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Magnesium in PDB 5olc: Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans

Enzymatic activity of Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans

All present enzymatic activity of Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans:
4.2.1.6;

Protein crystallography data

The structure of Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans, PDB code: 5olc was solved by G.Michel, M.Czjzek, M.Jam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.17 / 2.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.840, 154.070, 150.870, 90.00, 104.38, 90.00
R / Rfree (%) 23.1 / 26.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans (pdb code 5olc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans, PDB code: 5olc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5olc

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Magnesium binding site 1 out of 5 in the Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:59.7
occ:1.00
 OE1 C:GLU246 1.9 0.5 1.0
OE2 C:GLU220 2.0 0.9 1.0
OD2 C:ASP194 2.4 98.2 1.0
OD1 C:ASP194 2.7 88.4 1.0
CG C:ASP194 2.8 87.9 1.0
O C:HOH502 3.0 64.1 1.0
CD C:GLU220 3.0 0.2 1.0
CD C:GLU246 3.1 0.5 1.0
CG C:GLU220 3.5 85.4 1.0
NZ C:LYS164 3.8 0.3 1.0
OE2 C:GLU246 3.8 0.6 1.0
OE1 C:GLU220 4.0 0.9 1.0
CB C:ASP194 4.1 71.6 1.0
CG C:GLU246 4.1 72.5 1.0
CB C:GLU220 4.1 72.3 1.0
OD1 C:ASN196 4.2 0.4 1.0
CG C:GLU221 4.4 85.7 1.0
NZ C:LYS166 4.5 98.0 1.0
CE C:LYS164 4.5 0.1 1.0
NE2 C:HIS296 4.5 67.3 1.0
CD2 C:HIS296 4.6 67.6 1.0
CB C:GLU221 4.6 74.0 1.0
C C:GLU220 5.0 73.3 1.0

Magnesium binding site 2 out of 5 in 5olc

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Magnesium binding site 2 out of 5 in the Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:0.6
occ:1.00
 OE2 D:GLU220 1.9 0.1 1.0
OE1 D:GLU246 1.9 0.8 1.0
CD D:GLU246 2.8 0.8 1.0
OD2 D:ASP194 3.0 87.5 1.0
CD D:GLU220 3.1 0.7 1.0
NZ D:LYS164 3.4 70.3 1.0
OE2 D:GLU246 3.4 0.7 1.0
NE2 D:HIS296 3.5 69.7 1.0
CD2 D:HIS296 3.5 69.8 1.0
CG D:ASP194 3.6 80.6 1.0
CG D:GLU246 3.7 83.6 1.0
OD1 D:ASP194 3.8 81.9 1.0
CG D:GLU220 4.0 81.0 1.0
OE1 D:GLU220 4.0 0.6 1.0
NZ D:LYS166 4.3 0.8 1.0
CE D:LYS164 4.4 69.8 1.0
ND2 D:ASN196 4.5 0.1 1.0
OE1 D:GLU329 4.5 0.2 1.0
CE1 D:HIS296 4.7 69.7 1.0
CG D:HIS296 4.8 68.5 1.0
CB D:ASP194 4.8 68.0 1.0
OE2 D:GLU329 4.8 91.6 1.0
CB D:GLU220 4.9 68.0 1.0

Magnesium binding site 3 out of 5 in 5olc

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Magnesium binding site 3 out of 5 in the Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:64.7
occ:1.00
 OE1 F:GLU246 1.9 68.4 1.0
OE2 F:GLU220 2.2 95.6 1.0
OD2 F:ASP194 2.3 87.7 1.0
OD1 F:ASP194 2.8 81.9 1.0
CG F:ASP194 2.8 81.2 1.0
CD F:GLU246 3.1 75.6 1.0
CD F:GLU220 3.2 100.0 1.0
OE2 F:GLU246 3.7 55.8 1.0
CG F:GLU220 3.7 70.5 1.0
NZ F:LYS164 3.8 84.0 1.0
OD1 F:ASN196 3.9 97.3 1.0
CB F:ASP194 4.1 68.4 1.0
CG F:GLU246 4.2 66.2 1.0
OE1 F:GLU220 4.2 0.7 1.0
CB F:GLU220 4.4 57.1 1.0
CG F:GLU221 4.5 69.2 1.0
NE2 F:HIS296 4.5 65.4 1.0
CE F:LYS164 4.5 71.1 1.0
CD2 F:HIS296 4.6 65.7 1.0
CB F:GLU221 4.7 58.1 1.0
CG F:ASN196 4.9 98.6 1.0
CE F:LYS166 4.9 0.5 1.0

Magnesium binding site 4 out of 5 in 5olc

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Magnesium binding site 4 out of 5 in the Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:61.9
occ:1.00
 OE1 G:GLU246 2.0 83.3 1.0
OE2 G:GLU220 2.5 0.0 1.0
OD2 G:ASP194 2.6 89.2 1.0
CD G:GLU246 2.9 81.5 1.0
O G:HOH504 3.2 77.6 1.0
CG G:ASP194 3.3 82.1 1.0
OE2 G:GLU246 3.4 66.8 1.0
OD1 G:ASP194 3.5 82.8 1.0
NZ G:LYS164 3.6 83.4 1.0
CD G:GLU220 3.6 0.9 1.0
NE2 G:HIS296 3.7 66.4 1.0
CD2 G:HIS296 4.0 66.7 1.0
OD1 G:ASN196 4.0 0.3 1.0
CG G:GLU246 4.1 63.8 1.0
CG G:GLU220 4.4 71.1 1.0
CE G:LYS164 4.5 73.9 1.0
OE1 G:GLU220 4.5 0.7 1.0
CB G:ASP194 4.7 68.3 1.0
CE G:LYS166 4.7 0.1 1.0
NZ G:LYS166 4.8 0.2 1.0
CE1 G:HIS296 4.9 66.0 1.0
O G:HOH516 4.9 52.8 1.0
OE1 G:GLU329 4.9 0.5 1.0

Magnesium binding site 5 out of 5 in 5olc

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Magnesium binding site 5 out of 5 in the Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the 3,6-Anhydro-D-Galactonate Cycloisomerase From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:73.9
occ:1.00
 OE1 H:GLU246 2.0 91.8 1.0
OE2 H:GLU220 2.2 87.0 1.0
OD2 H:ASP194 2.4 86.1 1.0
O H:HOH502 2.6 46.3 1.0
CD H:GLU246 3.0 87.4 1.0
CG H:ASP194 3.1 79.0 1.0
OD1 H:ASP194 3.2 78.8 1.0
CD H:GLU220 3.3 93.7 1.0
NZ H:LYS164 3.5 94.2 1.0
OE2 H:GLU246 3.6 69.5 1.0
NE2 H:HIS296 4.0 66.1 1.0
CG H:GLU220 4.0 65.0 1.0
OD1 H:ASN196 4.1 84.4 1.0
CG H:GLU246 4.1 69.3 1.0
CD2 H:HIS296 4.2 66.3 1.0
OE1 H:GLU220 4.2 0.9 1.0
CE H:LYS164 4.3 82.7 1.0
CB H:ASP194 4.4 69.7 1.0
CB H:GLU220 4.7 53.8 1.0
CE H:LYS166 4.8 0.9 1.0
CG H:GLU221 4.9 64.8 1.0
OE2 H:GLU329 4.9 0.5 1.0
NZ H:LYS166 4.9 1.0 1.0
OE1 H:GLU329 5.0 0.7 1.0

Reference:

E.Ficko-Blean, A.Prechoux, F.Thomas, T.Rochat, R.Larocque, Y.Zhu, M.Stam, S.Genicot, M.Jam, A.Calteau, B.Viart, D.Ropartz, D.Perez-Pascual, G.Correc, M.Matard-Mann, K.A.Stubbs, H.Rogniaux, A.Jeudy, T.Barbeyron, C.Medigue, M.Czjzek, D.Vallenet, M.J.Mcbride, E.Duchaud, G.Michel. Carrageenan Catabolism Is Encoded By A Complex Regulon in Marine Heterotrophic Bacteria. Nat Commun V. 8 1685 2017.
ISSN: ESSN 2041-1723
PubMed: 29162826
DOI: 10.1038/S41467-017-01832-6
Page generated: Mon Sep 30 01:02:11 2024

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