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Magnesium in PDB 5d8g: A Structural View on the Dissociation of E. Coli Tryptophanase

Enzymatic activity of A Structural View on the Dissociation of E. Coli Tryptophanase

All present enzymatic activity of A Structural View on the Dissociation of E. Coli Tryptophanase:
4.1.99.1;

Protein crystallography data

The structure of A Structural View on the Dissociation of E. Coli Tryptophanase, PDB code: 5d8g was solved by O.Almog, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.20 / 1.89
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 118.287, 120.267, 171.709, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.4

Other elements in 5d8g:

The structure of A Structural View on the Dissociation of E. Coli Tryptophanase also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A Structural View on the Dissociation of E. Coli Tryptophanase (pdb code 5d8g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the A Structural View on the Dissociation of E. Coli Tryptophanase, PDB code: 5d8g:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5d8g

Go back to Magnesium Binding Sites List in 5d8g
Magnesium binding site 1 out of 3 in the A Structural View on the Dissociation of E. Coli Tryptophanase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Structural View on the Dissociation of E. Coli Tryptophanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:18.3
occ:1.00
O A:HOH1419 2.0 21.2 1.0
O A:HOH1180 2.0 19.8 1.0
O A:HOH1305 4.0 20.3 1.0
O A:PRO275 4.1 24.3 1.0
O A:GLY55 4.4 15.2 1.0
C A:GLY55 4.9 14.9 1.0
O A:SER54 4.9 16.8 1.0

Magnesium binding site 2 out of 3 in 5d8g

Go back to Magnesium Binding Sites List in 5d8g
Magnesium binding site 2 out of 3 in the A Structural View on the Dissociation of E. Coli Tryptophanase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Structural View on the Dissociation of E. Coli Tryptophanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:62.8
occ:1.00
O A:HOH1111 1.9 39.5 1.0
O A:HOH1125 2.3 39.7 1.0
OE2 A:GLU293 2.4 48.9 1.0
NE2 A:GLN119 2.9 53.4 1.0
CD A:GLU293 3.3 46.2 1.0
OE1 A:GLU293 3.5 47.5 1.0
O A:HOH1115 4.0 31.0 1.0
CD A:GLN119 4.1 52.4 1.0
O A:HOH1337 4.5 33.9 1.0
OE2 A:GLU120 4.6 32.4 1.0
OE1 A:GLN119 4.7 55.8 1.0
CG A:GLU293 4.7 37.0 1.0
CA A:LYS116 4.8 29.2 1.0

Magnesium binding site 3 out of 3 in 5d8g

Go back to Magnesium Binding Sites List in 5d8g
Magnesium binding site 3 out of 3 in the A Structural View on the Dissociation of E. Coli Tryptophanase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Structural View on the Dissociation of E. Coli Tryptophanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1005

b:36.9
occ:1.00
O A:HOH1383 2.5 32.7 1.0
O A:HIS358 2.6 22.4 1.0
N A:ILE422 2.9 14.3 1.0
OD2 A:ASP53 3.1 21.8 1.0
CG A:ASP53 3.3 18.2 1.0
NH2 A:ARG334 3.3 10.9 1.0
O A:ILE422 3.6 14.7 1.0
C A:HIS358 3.6 23.7 1.0
CB A:ASP53 3.6 15.0 1.0
O A:HOH1157 3.7 34.5 1.0
CA A:THR421 3.7 16.5 1.0
CB A:THR421 3.7 17.8 1.0
C A:THR421 3.8 16.7 1.0
OD1 A:ASP53 3.8 20.2 1.0
CA A:ILE422 4.0 13.3 1.0
C A:ILE422 4.1 14.6 1.0
CA A:HIS358 4.2 21.6 1.0
O A:HOH1175 4.3 14.6 1.0
CZ A:ARG334 4.3 11.0 1.0
O A:GLY357 4.3 21.1 1.0
CB A:ILE422 4.3 12.7 1.0
NH1 A:ARG334 4.6 12.6 1.0
CG2 A:THR421 4.6 17.0 1.0
N A:ALA359 4.6 21.8 1.0
NH2 A:ARG230 4.7 28.6 1.0
OG1 A:THR421 4.7 20.4 1.0
CG1 A:ILE422 4.9 16.5 1.0
CA A:ASP53 5.0 14.6 1.0
CA A:ALA359 5.0 21.4 1.0

Reference:

K.Green, N.Qasim, G.Gdaelvsky, A.Kogan, Y.Goldgur, A.H.Parola, O.Lotan, O.Almog. A Structural View of the Dissociation of Escherichia Coli Tryptophanase. Acta Crystallogr.,Sect.D V. 71 2364 2015.
ISSN: ESSN 1399-0047
PubMed: 26627645
DOI: 10.1107/S139900471501799X
Page generated: Mon Dec 14 20:10:29 2020

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