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Magnesium in PDB 3udz: 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: 3udz was solved by V.Gosein, T.-F.Leung, O.Krajden, G.J.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.44 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.057, 59.394, 82.755, 89.84, 82.58, 63.36
R / Rfree (%) 18.9 / 26

Other elements in 3udz:

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) 1 atom

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 3udz). 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: 3udz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3udz

Go back to Magnesium Binding Sites List in 3udz
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:Mg700

b:32.2
occ:1.00
 OD1 A:ASP407 2.3 24.8 1.0
O23 A:IHP500 2.5 28.3 1.0
O A:HOH474 2.7 22.5 1.0
O1B A:ADP600 2.8 32.8 1.0
O2B A:ADP600 3.1 32.7 1.0
OG A:SER409 3.2 32.5 1.0
CG A:ASP407 3.2 24.9 1.0
OD2 A:ASP407 3.2 28.4 1.0
PB A:ADP600 3.4 32.2 1.0
CB A:SER409 3.8 25.9 1.0
P3 A:IHP500 3.9 38.9 1.0
O32 A:IHP500 4.0 26.8 1.0
MG A:MG701 4.1 38.2 1.0
O43 A:IHP500 4.1 31.1 1.0
NH2 A:ARG40 4.1 26.9 1.0
O3B A:ADP600 4.3 31.9 1.0
CB A:ALA21 4.4 33.9 1.0
NZ A:LYS411 4.4 18.6 1.0
OD2 A:ASP368 4.4 24.2 1.0
O22 A:IHP500 4.4 24.0 1.0
ND2 A:ASN22 4.5 30.2 1.0
O A:HOH620 4.6 30.4 1.0
P2 A:IHP500 4.6 32.3 1.0
O12 A:IHP500 4.6 23.2 1.0
CB A:ASP407 4.6 25.7 1.0
O33 A:IHP500 4.7 28.3 1.0
O A:HOH472 4.8 22.3 1.0
O3A A:ADP600 4.8 28.2 1.0

Magnesium binding site 2 out of 4 in 3udz

Go back to Magnesium Binding Sites List in 3udz
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:Mg701

b:38.2
occ:1.00
 OD2 A:ASP407 2.0 28.4 1.0
O2B A:ADP600 2.3 32.7 1.0
O1A A:ADP600 2.3 29.3 1.0
O A:HOH568 2.4 32.8 1.0
O33 A:IHP500 2.6 28.3 1.0
CG A:ASP407 2.7 24.9 1.0
O A:HOH489 2.8 28.4 1.0
O23 A:IHP500 3.0 28.3 1.0
P3 A:IHP500 3.3 38.9 1.0
CB A:ASP407 3.5 25.7 1.0
OD1 A:ASP407 3.5 24.8 1.0
PA A:ADP600 3.5 30.8 1.0
PB A:ADP600 3.5 32.2 1.0
O3A A:ADP600 3.8 28.2 1.0
O43 A:IHP500 4.0 31.1 1.0
MG A:MG700 4.1 32.2 1.0
O1B A:ADP600 4.2 32.8 1.0
O2A A:ADP600 4.4 28.1 1.0
O A:HOH530 4.4 20.5 1.0
O A:ASP368 4.5 19.6 1.0
CE A:LYS168 4.6 20.4 1.0
NZ A:LYS168 4.6 23.5 1.0
CA A:GLY19 4.6 25.7 1.0
O13 A:IHP500 4.7 24.4 1.0
O5' A:ADP600 4.7 27.8 1.0
O3B A:ADP600 4.7 31.9 1.0
OD2 A:ASP368 4.8 24.2 1.0
O3' A:ADP600 4.9 24.2 1.0
CA A:ASP407 4.9 25.0 1.0

Magnesium binding site 3 out of 4 in 3udz

Go back to Magnesium Binding Sites List in 3udz
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:Mg700

b:29.9
occ:1.00
 OD1 B:ASP407 2.3 27.8 1.0
O42 B:IHP500 2.5 30.3 1.0
O1B B:ADP600 2.5 31.9 1.0
O B:HOH499 2.8 30.3 1.0
OG B:SER409 2.9 30.8 1.0
CG B:ASP407 3.1 30.9 1.0
O2B B:ADP600 3.2 32.8 1.0
OD2 B:ASP407 3.3 31.2 1.0
PB B:ADP600 3.4 32.3 1.0
CB B:SER409 3.6 27.1 1.0
O23 B:IHP500 3.9 29.0 1.0
P2 B:IHP500 4.0 45.2 1.0
NZ B:LYS411 4.2 23.5 1.0
NH2 B:ARG40 4.2 29.9 1.0
O3B B:ADP600 4.3 29.3 1.0
ND2 B:ASN22 4.3 30.9 1.0
CB B:ALA21 4.3 32.1 1.0
OD2 B:ASP368 4.4 27.0 1.0
O43 B:IHP500 4.4 26.5 1.0
P3 B:IHP500 4.5 31.4 1.0
O B:HOH615 4.6 38.5 1.0
CB B:ASP407 4.6 28.2 1.0
O13 B:IHP500 4.7 27.9 1.0
O3A B:ADP600 4.7 30.6 1.0
O32 B:IHP500 4.7 33.8 1.0
O22 B:IHP500 4.7 39.6 1.0
O B:HOH539 4.8 26.2 1.0
O12 B:IHP500 4.8 31.9 1.0
CA B:SER409 4.9 29.7 1.0
O B:ASP407 5.0 27.1 1.0
N B:ALA21 5.0 30.7 1.0
N B:SER409 5.0 29.6 1.0

Magnesium binding site 4 out of 4 in 3udz

Go back to Magnesium Binding Sites List in 3udz
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:Mg701

b:41.1
occ:1.00
 O1A B:ADP600 2.2 28.9 1.0
O2B B:ADP600 2.8 32.8 1.0
OD2 B:ASP407 3.0 31.2 1.0
O B:HOH558 3.1 31.7 1.0
O B:HOH572 3.2 35.4 1.0
O3' B:ADP600 3.3 29.4 1.0
O32 B:IHP500 3.4 33.8 1.0
PA B:ADP600 3.5 27.6 1.0
O B:HOH587 3.5 31.9 1.0
O22 B:IHP500 3.7 39.6 1.0
O3A B:ADP600 3.9 30.6 1.0
PB B:ADP600 4.0 32.3 1.0
P2 B:IHP500 4.0 45.2 1.0
O B:HOH522 4.0 28.3 1.0
CG B:ASP407 4.0 30.9 1.0
C3' B:ADP600 4.0 29.5 1.0
C5' B:ADP600 4.1 31.1 1.0
O5' B:ADP600 4.2 29.7 1.0
CA B:GLY19 4.2 28.5 1.0
O42 B:IHP500 4.3 30.3 1.0
OE2 B:GLU166 4.5 35.9 1.0
CB B:ASP407 4.6 28.2 1.0
C4' B:ADP600 4.6 32.3 1.0
OG B:SER370 4.6 32.1 1.0
CE B:LYS168 4.6 24.9 1.0
N B:GLY19 4.7 30.1 1.0
O2A B:ADP600 4.8 27.6 1.0
O3B B:ADP600 4.9 29.3 1.0
O B:GLU18 4.9 30.6 1.0
OD1 B:ASP407 5.0 27.8 1.0
O B:HOH601 5.0 31.9 1.0
O1B B:ADP600 5.0 31.9 1.0

Reference:

V.Gosein, T.F.Leung, O.Krajden, G.J.Miller. Inositol Phosphate-Induced Stabilization of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase and Its Role in Substrate Specificity. Protein Sci. V. 21 737 2012.
ISSN: ISSN 0961-8368
PubMed: 22362712
DOI: 10.1002/PRO.2049
Page generated: Thu Aug 15 12:29:09 2024

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