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Magnesium in PDB 2xam: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6.

Enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6.

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6.:
2.7.1.158;

Protein crystallography data

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6., PDB code: 2xam was solved by B.Gonzalez, J.I.Banos-Sanz, M.Villate, C.A.Brearley, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.74 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.124, 113.591, 142.478, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 27

Other elements in 2xam:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6. (pdb code 2xam). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6., PDB code: 2xam:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2xam

Go back to Magnesium Binding Sites List in 2xam
Magnesium binding site 1 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1128

b:44.1
occ:1.00
 OD1 A:ASP407 2.7 18.5 1.0
O2B A:ADP600 2.9 27.7 1.0
OG A:SER409 2.9 18.2 1.0
CG A:ASP407 3.5 18.7 1.0
CB A:SER409 3.5 19.1 1.0
OD2 A:ASP407 3.6 18.8 1.0
O3B A:ADP600 3.6 27.4 1.0
PB A:ADP600 3.7 27.9 1.0
O42 A:I6P500 3.8 28.6 1.0
CB A:ALA21 3.8 19.1 1.0
O32 A:I6P500 4.0 27.9 1.0
NH2 A:ARG40 4.2 27.0 1.0
O43 A:I6P500 4.3 21.7 1.0
O23 A:I6P500 4.3 22.5 1.0
NZ A:LYS411 4.4 15.7 1.0
P2 A:I6P500 4.4 27.3 1.0
OD1 A:ASN22 4.5 17.3 1.0
O1B A:ADP600 4.6 27.1 1.0
MG A:MG1129 4.7 27.0 1.0
OD2 A:ASP368 4.7 19.5 1.0
P3 A:I6P500 4.8 21.0 1.0
O A:HOH2077 4.8 28.5 1.0
O13 A:I6P500 4.8 20.3 1.0
CA A:SER409 4.9 19.0 1.0
CB A:ASP407 4.9 18.7 1.0
N A:ALA21 5.0 19.2 1.0
CA A:ALA21 5.0 19.1 1.0

Magnesium binding site 2 out of 4 in 2xam

Go back to Magnesium Binding Sites List in 2xam
Magnesium binding site 2 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1129

b:27.0
occ:1.00
 OD2 A:ASP407 2.0 18.8 1.0
O3B A:ADP600 2.2 27.4 1.0
O A:HOH2091 2.3 28.1 1.0
O1A A:ADP600 2.3 25.3 1.0
O42 A:I6P500 2.4 28.6 1.0
O A:HOH2076 2.6 32.9 1.0
CG A:ASP407 3.0 18.7 1.0
P2 A:I6P500 3.3 27.3 1.0
O22 A:I6P500 3.3 30.2 1.0
PB A:ADP600 3.5 27.9 1.0
PA A:ADP600 3.6 25.1 1.0
CB A:ASP407 3.7 18.7 1.0
O3A A:ADP600 3.8 26.0 1.0
OD1 A:ASP407 3.9 18.5 1.0
O32 A:I6P500 4.0 27.9 1.0
O2B A:ADP600 4.2 27.7 1.0
NZ A:LYS168 4.3 18.5 1.0
O A:HOH2086 4.4 16.3 1.0
O2A A:ADP600 4.6 25.1 1.0
O A:ASP368 4.6 15.1 1.0
O1B A:ADP600 4.6 27.1 1.0
CA A:GLY19 4.6 17.0 1.0
MG A:MG1128 4.7 44.1 1.0
O12 A:I6P500 4.7 22.5 1.0
O5' A:ADP600 4.7 24.0 1.0
OD2 A:ASP368 4.8 19.5 1.0
O3' A:ADP600 4.8 23.2 1.0
C5' A:ADP600 4.9 22.1 1.0
OG A:SER370 4.9 16.8 1.0

Magnesium binding site 3 out of 4 in 2xam

Go back to Magnesium Binding Sites List in 2xam
Magnesium binding site 3 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1030

b:23.1
occ:1.00
 OD2 B:ASP407 2.0 18.1 1.0
O2B B:ADP600 2.3 23.1 1.0
O1A B:ADP600 2.3 20.1 1.0
O42 B:I6P500 2.3 33.1 1.0
O B:HOH2097 2.3 30.1 1.0
O B:HOH2087 2.5 17.2 1.0
CG B:ASP407 3.0 17.1 1.0
P2 B:I6P500 3.4 31.5 1.0
PB B:ADP600 3.6 23.1 1.0
PA B:ADP600 3.6 22.6 1.0
O22 B:I6P500 3.7 35.3 1.0
CB B:ASP407 3.7 15.5 1.0
O3A B:ADP600 3.8 21.7 1.0
OD1 B:ASP407 4.0 18.5 1.0
MG B:MG1031 4.1 43.3 1.0
O B:HOH2092 4.2 17.8 1.0
O32 B:I6P500 4.3 34.8 1.0
O1B B:ADP600 4.3 20.7 1.0
O B:ASP368 4.5 13.5 1.0
O2A B:ADP600 4.5 20.6 1.0
CA B:GLY19 4.6 17.4 1.0
O12 B:I6P500 4.7 26.1 1.0
O3B B:ADP600 4.7 22.4 1.0
O5' B:ADP600 4.7 20.4 1.0
O3' B:ADP600 4.8 16.3 1.0
OD2 B:ASP368 4.8 17.0 1.0
C5' B:ADP600 4.9 17.8 1.0
O B:HOH2047 4.9 9.8 1.0

Magnesium binding site 4 out of 4 in 2xam

Go back to Magnesium Binding Sites List in 2xam
Magnesium binding site 4 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP6. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1031

b:43.3
occ:1.00
 OD1 B:ASP407 2.7 18.5 1.0
O1B B:ADP600 2.8 20.7 1.0
O2B B:ADP600 2.9 23.1 1.0
O B:HOH2094 2.9 15.2 1.0
OD2 B:ASP407 3.0 18.1 1.0
O32 B:I6P500 3.1 34.8 1.0
OG B:SER409 3.2 17.0 1.0
CG B:ASP407 3.2 17.1 1.0
PB B:ADP600 3.2 23.1 1.0
O42 B:I6P500 3.3 33.1 1.0
P2 B:I6P500 3.8 31.5 1.0
O23 B:I6P500 3.9 24.1 1.0
CB B:ALA21 4.0 18.3 1.0
MG B:MG1030 4.1 23.1 1.0
O3B B:ADP600 4.1 22.4 1.0
CB B:SER409 4.1 15.7 1.0
OD2 B:ASP368 4.2 17.0 1.0
O43 B:I6P500 4.4 22.0 1.0
NZ B:LYS411 4.6 16.1 1.0
P3 B:I6P500 4.6 24.9 1.0
OD1 B:ASN22 4.6 18.1 1.0
NH1 B:ARG40 4.6 28.8 1.0
O3A B:ADP600 4.6 21.7 1.0
O13 B:I6P500 4.7 21.6 1.0
CB B:ASP407 4.7 15.5 1.0
N B:ALA21 4.8 18.5 1.0
O12 B:I6P500 4.8 26.1 1.0
O22 B:I6P500 4.9 35.3 1.0
O1A B:ADP600 5.0 20.1 1.0
CA B:ALA21 5.0 18.3 1.0

Reference:

B.Gonzalez, J.I.Banos-Sanz, M.Villate, C.A.Brearley, J.Sanz-Aparicio. Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase Is A Distant Ipk Member with A Singular Inositide Binding Site For Axial 2-Oh Recognition. Proc.Natl.Acad.Sci.Usa V. 107 9608 2010.
ISSN: ISSN 0027-8424
PubMed: 20453199
DOI: 10.1073/PNAS.0912979107
Page generated: Wed Aug 14 07:02:37 2024

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