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Manganese in PDB 8pp8: Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/Mn

Enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/Mn

All present enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/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 L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/Mn, PDB code: 8pp8 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) 95.59 / 1.59
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.561, 97.351, 191.177, 90, 90, 90
R / Rfree (%) 19.3 / 21.2

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 L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/Mn (pdb code 8pp8). 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 L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/Mn, PDB code: 8pp8:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8pp8

Go back to Manganese Binding Sites List in 8pp8
Manganese binding site 1 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/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 L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:42.6
occ:0.40
 O2G A:ANP501 1.9 52.4 0.6
OD2 A:ASP416 1.9 35.6 1.0
O A:HOH704 2.2 28.2 1.0
O2A A:ANP501 2.3 29.8 0.6
O2B A:ANP501 2.9 44.0 0.6
CG A:ASP416 3.0 32.6 1.0
PG A:ANP501 3.1 56.5 0.6
CB A:ASP416 3.5 27.1 1.0
O A:HOH731 3.5 51.1 1.0
PA A:ANP501 3.6 30.9 0.6
N3B A:ANP501 3.6 48.4 0.6
PB A:ANP501 3.7 45.5 0.6
O1G A:ANP501 3.8 58.0 0.6
O A:HOH728 3.8 50.1 1.0
O A:GLY397 3.9 26.9 1.0
O3A A:ANP501 3.9 36.9 0.6
OD1 A:ASP416 4.1 34.8 1.0
O3G A:ANP501 4.2 56.4 0.6
O1A A:ANP501 4.3 31.0 0.6
OG A:SER399 4.7 25.8 1.0
O5' A:ANP501 4.7 33.1 0.6
O A:HOH657 4.8 47.9 1.0
CE A:LYS264 4.9 30.9 1.0
CA A:ASP416 4.9 26.8 1.0

Manganese binding site 2 out of 2 in 8pp8

Go back to Manganese Binding Sites List in 8pp8
Manganese binding site 2 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/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 L-Scyllo-Inositol 1,2,4-Trisphosphate/Amp-Pnp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:60.4
occ:0.50
 O2G B:ANP502 1.7 55.2 0.6
OD2 B:ASP416 1.9 39.1 1.0
O2A B:ANP502 2.1 34.6 0.6
O B:HOH701 2.5 33.8 1.0
O2B B:ANP502 2.7 49.9 0.6
PG B:ANP502 2.8 60.5 0.6
CG B:ASP416 2.9 35.0 1.0
N3B B:ANP502 3.2 52.4 0.6
PA B:ANP502 3.3 35.1 0.6
PB B:ANP502 3.4 48.3 0.6
O3G B:ANP502 3.4 57.7 0.6
CB B:ASP416 3.4 30.8 1.0
O3A B:ANP502 3.6 41.9 0.6
O B:HOH623 3.7 55.6 1.0
O B:HOH720 4.0 53.1 1.0
OD1 B:ASP416 4.0 36.9 1.0
O1G B:ANP502 4.1 56.6 0.6
O1A B:ANP502 4.1 35.0 0.6
O B:GLY397 4.2 29.0 1.0
O5' B:ANP502 4.5 36.3 0.6
O1B B:ANP502 4.9 49.3 0.6
CA B:ASP416 4.9 28.0 1.0
C5' B:ANP502 4.9 39.0 0.6
OG B:SER399 4.9 28.5 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 13:32:18 2024

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