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Magnesium in PDB 4oec: Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1

Enzymatic activity of Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1

All present enzymatic activity of Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1:
3.1.4.46;

Protein crystallography data

The structure of Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1, PDB code: 4oec was solved by Y.Atsuta, D.J.You, K.Takano, Y.Koga, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.724, 132.034, 171.639, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1 (pdb code 4oec). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1, PDB code: 4oec:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4oec

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Magnesium binding site 1 out of 4 in the Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1


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 Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:21.0
occ:1.00
 OE1 A:GLU106 1.9 18.4 1.0
O A:HOH713 2.0 22.7 1.0
OD1 A:ASP41 2.1 15.6 1.0
OE2 A:GLU39 2.1 19.7 1.0
O A:HOH718 2.2 34.5 1.0
CD A:GLU106 3.1 21.5 1.0
CD A:GLU39 3.1 18.3 1.0
CG A:ASP41 3.1 23.3 1.0
OE1 A:GLU39 3.4 18.5 1.0
OD2 A:ASP41 3.5 21.4 1.0
CB A:GLU106 3.9 18.0 1.0
O A:HOH506 3.9 20.0 1.0
OE2 A:GLU106 3.9 21.0 1.0
CG A:GLU106 4.0 22.3 1.0
NE2 A:HIS12 4.1 22.6 1.0
ND1 A:HIS54 4.3 24.6 1.0
O A:HOH722 4.3 40.6 1.0
CG A:GLU39 4.4 16.6 1.0
CB A:ASP41 4.4 18.9 1.0
NZ A:LYS108 4.4 29.8 1.0
CE A:LYS108 4.5 24.9 1.0
CD2 A:HIS12 4.5 18.8 1.0
C A:LEU40 4.6 20.1 1.0
O A:LEU40 4.7 20.1 1.0
O A:HOH564 4.7 34.7 1.0
CE1 A:HIS54 4.8 21.2 1.0
N A:ASP41 4.8 20.5 1.0
NE A:ARG13 4.8 20.0 1.0
CA A:ASP41 4.8 19.6 1.0

Magnesium binding site 2 out of 4 in 4oec

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Magnesium binding site 2 out of 4 in the Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1


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 Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:24.8
occ:1.00
 OE1 B:GLU106 1.9 19.8 1.0
OE2 B:GLU39 2.0 20.1 1.0
OD1 B:ASP41 2.0 20.2 1.0
O B:HOH530 2.2 24.0 1.0
O B:HOH570 2.2 29.1 1.0
CG B:ASP41 3.0 25.6 1.0
CD B:GLU106 3.0 25.1 1.0
CD B:GLU39 3.1 17.8 1.0
OD2 B:ASP41 3.4 19.9 1.0
OE1 B:GLU39 3.5 23.8 1.0
O B:HOH522 3.7 20.5 1.0
CB B:GLU106 3.8 23.2 1.0
OE2 B:GLU106 3.8 21.8 1.0
CG B:GLU106 4.0 17.4 1.0
NZ B:LYS108 4.1 34.1 1.0
CB B:ASP41 4.3 20.3 1.0
CG B:GLU39 4.3 15.4 1.0
NE2 B:HIS12 4.3 21.5 1.0
ND1 B:HIS54 4.6 30.1 1.0
CE B:LYS108 4.6 32.1 1.0
CD2 B:HIS12 4.7 19.4 1.0
O B:LEU40 4.7 22.2 1.0
C B:LEU40 4.7 21.3 1.0
O B:HOH674 4.8 34.0 1.0
CA B:ASP41 4.8 22.0 1.0
N B:ASP41 4.8 21.0 1.0
NE B:ARG13 4.9 19.7 1.0

Magnesium binding site 3 out of 4 in 4oec

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Magnesium binding site 3 out of 4 in the Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1


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 Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:30.2
occ:1.00
 OE2 C:GLU106 1.9 30.1 1.0
OD1 C:ASP41 1.9 30.7 1.0
OE2 C:GLU39 2.0 28.6 1.0
O C:HOH592 2.1 26.3 1.0
O C:HOH606 2.1 32.8 1.0
CG C:ASP41 2.9 28.1 1.0
CD C:GLU106 3.0 27.6 1.0
CD C:GLU39 3.0 28.9 1.0
OD2 C:ASP41 3.4 28.4 1.0
OE1 C:GLU39 3.4 28.3 1.0
O C:HOH594 3.6 29.3 1.0
OE1 C:GLU106 3.7 31.2 1.0
CB C:GLU106 3.8 29.7 1.0
CG C:GLU106 3.9 32.1 1.0
CB C:ASP41 4.2 26.6 1.0
CE1 C:HIS12 4.3 28.2 1.0
NZ C:LYS108 4.3 38.0 1.0
CG C:GLU39 4.3 25.8 1.0
ND1 C:HIS54 4.5 32.4 1.0
CE C:LYS108 4.6 39.6 1.0
O C:LEU40 4.6 28.2 1.0
C C:LEU40 4.7 27.7 1.0
ND1 C:HIS12 4.7 31.4 1.0
N C:ASP41 4.8 26.9 1.0
CA C:ASP41 4.8 27.3 1.0
NE C:ARG13 4.9 32.6 1.0
CE1 C:HIS54 4.9 32.3 1.0

Magnesium binding site 4 out of 4 in 4oec

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Magnesium binding site 4 out of 4 in the Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1


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 Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:20.3
occ:1.00
 O D:HOH666 2.0 18.6 1.0
OE1 D:GLU106 2.0 22.2 1.0
OE2 D:GLU39 2.0 20.0 1.0
O D:HOH672 2.1 33.5 1.0
OD1 D:ASP41 2.2 16.2 1.0
CD D:GLU39 3.0 23.1 1.0
CD D:GLU106 3.1 26.4 1.0
CG D:ASP41 3.2 21.0 1.0
OE1 D:GLU39 3.4 19.3 1.0
OD2 D:ASP41 3.6 21.9 1.0
O D:HOH516 3.8 23.3 1.0
CB D:GLU106 3.9 17.6 1.0
OE2 D:GLU106 4.0 18.8 1.0
CG D:GLU106 4.1 17.5 1.0
CE1 D:HIS12 4.1 23.8 1.0
ND1 D:HIS54 4.3 26.7 1.0
CG D:GLU39 4.4 19.9 1.0
CB D:ASP41 4.5 18.0 1.0
NZ D:LYS108 4.5 27.7 1.0
ND1 D:HIS12 4.6 23.8 1.0
CE D:LYS108 4.7 28.0 1.0
O D:LEU40 4.7 17.9 1.0
C D:LEU40 4.7 17.8 1.0
O D:HOH611 4.7 33.9 1.0
NE D:ARG13 4.8 20.9 1.0
N D:ASP41 4.8 18.0 1.0
CE1 D:HIS54 4.8 22.6 1.0
CA D:ASP41 4.9 18.3 1.0

Reference:

Y.Atsuta, D.J.You, K.Takano, Y.Koga, S.Kanaya. Crystal Structure of Glycerophosphodiester Phosphodiesterase From Thermococcus Kodakarensis KOD1 To Be Published.
Page generated: Mon Aug 11 21:28:34 2025

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