Atomistry » Magnesium » PDB 3u87-3umb » 3udz
Atomistry »
  Magnesium »
    PDB 3u87-3umb »
      3udz »

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: Mon Dec 14 08:56:30 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy