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Calcium in PDB 6eew: Crystal Structure of Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan

Enzymatic activity of Crystal Structure of Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan

All present enzymatic activity of Crystal Structure of Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan:
4.1.1.28;

Protein crystallography data

The structure of Crystal Structure of Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan, PDB code: 6eew was solved by M.P.Torrens-Spence, Y.Chiang, T.Smith, M.A.Vicent, Y.Wang, J.K.Weng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 133.18 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.612, 69.607, 133.472, 90.00, 93.78, 90.00
R / Rfree (%) 22 / 25.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan (pdb code 6eew). 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 Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan, PDB code: 6eew:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6eew

Go back to Calcium Binding Sites List in 6eew
Calcium binding site 1 out of 4 in the Crystal Structure of Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan


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 Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:71.2
occ:1.00
 O A:HOH728 2.5 55.2 1.0
O A:HOH716 2.5 67.0 1.0
OD1 A:ASP397 2.7 49.4 1.0
CG A:ASP397 3.7 48.7 1.0
O A:THR477 3.9 61.2 1.0
O A:GLY473 4.0 63.2 1.0
O A:SER475 4.1 62.5 1.0
OD2 A:ASP397 4.1 47.0 1.0
O A:SER474 4.2 57.6 1.0
SD A:MET400 4.5 60.2 0.3
CA A:SER475 4.6 50.0 1.0
C A:GLY473 4.6 59.8 1.0
C A:SER475 4.6 57.2 1.0
OG A:SER396 4.6 53.4 1.0
ND1 A:HIS393 4.6 57.9 1.0
C A:SER474 4.8 58.5 1.0
CA A:GLY473 4.8 61.1 1.0
C A:THR477 5.0 57.8 1.0

Calcium binding site 2 out of 4 in 6eew

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Calcium binding site 2 out of 4 in the Crystal Structure of Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan


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 Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:64.2
occ:1.00
 O B:HOH745 2.3 46.3 1.0
O B:HOH749 2.4 63.1 1.0
O B:HOH709 2.6 56.4 1.0
OD1 B:ASP397 2.6 43.5 1.0
CG B:ASP397 3.7 48.1 1.0
O B:THR477 4.0 43.2 1.0
OD2 B:ASP397 4.1 44.1 1.0
O B:GLY473 4.4 59.6 1.0
O B:SER475 4.4 56.5 1.0
O B:SER474 4.4 55.9 1.0
SD B:MET400 4.5 38.3 0.4
OG B:SER396 4.7 66.3 1.0
ND1 B:HIS393 4.7 46.6 1.0
C B:GLY473 4.8 57.0 1.0
CA B:SER475 4.8 45.2 1.0
C B:SER475 4.9 46.3 1.0
CA B:GLY473 5.0 49.6 1.0

Calcium binding site 3 out of 4 in 6eew

Go back to Calcium Binding Sites List in 6eew
Calcium binding site 3 out of 4 in the Crystal Structure of Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan


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 Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:89.5
occ:1.00
 OD1 C:ASP397 2.4 64.9 1.0
O C:HOH715 2.7 52.4 1.0
O C:HOH738 3.0 63.6 1.0
CG C:ASP397 3.5 69.8 1.0
OD2 C:ASP397 3.8 73.5 1.0
O C:THR477 3.8 84.5 1.0
O C:SER475 4.2 80.5 1.0
O C:GLY473 4.2 77.4 1.0
O C:SER474 4.3 76.9 1.0
SD C:MET400 4.4 81.7 0.6
CA C:SER475 4.7 73.0 1.0
C C:GLY473 4.7 71.9 1.0
ND1 C:HIS393 4.7 72.4 1.0
C C:SER475 4.7 75.5 1.0
CB C:ASP397 4.8 67.6 1.0
CA C:GLY473 4.8 68.1 1.0
OG C:SER396 4.9 89.6 1.0
C C:SER474 5.0 73.3 1.0
C C:THR477 5.0 82.8 1.0

Calcium binding site 4 out of 4 in 6eew

Go back to Calcium Binding Sites List in 6eew
Calcium binding site 4 out of 4 in the Crystal Structure of Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan


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 Catharanthus Roseus Tryptophan Decarboxylase in Complex with L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca602

b:80.6
occ:1.00
 OD1 D:ASP397 2.5 68.1 1.0
CG D:ASP397 3.5 73.7 1.0
OD2 D:ASP397 3.8 79.4 1.0
O D:THR477 4.0 83.8 1.0
O D:GLY473 4.2 71.8 1.0
O D:SER474 4.3 86.4 1.0
ND1 D:HIS393 4.4 75.0 1.0
O D:SER475 4.4 73.0 1.0
C D:GLY473 4.7 75.5 1.0
CA D:SER475 4.8 73.2 1.0
CB D:ASP397 4.8 74.7 1.0
OG D:SER396 4.9 98.1 1.0
C D:SER475 4.9 77.2 1.0
CA D:GLY473 4.9 74.6 1.0
CE1 D:HIS393 4.9 73.4 1.0
O D:HIS393 5.0 79.6 1.0
N D:ASP397 5.0 77.5 1.0
C D:SER474 5.0 81.1 1.0

Reference:

M.P.Torrens-Spence, Y.-C.Chiang, T.Smith, M.A.Vicent, Y.Wang, J.K.Weng. Structural Basis For Independent Origins of New Catalytic Machineries in Plant Aaad Proteins Biorxiv 2019.
DOI: 10.1101/404970
Page generated: Wed Jul 9 13:41:28 2025

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