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Magnesium in PDB 1un9: Crystal Structure of the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+

Enzymatic activity of Crystal Structure of the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+

All present enzymatic activity of Crystal Structure of the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+:
2.7.1.29;

Protein crystallography data

The structure of Crystal Structure of the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+, PDB code: 1un9 was solved by C.Siebold, I.Arnold, L.F.Garcia-Alles, U.Baumann, B.Erni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25 / 3.1
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 100.788, 124.869, 236.530, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+ (pdb code 1un9). 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 the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+, PDB code: 1un9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1un9

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+


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 Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1552

b:90.1
occ:1.00
 O1B A:ANP1551 2.1 75.9 1.0
OD2 A:ASP385 2.2 99.2 1.0
OD1 A:ASP387 2.3 98.9 1.0
OD2 A:ASP380 2.3 91.6 1.0
O3A A:ANP1551 2.4 71.0 1.0
PB A:ANP1551 2.8 72.7 1.0
OD1 A:ASP380 2.8 91.3 1.0
CG A:ASP380 2.9 93.5 1.0
CG A:ASP387 3.4 100.0 1.0
CG A:ASP385 3.4 99.0 1.0
O5' A:ANP1551 3.4 67.1 1.0
PA A:ANP1551 3.5 69.2 1.0
OD2 A:ASP387 3.8 0.4 1.0
N3B A:ANP1551 3.8 74.6 1.0
N A:ASP385 3.9 99.4 1.0
OD1 A:ASP385 4.0 98.3 1.0
OG1 A:THR388 4.0 98.7 1.0
C5' A:ANP1551 4.1 66.4 1.0
O2B A:ANP1551 4.1 73.6 1.0
O1A A:ANP1551 4.2 70.3 1.0
N A:THR388 4.2 0.8 1.0
N A:ASP387 4.2 0.3 1.0
CB A:ASP380 4.4 95.1 1.0
CA A:ASP385 4.5 97.8 1.0
CB A:ASP385 4.5 98.3 1.0
C A:ASP385 4.6 97.3 1.0
MG A:MG1553 4.6 76.7 1.0
CB A:ASP387 4.6 0.5 1.0
N A:GLY386 4.6 98.2 1.0
CA A:ASP387 4.7 0.5 1.0
C A:ASP387 4.8 0.8 1.0
C A:GLY384 4.8 0.9 1.0
O2A A:ANP1551 4.8 70.7 1.0
CA A:GLY384 4.8 0.4 1.0
CA A:THR388 4.9 99.6 1.0
CB A:THR388 5.0 99.1 1.0

Magnesium binding site 2 out of 4 in 1un9

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+


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 Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1553

b:76.7
occ:1.00
 OD2 A:ASP387 2.1 0.4 1.0
N3B A:ANP1551 2.2 74.6 1.0
OD1 A:ASP385 2.3 98.3 1.0
O3G A:ANP1551 2.6 79.3 1.0
PG A:ANP1551 2.9 77.2 1.0
CG A:ASP387 3.3 100.0 1.0
CG A:ASP385 3.3 99.0 1.0
PB A:ANP1551 3.5 72.7 1.0
OD2 A:ASP385 3.7 99.2 1.0
O3A A:ANP1551 3.7 71.0 1.0
O1G A:ANP1551 3.8 78.8 1.0
OD1 A:ASP387 3.8 98.9 1.0
O2G A:ANP1551 4.3 75.5 1.0
O1B A:ANP1551 4.4 75.9 1.0
CB A:ASP387 4.5 0.5 1.0
MG A:MG1552 4.6 90.1 1.0
CB A:ASP385 4.6 98.3 1.0
O2B A:ANP1551 4.7 73.6 1.0

Magnesium binding site 3 out of 4 in 1un9

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+


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 Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1552

b:65.2
occ:1.00
 OD1 B:ASP387 2.0 90.8 1.0
O3A B:ANP1551 2.0 66.7 1.0
OD2 B:ASP380 2.1 96.1 1.0
OD2 B:ASP385 2.1 97.0 1.0
CG B:ASP380 2.8 97.4 1.0
OD1 B:ASP380 2.9 98.3 1.0
PA B:ANP1551 3.1 64.0 1.0
CG B:ASP387 3.1 90.0 1.0
O1A B:ANP1551 3.1 66.0 1.0
PB B:ANP1551 3.2 67.9 1.0
O1B B:ANP1551 3.2 73.0 1.0
CG B:ASP385 3.3 96.3 1.0
OD2 B:ASP387 3.6 88.7 1.0
O5' B:ANP1551 3.7 63.9 1.0
N B:ASP385 3.8 95.2 1.0
N B:ASP387 3.9 91.0 1.0
OD1 B:ASP385 3.9 95.7 1.0
OG1 B:THR388 4.0 84.5 1.0
N B:THR388 4.0 88.6 1.0
O2B B:ANP1551 4.2 71.1 1.0
CB B:ASP380 4.3 96.9 1.0
CB B:ASP387 4.3 89.1 1.0
C B:ASP385 4.3 92.3 1.0
CA B:ASP385 4.3 93.5 1.0
CA B:ASP387 4.4 89.5 1.0
CB B:ASP385 4.4 94.7 1.0
N B:GLY386 4.4 91.3 1.0
C B:ASP387 4.4 89.5 1.0
O2A B:ANP1551 4.4 63.5 1.0
N3B B:ANP1551 4.5 69.4 1.0
MG B:MG1553 4.6 0.9 1.0
CA B:THR388 4.7 87.9 1.0
C5' B:ANP1551 4.7 60.0 1.0
C B:GLY384 4.8 96.3 1.0
O B:ASP385 4.8 92.2 1.0
CB B:THR388 4.9 87.0 1.0
CA B:GLY384 4.9 97.5 1.0
C B:GLY386 5.0 91.4 1.0

Magnesium binding site 4 out of 4 in 1un9

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+


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 Dihydroxyacetone Kinase From C. Freundii in Complex with Amp-Pnp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1553

b:0.9
occ:1.00
 OD2 B:ASP387 2.0 88.7 1.0
O2G B:ANP1551 2.1 70.3 1.0
N3B B:ANP1551 2.9 69.4 1.0
PG B:ANP1551 2.9 70.0 1.0
OD1 B:ASP385 3.0 95.7 1.0
CG B:ASP387 3.2 90.0 1.0
O3G B:ANP1551 3.6 70.4 1.0
PB B:ANP1551 3.7 67.9 1.0
OD1 B:ASP387 3.8 90.8 1.0
O1B B:ANP1551 3.8 73.0 1.0
CG B:ASP385 3.9 96.3 1.0
O3A B:ANP1551 3.9 66.7 1.0
OD2 B:ASP385 4.1 97.0 1.0
O1G B:ANP1551 4.3 69.2 1.0
CB B:ASP387 4.4 89.1 1.0
MG B:MG1552 4.6 65.2 1.0
O2A B:ANP1551 4.6 63.5 1.0
PA B:ANP1551 4.8 64.0 1.0
CA B:GLY430 4.8 89.9 1.0
OG1 B:THR391 5.0 84.4 1.0

Reference:

C.Siebold, I.Arnold, L.F.Garcia-Alles, U.Baumann, B.Erni. Crystal Structure of the Citrobacter Freundii Dihydroxyacetone Kinase Reveals An Eight-Stranded Alpha-Helical Barrel Atp-Binding Domain J.Biol.Chem. V. 278 48236 2003.
ISSN: ISSN 0021-9258
PubMed: 12966101
DOI: 10.1074/JBC.M305942200
Page generated: Tue Aug 13 14:52:40 2024

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