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Manganese in PDB 8ppi: Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn

Enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn

All present enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn:
2.7.1.127;

Protein crystallography data

The structure of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn, PDB code: 8ppi was solved by M.A.Marquez-Monino, B.Gonzalez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 96.58 / 1.65
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 73.953, 98.124, 193.163, 90, 90, 90
R / Rfree (%) 18.5 / 21.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn (pdb code 8ppi). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn, PDB code: 8ppi:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8ppi

Go back to Manganese Binding Sites List in 8ppi
Manganese binding site 1 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:54.7
occ:0.50
 O1G A:ATP502 1.8 66.7 1.0
O1A A:ATP502 2.0 25.9 1.0
O A:HOH704 2.1 27.6 1.0
OD2 A:ASP416 2.2 26.2 1.0
PG A:ATP502 2.8 73.3 1.0
O3B A:ATP502 3.1 54.9 1.0
CG A:ASP416 3.2 26.9 1.0
O2G A:ATP502 3.2 73.0 1.0
PA A:ATP502 3.3 27.8 1.0
CB A:ASP416 3.5 22.3 1.0
O1B A:ATP502 3.7 46.0 1.0
O3A A:ATP502 3.8 34.7 1.0
PB A:ATP502 3.8 43.2 1.0
O A:HOH707 3.9 31.8 1.0
O A:GLY397 4.0 25.1 1.0
O3G A:ATP502 4.2 71.0 1.0
O2A A:ATP502 4.2 28.7 1.0
OD1 A:ASP416 4.3 27.0 1.0
OG A:SER399 4.5 22.3 1.0
O5' A:ATP502 4.5 28.4 1.0
C5' A:ATP502 4.9 30.7 1.0

Manganese binding site 2 out of 2 in 8ppi

Go back to Manganese Binding Sites List in 8ppi
Manganese binding site 2 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,1'- Trisphosphate/Atp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn507

b:62.2
occ:0.50
 O1G B:ATP502 1.7 44.5 0.5
OD2 B:ASP416 1.9 32.7 1.0
O1A B:ATP502 2.1 36.4 0.5
O2A B:ATP502 2.2 33.0 0.5
O B:HOH687 2.2 30.1 1.0
O3B B:ATP502 2.5 46.2 0.5
PG B:ATP502 2.6 49.5 0.5
CG B:ASP416 3.0 31.3 1.0
CB B:ASP416 3.4 26.1 1.0
PA B:ATP502 3.4 35.7 0.5
PA B:ATP502 3.4 32.1 0.5
O1B B:ATP502 3.4 39.0 0.5
O B:HOH651 3.5 52.0 1.0
O2B B:ATP502 3.6 40.8 0.5
O3G B:ATP502 3.7 51.2 0.5
O2G B:ATP502 3.7 49.9 0.5
PB B:ATP502 3.7 40.3 0.5
O B:HOH667 3.8 46.2 1.0
O3A B:ATP502 3.9 36.7 0.5
O3A B:ATP502 3.9 41.0 0.5
PB B:ATP502 3.9 47.0 0.5
O B:GLY397 4.0 26.3 1.0
OD1 B:ASP416 4.1 31.8 1.0
O2A B:ATP502 4.1 35.7 0.5
O1A B:ATP502 4.2 31.9 0.5
O B:HOH602 4.4 53.1 1.0
O5' B:ATP502 4.6 33.2 0.5
OG B:SER399 4.6 25.9 1.0
O5' B:ATP502 4.7 30.8 0.5
O2B B:ATP502 4.7 46.9 0.5
O1B B:ATP502 4.8 46.0 0.5
CA B:ASP416 4.9 23.9 1.0
C5' B:ATP502 5.0 32.6 0.5

Reference:

M.A.Marquez-Monino, R.Ortega-Garcia, H.Whitfield, A.M.Riley, L.Infantes, S.W.Garrett, M.L.Shipton, C.A.Brearley, B.V.L.Potter, B.Gonzalez. Substrate Promiscuity of Inositol 1,4,5-Trisphosphate Kinase Driven By Structurally-Modified Ligands and Active Site Plasticity Nat Commun V. 15 1502 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-45917-5
Page generated: Sun Oct 6 13:34:23 2024

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