190 4.9 64.7 1.0

Calcium binding site 4 out of 4 in 7wrt

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Calcium binding site 4 out of 4 in the X-Ray Structure Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate


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 Ofthermus Thermophilus HB8 Transketorase Demonstrate in Complex with Tpp and D-Erythrose-4-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca803

b:73.8
occ:1.00
 O D:ILE191 2.1 53.0 1.0
OD2 D:ASP159 2.4 57.5 1.0
O D:HOH901 2.5 52.0 1.0
OD1 D:ASN189 2.6 80.4 1.0
O1A D:TPP802 2.8 125.2 1.0
O1B D:TPP802 3.0 110.8 1.0
CG D:ASP159 3.2 63.3 1.0
C D:ILE191 3.3 68.1 1.0
CG D:ASN189 3.4 80.5 1.0
ND2 D:ASN189 3.7 81.2 1.0
CB D:ASP159 3.8 63.9 1.0
PB D:TPP802 3.8 111.8 1.0
N D:ILE191 3.9 76.2 1.0
O3B D:TPP802 3.9 81.7 1.0
PA D:TPP802 3.9 105.3 1.0
O3A D:TPP802 4.1 115.5 1.0
OD1 D:ASP159 4.1 55.5 1.0
CA D:ILE191 4.1 76.9 1.0
N D:SER192 4.3 67.2 1.0
O7 D:TPP802 4.3 121.4 1.0
O D:ASP187 4.3 69.9 1.0
CG2 D:THR197 4.4 73.7 1.0
N D:ASP159 4.5 55.2 1.0
OG D:SER192 4.6 83.0 1.0
N D:ARG190 4.6 62.3 1.0
N D:ASN189 4.6 65.2 1.0
CA D:SER192 4.7 71.5 1.0
CB D:ASN189 4.7 71.0 1.0
C D:ASN189 4.7 71.1 1.0
CA D:ASP159 4.8 63.9 1.0
CB D:ILE191 4.8 75.6 1.0
CA D:ASN189 5.0 58.9 1.0

Reference:

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
Page generated: Tue Apr 4 19:12:58 2023

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