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Manganese in PDB 8pph: Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Alpha-D-Glucopyranosyl 1,3,4-Trisphosphate/Atp/Mn

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

All present enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Alpha-D-Glucopyranosyl 1,3,4-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 Alpha-D-Glucopyranosyl 1,3,4-Trisphosphate/Atp/Mn, PDB code: 8pph 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) 47.77 / 1.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.046, 97.503, 190.879, 90, 90, 90
R / Rfree (%) 19.8 / 23.1

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 Alpha-D-Glucopyranosyl 1,3,4-Trisphosphate/Atp/Mn (pdb code 8pph). 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 Alpha-D-Glucopyranosyl 1,3,4-Trisphosphate/Atp/Mn, PDB code: 8pph:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8pph

Go back to Manganese Binding Sites List in 8pph
Manganese binding site 1 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Alpha-D-Glucopyranosyl 1,3,4-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 Alpha-D-Glucopyranosyl 1,3,4-Trisphosphate/Atp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:37.1
occ:0.10
 O1G A:ATP501 1.8 64.8 0.8
O A:HOH680 1.9 38.0 1.0
O1A A:ATP501 2.0 36.3 0.8
OD2 A:ASP416 2.0 41.3 1.0
CG A:ASP416 3.0 35.3 1.0
O A:HOH613 3.0 67.3 1.0
PG A:ATP501 3.1 78.7 0.8
CB A:ASP416 3.3 31.5 1.0
PA A:ATP501 3.4 38.8 0.8
O3B A:ATP501 3.4 61.3 0.8
O2B A:ATP501 3.6 51.0 0.8
O A:GLY397 3.9 33.1 1.0
PB A:ATP501 4.0 55.3 0.8
O2G A:ATP501 4.0 71.3 0.8
O3A A:ATP501 4.0 46.9 0.8
O3G A:ATP501 4.2 71.9 0.8
O2A A:ATP501 4.2 40.2 0.8
OD1 A:ASP416 4.2 40.3 1.0
MN A:MN507 4.2 68.7 0.5
OG A:SER399 4.4 29.4 1.0
O A:HOH682 4.5 61.8 1.0
O5' A:ATP501 4.5 38.1 0.8
CA A:ASP416 4.8 31.3 1.0
OD2 A:ASP262 4.9 57.6 1.0
C5' A:ATP501 5.0 41.2 0.8

Manganese binding site 2 out of 2 in 8pph

Go back to Manganese Binding Sites List in 8pph
Manganese binding site 2 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Alpha-D-Glucopyranosyl 1,3,4-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 Alpha-D-Glucopyranosyl 1,3,4-Trisphosphate/Atp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:68.7
occ:0.50
 O A:HOH615 2.0 58.5 1.0
O2B A:ATP501 2.0 51.0 0.8
OD2 A:ASP416 2.7 41.3 1.0
OD1 A:ASP416 2.7 40.3 1.0
O A:HOH647 2.9 57.7 1.0
CG A:ASP416 3.0 35.3 1.0
PB A:ATP501 3.5 55.3 0.8
O A:HOH682 4.1 61.8 1.0
NZ A:LYS209 4.1 44.5 1.0
O1G A:ATP501 4.2 64.8 0.8
O3G A:ATP501 4.2 71.9 0.8
MN A:MN506 4.2 37.1 0.1
O3B A:ATP501 4.3 61.3 0.8
O3A A:ATP501 4.3 46.9 0.8
O1B A:ATP501 4.4 60.6 0.8
CB A:ASP416 4.4 31.5 1.0
O A:HOH613 4.4 67.3 1.0
PG A:ATP501 4.5 78.7 0.8
O1A A:ATP501 4.7 36.3 0.8
CE A:LYS209 4.8 41.5 1.0
O11 A:5AI502 4.8 76.8 0.9
CA A:GLY418 4.9 34.7 1.0
PA A:ATP501 4.9 38.8 0.8
N A:GLY418 5.0 35.4 1.0

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 13:34:19 2024

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