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Magnesium in PDB 5w2i: Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp

Enzymatic activity of Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp

All present enzymatic activity of Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp:
2.7.1.151;

Protein crystallography data

The structure of Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp, PDB code: 5w2i was solved by H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.03 / 1.60
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.090, 78.090, 86.320, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp (pdb code 5w2i). 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 the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp, PDB code: 5w2i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5w2i

Go back to Magnesium Binding Sites List in 5w2i
Magnesium binding site 1 out of 2 in the Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp


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 the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:13.7
occ:1.00
 O A:HOH855 2.0 27.5 1.0
O A:HOH906 2.0 18.8 1.0
O3B A:ADP703 2.0 19.8 1.0
O A:HOH826 2.0 22.4 1.0
O2A A:ADP703 2.1 13.7 1.0
OD2 A:ASP385 2.1 14.5 1.0
PB A:ADP703 3.2 18.3 1.0
CG A:ASP385 3.2 11.5 1.0
PA A:ADP703 3.3 13.5 1.0
O3A A:ADP703 3.6 18.2 1.0
O A:HOH928 3.6 30.9 1.0
MG A:MG702 3.7 17.6 1.0
O A:HOH829 3.8 18.1 1.0
O1B A:ADP703 3.8 22.8 1.0
CB A:ASP385 3.8 8.7 1.0
OD2 A:ASP144 4.0 17.9 1.0
OD1 A:ASP385 4.2 14.4 1.0
CD1 A:LEU179 4.2 13.2 1.0
O1A A:ADP703 4.3 14.3 1.0
O5' A:ADP703 4.3 16.1 1.0
C5' A:ADP703 4.4 16.7 1.0
O A:HOH862 4.4 33.8 1.0
O2B A:ADP703 4.5 23.1 1.0
OG A:SER252 4.5 12.5 1.0
O A:HOH887 4.8 32.2 1.0

Magnesium binding site 2 out of 2 in 5w2i

Go back to Magnesium Binding Sites List in 5w2i
Magnesium binding site 2 out of 2 in the Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp


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 the Core Catalytic Domain of Human Inositol Phosphate Multikinase Soaked with C4-Analogue of Ptdins(4,5)P2 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:17.6
occ:1.00
 O A:HOH928 2.0 30.9 1.0
O A:HOH913 2.1 29.8 1.0
OD2 A:ASP385 2.3 14.5 1.0
O A:HOH887 2.3 32.2 1.0
O1B A:ADP703 2.4 22.8 1.0
OD1 A:ASP385 2.4 14.4 1.0
CG A:ASP385 2.7 11.5 1.0
O A:HOH801 2.9 34.7 1.0
O3B A:ADP703 3.2 19.8 1.0
PB A:ADP703 3.3 18.3 1.0
O A:HOH906 3.6 18.8 1.0
MG A:MG701 3.7 13.7 1.0
O A:HOH886 3.8 46.3 1.0
OE1 A:GLN78 4.1 29.3 1.0
CB A:ASP385 4.2 8.7 1.0
NE2 A:GLN78 4.3 35.9 1.0
O41 A:I3P704 4.4 14.7 1.0
O42 A:I3P704 4.4 18.8 1.0
O3A A:ADP703 4.4 18.2 1.0
O2B A:ADP703 4.5 23.1 1.0
O A:ALA250 4.6 9.4 1.0
CD A:GLN78 4.6 27.8 1.0
NZ A:LYS75 4.6 15.8 1.0
O2A A:ADP703 4.7 13.7 1.0
P4 A:I3P704 4.9 17.9 1.0
O A:HOH829 5.0 18.1 1.0
CB A:ALA387 5.0 13.4 1.0

Reference:

H.Wang, S.B.Shears. Structural Features of Human Inositol Phosphate Multikinase Rationalize Its Inositol Phosphate Kinase and Phosphoinositide 3-Kinase Activities. J. Biol. Chem. V. 292 18192 2017.
ISSN: ESSN 1083-351X
PubMed: 28882892
DOI: 10.1074/JBC.M117.801845
Page generated: Mon Sep 30 06:27:12 2024

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