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Manganese in PDB 8ppe: Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/Mn

Enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/Mn

All present enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/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 Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/Mn, PDB code: 8ppe 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) 58.28 / 1.59
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.554, 97.547, 190.44, 90, 90, 90
R / Rfree (%) 20 / 24

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 Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/Mn (pdb code 8ppe). 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 Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/Mn, PDB code: 8ppe:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8ppe

Go back to Manganese Binding Sites List in 8ppe
Manganese binding site 1 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/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 Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:35.1
occ:0.50
 OD2 A:ASP416 2.0 38.3 1.0
O2B A:ADP501 2.3 55.0 0.8
O1A A:ADP501 2.3 47.4 0.8
O56 A:7I8502 2.4 47.2 0.5
O A:HOH672 2.5 29.1 1.0
O56 A:7I8502 2.5 64.4 0.5
CG A:ASP416 3.1 33.3 1.0
P6 A:7I8502 3.3 50.2 0.5
O46 A:7I8502 3.5 43.1 0.5
O A:HOH683 3.5 62.0 1.0
PA A:ADP501 3.5 48.1 0.8
CB A:ASP416 3.5 27.7 1.0
PB A:ADP501 3.6 56.1 0.8
O A:HOH604 3.6 42.9 1.0
O3A A:ADP501 3.8 50.1 0.8
P6 A:7I8502 3.8 65.3 0.5
O66 A:7I8502 4.0 46.5 0.5
O A:GLY397 4.1 27.1 1.0
OD1 A:ASP416 4.2 34.5 1.0
O66 A:7I8502 4.2 62.2 0.5
O1B A:ADP501 4.3 58.0 0.8
O2A A:ADP501 4.4 46.4 0.8
O36 A:7I8502 4.5 66.5 0.5
O A:HOH634 4.5 59.0 1.0
O36 A:7I8502 4.7 48.4 0.5
O5' A:ADP501 4.8 44.7 0.8
O3B A:ADP501 4.8 53.7 0.8
O46 A:7I8502 5.0 63.3 0.5
C5' A:ADP501 5.0 45.8 0.8

Manganese binding site 2 out of 2 in 8ppe

Go back to Manganese Binding Sites List in 8ppe
Manganese binding site 2 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/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 Dl-6-Deoxy-6-Phosphoryloxymethyl-Scyllo-Inositol 1,2, 4-Trisphosphate/Adp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:51.1
occ:0.50
 OD2 B:ASP416 2.0 42.2 1.0
O1B B:ADP501 2.4 63.6 0.8
O1A B:ADP501 2.4 50.9 0.8
O B:HOH665 2.6 32.8 1.0
O66 B:7I8502 3.1 109.5 1.0
CG B:ASP416 3.1 39.2 1.0
PA B:ADP501 3.5 54.0 0.8
PB B:ADP501 3.6 65.0 0.8
CB B:ASP416 3.7 31.6 1.0
O3A B:ADP501 3.8 60.0 0.8
O B:HOH604 3.8 46.3 1.0
O56 B:7I8502 4.1 107.6 1.0
P6 B:7I8502 4.1 108.1 1.0
OD1 B:ASP416 4.2 39.4 1.0
O B:GLY397 4.2 28.9 1.0
O B:HOH683 4.2 60.0 1.0
O2A B:ADP501 4.3 51.2 0.8
O3B B:ADP501 4.5 61.5 0.8
O2B B:ADP501 4.7 61.8 0.8
O5' B:ADP501 4.8 49.9 0.8

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 13:34:02 2024

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