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Magnesium in PDB 4lv7: Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C

Enzymatic activity of Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C

All present enzymatic activity of Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C:
2.7.1.158;

Protein crystallography data

The structure of Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C, PDB code: 4lv7 was solved by V.Gosein, G.J.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.55 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.763, 59.353, 82.232, 83.01, 89.92, 63.41
R / Rfree (%) 22.4 / 29.4

Other elements in 4lv7:

The structure of Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C (pdb code 4lv7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C, PDB code: 4lv7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4lv7

Go back to Magnesium Binding Sites List in 4lv7
Magnesium binding site 1 out of 2 in the Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C


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 Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:29.4
occ:1.00
OD1 A:ASP407 2.4 29.0 1.0
O1B A:ADP502 2.6 45.6 1.0
OG A:SER409 3.0 26.6 1.0
O42 A:IHP501 3.1 27.4 1.0
PB A:ADP502 3.4 53.2 1.0
CB A:SER409 3.5 23.5 1.0
CG A:ASP407 3.6 26.1 1.0
O2B A:ADP502 3.6 48.7 1.0
NH2 A:ARG40 3.6 30.9 1.0
O23 A:IHP501 3.6 18.5 1.0
O32 A:IHP501 3.8 32.2 1.0
O3B A:ADP502 3.9 29.7 1.0
OD2 A:ASP407 4.0 24.9 1.0
P2 A:IHP501 4.2 25.7 1.0
OD1 A:ASN22 4.3 35.6 1.0
CB A:ALA21 4.3 24.3 1.0
OD2 A:ASP368 4.4 26.3 1.0
NZ A:LYS411 4.5 20.3 1.0
O A:ASP407 4.5 31.6 1.0
P3 A:IHP501 4.5 23.4 1.0
O43 A:IHP501 4.6 15.2 1.0
O13 A:IHP501 4.7 20.6 1.0
CZ A:ARG40 4.8 31.4 1.0
CB A:ASP407 4.8 24.8 1.0
C A:ASP407 4.8 26.0 1.0
CA A:SER409 4.9 26.2 1.0
O3A A:ADP502 4.9 33.6 1.0
CA A:ASP407 5.0 28.3 1.0

Magnesium binding site 2 out of 2 in 4lv7

Go back to Magnesium Binding Sites List in 4lv7
Magnesium binding site 2 out of 2 in the Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C


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 Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:29.6
occ:1.00
O2B B:ADP502 2.7 42.2 1.0
O1A B:ADP502 2.9 23.3 1.0
O22 B:IHP501 2.9 23.7 1.0
OD2 B:ASP407 3.4 20.5 1.0
CA B:GLY19 3.6 23.2 1.0
O3' B:ADP502 3.7 21.9 1.0
N B:GLY19 3.9 30.0 1.0
O32 B:IHP501 3.9 31.5 1.0
P2 B:IHP501 4.0 21.4 1.0
PA B:ADP502 4.0 25.9 1.0
PB B:ADP502 4.0 40.3 1.0
O3A B:ADP502 4.1 22.5 1.0
CG B:ASP407 4.1 24.9 1.0
C5' B:ADP502 4.3 27.1 1.0
C3' B:ADP502 4.3 20.2 1.0
O B:GLU18 4.4 24.2 1.0
C B:GLU18 4.4 30.9 1.0
O5' B:ADP502 4.5 33.1 1.0
O42 B:IHP501 4.5 28.4 1.0
CB B:ASP407 4.7 19.8 1.0
O3B B:ADP502 4.7 38.5 1.0
OE2 B:GLU166 4.7 19.9 1.0
C4' B:ADP502 4.8 23.7 1.0
OD1 B:ASP407 4.9 34.6 1.0
NZ B:LYS168 5.0 18.3 1.0

Reference:

V.Gosein, G.J.Miller. Conformational Stability of IPK1 Dictates Its Substrate Selectivity J.Biol.Chem. 2013.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M113.512731
Page generated: Mon Dec 14 19:10:46 2020

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