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Magnesium in PDB 6ilt: Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion

Enzymatic activity of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion

All present enzymatic activity of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion:
2.7.1.15;

Protein crystallography data

The structure of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion, PDB code: 6ilt was solved by P.Kang, J.Oh, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.34 / 2.20
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.445, 99.445, 164.952, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.8

Other elements in 6ilt:

The structure of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion (pdb code 6ilt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion, PDB code: 6ilt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ilt

Go back to Magnesium Binding Sites List in 6ilt
Magnesium binding site 1 out of 4 in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:75.5
occ:1.00
 O A:HOH530 2.0 63.3 1.0
O1A A:ATP401 2.3 48.9 1.0
O1B A:ATP401 2.5 66.7 1.0
O A:HOH501 2.7 55.2 1.0
O A:HOH506 2.8 64.0 1.0
PB A:ATP401 3.6 73.8 1.0
PA A:ATP401 3.7 56.6 1.0
O3B A:ATP401 3.8 74.2 1.0
O1G A:ATP401 3.9 78.1 1.0
O3A A:ATP401 4.1 68.0 1.0
OE2 A:GLU256 4.4 91.2 1.0
O2A A:ATP401 4.5 53.6 1.0
PG A:ATP401 4.6 80.2 1.0
ND2 A:ASN255 4.7 68.1 1.0
O5' A:ATP401 4.8 60.0 1.0
CA A:GLY293 5.0 60.4 1.0

Magnesium binding site 2 out of 4 in 6ilt

Go back to Magnesium Binding Sites List in 6ilt
Magnesium binding site 2 out of 4 in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:76.4
occ:1.00
 O2B A:ATP401 2.2 61.5 1.0
O A:HOH514 2.3 60.8 1.0
O A:HOH517 2.6 57.9 1.0
O3G A:ATP401 2.6 66.6 1.0
NZ A:LYS107 3.1 58.2 1.0
PB A:ATP401 3.5 73.8 1.0
OE2 A:GLU258 3.8 77.9 1.0
PG A:ATP401 3.8 80.2 1.0
O3B A:ATP401 3.9 74.2 1.0
NZ A:LYS291 4.0 63.0 1.0
OD2 A:ASP233 4.1 70.6 1.0
OD1 A:ASP233 4.1 65.3 1.0
CE A:LYS107 4.3 61.6 1.0
CE A:LYS291 4.4 58.0 1.0
CA A:GLY324 4.4 41.7 1.0
O1B A:ATP401 4.5 66.7 1.0
OE1 A:GLU258 4.5 58.2 1.0
CG A:ASP233 4.5 60.9 1.0
O3A A:ATP401 4.6 68.0 1.0
CD A:GLU258 4.6 64.5 1.0
OD1 A:ASP325 4.7 41.3 1.0
ND2 A:ASN255 4.7 68.1 1.0
C A:GLY324 4.8 49.5 1.0
O2G A:ATP401 4.8 73.9 1.0
O1G A:ATP401 4.8 78.1 1.0
CA A:GLY235 4.9 63.9 1.0

Magnesium binding site 3 out of 4 in 6ilt

Go back to Magnesium Binding Sites List in 6ilt
Magnesium binding site 3 out of 4 in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:71.2
occ:1.00
 O B:HOH546 2.2 74.8 1.0
O2B B:ATP401 2.2 61.6 1.0
O B:HOH542 2.6 69.1 1.0
O2A B:ATP401 2.6 55.2 1.0
O B:HOH501 2.8 46.3 1.0
PB B:ATP401 3.5 61.5 1.0
PA B:ATP401 3.7 55.0 1.0
O B:HOH505 3.9 58.6 1.0
O3A B:ATP401 4.0 54.0 1.0
ND2 B:ASN255 4.0 40.8 1.0
O3B B:ATP401 4.1 60.2 1.0
O2G B:ATP401 4.2 75.5 1.0
O1A B:ATP401 4.2 50.2 1.0
OE2 B:GLU256 4.4 79.7 1.0
CB B:ASN255 4.7 43.7 1.0
CG B:ASN255 4.7 49.5 1.0
O1B B:ATP401 4.7 55.9 1.0
OE1 B:GLU256 4.8 64.2 1.0
PG B:ATP401 4.9 69.2 1.0

Magnesium binding site 4 out of 4 in 6ilt

Go back to Magnesium Binding Sites List in 6ilt
Magnesium binding site 4 out of 4 in the Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Arabidopsis Thaliana Ribokinase Complexed with Atp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:65.2
occ:1.00
 O1B B:ATP401 2.3 55.9 1.0
O1G B:ATP401 2.4 61.2 1.0
O B:HOH511 2.8 45.7 1.0
NZ B:LYS107 2.9 53.3 1.0
PB B:ATP401 3.5 61.5 1.0
PG B:ATP401 3.6 69.2 1.0
O3B B:ATP401 3.7 60.2 1.0
OD2 B:ASP233 3.9 44.9 1.0
NZ B:LYS291 4.0 52.7 1.0
CE B:LYS107 4.2 58.9 1.0
CA B:GLY324 4.2 34.4 1.0
OD1 B:ASP233 4.2 64.5 1.0
OE2 B:GLU258 4.3 70.2 1.0
O2B B:ATP401 4.4 61.6 1.0
C B:GLY324 4.5 32.3 1.0
CG B:ASP233 4.5 48.8 1.0
O3G B:ATP401 4.5 63.7 1.0
O B:HOH515 4.6 46.6 1.0
O3A B:ATP401 4.6 54.0 1.0
OD1 B:ASP325 4.6 36.8 1.0
O2G B:ATP401 4.6 75.5 1.0
CE B:LYS291 4.7 49.8 1.0
CA B:GLY235 4.7 41.8 1.0
N B:ASP325 4.8 30.1 1.0
OE1 B:GLU258 4.8 53.2 1.0
ND2 B:ASN255 4.9 40.8 1.0
CD B:LYS107 4.9 65.5 1.0
O B:GLY324 4.9 34.6 1.0
CD B:GLU258 5.0 62.5 1.0

Reference:

P.A.Kang, J.Oh, H.Lee, C.P.Witte, S.Rhee. Crystal Structure and Mutational Analyses of Ribokinase From Arabidopsis Thaliana. J. Struct. Biol. V. 206 110 2019.
ISSN: ESSN 1095-8657
PubMed: 30822455
DOI: 10.1016/J.JSB.2019.02.007
Page generated: Wed Aug 13 08:45:19 2025

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