Atomistry » Calcium » PDB 7wa2-7wwn » 7wrt
Atomistry »
  Calcium »
    PDB 7wa2-7wwn »
      7wrt »

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

Go back to Calcium Binding Sites List in 7wrt
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

Go back to Calcium Binding Sites List in 7wrt
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

Go back to Calcium Binding Sites List in 7wrt
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

Go back to Calcium Binding Sites List in 7wrt
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: Fri Jul 19 05:52:48 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy