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Magnesium in PDB 1k4i: Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Two Magnesium Ions

Protein crystallography data

The structure of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Two Magnesium Ions, PDB code: 1k4i was solved by D.-I.Liao, Y.-J.Zheng, P.V.Viitanen, D.B.Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 0.98
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.889, 88.147, 43.995, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Two Magnesium Ions (pdb code 1k4i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Two Magnesium Ions, PDB code: 1k4i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1k4i

Go back to Magnesium Binding Sites List in 1k4i
Magnesium binding site 1 out of 2 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Two Magnesium Ions


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 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Two Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:15.1
occ:1.00
O A:HOH1100 1.8 22.3 1.0
OE2 A:GLU37 2.2 18.9 1.0
ND1 A:HIS153 2.2 16.2 1.0
O A:HOH1139 2.3 28.5 1.0
O A:HOH1051 2.3 18.0 1.0
O2 A:SO41001 2.4 15.0 1.0
CE1 A:HIS153 3.1 17.6 1.0
O3 A:SO41001 3.1 20.6 1.0
CD A:GLU37 3.3 18.7 1.0
CG A:HIS153 3.3 11.5 1.0
S A:SO41001 3.3 12.9 1.0
OE1 A:GLU37 3.6 20.0 1.0
CB A:HIS153 3.7 10.4 1.0
MG A:MG1004 3.7 19.1 1.0
OD1 A:ASP41 4.0 16.4 1.0
O4 A:SO41001 4.1 17.4 1.0
OD2 A:ASP41 4.1 13.2 1.0
O A:HOH1075 4.1 30.5 1.0
NE2 A:HIS153 4.2 18.4 1.0
NH1 A:ARG36 4.2 15.8 1.0
O A:HOH1091 4.2 28.2 1.0
CD2 A:HIS153 4.3 14.2 1.0
O A:HOH1047 4.3 15.8 1.0
N A:HIS153 4.4 10.8 1.0
CG A:ASP41 4.4 12.0 1.0
O A:HOH1192 4.4 44.8 1.0
OE1 A:GLU39 4.5 17.9 1.0
O1 A:SO41001 4.5 12.7 1.0
CG A:GLU37 4.5 14.6 1.0
CA A:HIS153 4.6 10.3 1.0
CB A:GLU37 5.0 13.8 1.0

Magnesium binding site 2 out of 2 in 1k4i

Go back to Magnesium Binding Sites List in 1k4i
Magnesium binding site 2 out of 2 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Two Magnesium Ions


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 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Two Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:19.1
occ:1.00
OE1 A:GLU37 2.0 20.0 1.0
O A:HOH1091 2.0 28.2 1.0
O A:HOH1100 2.1 22.3 1.0
O A:HOH1047 2.1 15.8 1.0
CD A:GLU37 3.0 18.7 1.0
OE2 A:GLU37 3.5 18.9 1.0
O A:HOH1075 3.6 30.5 1.0
O A:HOH1153 3.6 44.2 1.0
MG A:MG1003 3.7 15.1 1.0
O A:HOH1145 3.9 30.0 1.0
OE2 A:GLU174 4.0 15.7 1.0
OE1 A:GLU39 4.2 17.9 1.0
O A:HOH1051 4.2 18.0 1.0
O3 A:SO41001 4.2 20.6 1.0
O A:HOH1139 4.3 28.5 1.0
CG A:GLU37 4.4 14.6 1.0
O4 A:SO41001 4.5 17.4 1.0
S A:SO41001 4.7 12.9 1.0
OG1 A:THR92 4.7 29.6 1.0
O2 A:SO41001 4.8 15.0 1.0
O A:HOH1192 5.0 44.8 1.0

Reference:

D.I.Liao, Y.J.Zheng, P.V.Viitanen, D.B.Jordan. Structural Definition of the Active Site and Catalytic Mechanism of 3,4-Dihydroxy-2-Butanone-4-Phosphate Synthase. Biochemistry V. 41 1795 2002.
ISSN: ISSN 0006-2960
PubMed: 11827524
DOI: 10.1021/BI015652U
Page generated: Mon Dec 14 06:12:47 2020

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