Atomistry » Calcium » PDB 1v3e-1vfm » 1ve5
Atomistry »
  Calcium »
    PDB 1v3e-1vfm »
      1ve5 »

Calcium in PDB 1ve5: Crystal Structure of T.Th. HB8 Threonine Deaminase

Enzymatic activity of Crystal Structure of T.Th. HB8 Threonine Deaminase

All present enzymatic activity of Crystal Structure of T.Th. HB8 Threonine Deaminase:
4.3.1.19;

Protein crystallography data

The structure of Crystal Structure of T.Th. HB8 Threonine Deaminase, PDB code: 1ve5 was solved by M.Goto, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.590, 158.190, 80.300, 90.00, 108.52, 90.00
R / Rfree (%) 20.2 / 24.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of T.Th. HB8 Threonine Deaminase (pdb code 1ve5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of T.Th. HB8 Threonine Deaminase, PDB code: 1ve5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1ve5

Go back to Calcium Binding Sites List in 1ve5
Calcium binding site 1 out of 4 in the Crystal Structure of T.Th. HB8 Threonine Deaminase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of T.Th. HB8 Threonine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:42.1
occ:1.00
O A:HOH1067 2.6 29.7 1.0
OE1 A:GLU203 2.7 33.8 1.0
O A:ALA207 2.7 41.2 1.0
OD2 A:ASP209 2.7 42.9 1.0
O A:HOH1223 2.7 39.1 1.0
O A:HOH1231 2.8 34.2 1.0
CG A:ASP209 3.4 42.3 1.0
OD1 A:ASP209 3.6 44.3 1.0
C A:ALA207 3.7 42.3 1.0
CD A:GLU203 3.8 36.2 1.0
N A:ASP209 4.1 42.4 1.0
CB A:ALA207 4.1 42.4 1.0
N A:ALA210 4.2 41.3 1.0
O A:VAL177 4.2 34.8 1.0
CB A:GLU203 4.2 33.5 1.0
O A:VAL233 4.4 37.7 1.0
CG A:GLU203 4.4 35.2 1.0
O A:THR235 4.5 43.8 1.0
CB A:ALA210 4.5 40.4 1.0
CA A:ALA207 4.5 42.6 1.0
CB A:ASP209 4.6 43.0 1.0
N A:ASP208 4.6 41.6 1.0
OE2 A:GLU203 4.7 37.3 1.0
CA A:ASP208 4.7 41.8 1.0
CA A:ASP209 4.8 42.4 1.0
C A:ASP208 4.8 41.9 1.0
O A:GLY178 4.9 29.1 1.0
OG1 A:THR235 4.9 49.7 1.0
C A:ASP209 5.0 42.1 1.0
CA A:ALA210 5.0 40.0 1.0

Calcium binding site 2 out of 4 in 1ve5

Go back to Calcium Binding Sites List in 1ve5
Calcium binding site 2 out of 4 in the Crystal Structure of T.Th. HB8 Threonine Deaminase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of T.Th. HB8 Threonine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:28.9
occ:1.00
OE1 B:GLU203 2.5 24.3 1.0
OD2 B:ASP209 2.5 19.2 1.0
O B:ALA207 2.6 27.0 1.0
O B:HOH1012 2.6 25.7 1.0
CD B:GLU203 3.3 26.1 1.0
CG B:ASP209 3.4 24.6 1.0
C B:ALA207 3.7 28.5 1.0
CG B:GLU203 3.7 24.4 1.0
OD1 B:ASP209 3.8 22.2 1.0
N B:ASP209 4.1 24.5 1.0
CB B:ALA207 4.1 29.6 1.0
O B:VAL233 4.2 27.4 1.0
N B:ALA210 4.3 23.2 1.0
OE2 B:GLU203 4.3 27.2 1.0
O B:VAL177 4.3 20.2 1.0
O B:THR235 4.3 27.9 1.0
CA B:ALA207 4.5 28.6 1.0
N B:ASP208 4.6 27.5 1.0
CA B:ASP208 4.6 27.6 1.0
CB B:ASP209 4.7 22.1 1.0
CB B:ALA210 4.7 25.6 1.0
C B:ASP208 4.8 26.4 1.0
CD1 B:LEU222 4.8 41.5 1.0
CB B:GLU203 4.8 23.6 1.0
O B:GLY178 4.8 19.7 1.0
CA B:ASP209 4.8 23.4 1.0

Calcium binding site 3 out of 4 in 1ve5

Go back to Calcium Binding Sites List in 1ve5
Calcium binding site 3 out of 4 in the Crystal Structure of T.Th. HB8 Threonine Deaminase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of T.Th. HB8 Threonine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2004

b:47.3
occ:1.00
OD2 C:ASP209 2.6 44.7 1.0
O C:ALA207 2.7 44.7 1.0
O C:HOH1063 2.7 33.9 1.0
OE1 C:GLU203 2.8 38.7 1.0
CG C:ASP209 3.3 43.9 1.0
OD1 C:ASP209 3.6 43.6 1.0
C C:ALA207 3.8 44.9 1.0
CD C:GLU203 3.9 41.9 1.0
N C:ASP209 4.0 42.2 1.0
CB C:ALA207 4.2 43.5 1.0
O C:VAL233 4.3 41.7 1.0
O C:VAL177 4.3 32.3 1.0
N C:ALA210 4.3 40.1 1.0
CB C:GLU203 4.4 35.9 1.0
OG1 C:THR235 4.5 51.0 1.0
O C:THR235 4.5 47.0 1.0
CG C:GLU203 4.5 38.8 1.0
CB C:ASP209 4.6 41.6 1.0
CA C:ALA207 4.6 44.9 1.0
O C:GLY178 4.6 33.0 1.0
CB C:ALA210 4.7 40.0 1.0
N C:ASP208 4.7 44.8 1.0
CA C:ASP209 4.7 42.1 1.0
CA C:ASP208 4.8 44.2 1.0
C C:ASP208 4.9 42.6 1.0
OE2 C:GLU203 4.9 41.5 1.0

Calcium binding site 4 out of 4 in 1ve5

Go back to Calcium Binding Sites List in 1ve5
Calcium binding site 4 out of 4 in the Crystal Structure of T.Th. HB8 Threonine Deaminase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of T.Th. HB8 Threonine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2002

b:41.1
occ:1.00
OE1 D:GLU203 2.6 36.4 1.0
O D:ALA207 2.7 47.2 1.0
OD2 D:ASP209 2.8 48.6 1.0
CG D:ASP209 3.4 47.4 1.0
OD1 D:ASP209 3.6 49.0 1.0
C D:ALA207 3.7 45.9 1.0
CD D:GLU203 3.8 38.9 1.0
CB D:ALA207 3.8 45.5 1.0
N D:ASP209 4.1 44.2 1.0
O D:VAL233 4.1 40.6 1.0
O D:VAL177 4.2 34.9 1.0
N D:ALA210 4.3 41.8 1.0
CB D:GLU203 4.3 34.6 1.0
CA D:ALA207 4.4 46.2 1.0
O D:THR235 4.4 42.8 1.0
CG D:GLU203 4.4 37.8 1.0
CB D:ASP209 4.5 45.9 1.0
N D:ASP208 4.7 45.1 1.0
CB D:ALA210 4.8 39.9 1.0
OE2 D:GLU203 4.8 39.0 1.0
CA D:ASP209 4.8 44.4 1.0
CD1 D:LEU222 4.8 58.9 1.0
CA D:ASP208 4.9 45.2 1.0
O D:GLY178 4.9 28.5 1.0
C D:ASP208 4.9 44.1 1.0

Reference:

M.Goto, M.Goto, Riken Structural Genomics/Proteomics Initiative (Rsgi). N/A N/A.
Page generated: Sat Dec 12 03:24:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy