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Manganese in PDB 8pp9: Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Scyllo-Inositol 1,2,3,5-Tetrakisphosphate/Adp/Mn

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

All present enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Scyllo-Inositol 1,2,3,5-Tetrakisphosphate/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 Scyllo-Inositol 1,2,3,5-Tetrakisphosphate/Adp/Mn, PDB code: 8pp9 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) 58.18 / 1.73
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.504, 97.509, 191.487, 90, 90, 90
R / Rfree (%) 19.4 / 21

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 Scyllo-Inositol 1,2,3,5-Tetrakisphosphate/Adp/Mn (pdb code 8pp9). 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 Scyllo-Inositol 1,2,3,5-Tetrakisphosphate/Adp/Mn, PDB code: 8pp9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8pp9

Go back to Manganese Binding Sites List in 8pp9
Manganese binding site 1 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Scyllo-Inositol 1,2,3,5-Tetrakisphosphate/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 Scyllo-Inositol 1,2,3,5-Tetrakisphosphate/Adp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:51.6
occ:0.50
 O13 A:4IM501 2.6 41.1 1.0
O1B A:ADP502 2.8 52.9 1.0
O1A A:ADP502 2.9 39.7 1.0
O A:HOH700 3.0 36.6 1.0
O A:HOH685 3.0 54.7 1.0
OD2 A:ASP416 3.1 34.0 1.0
O A:HOH602 3.1 54.1 1.0
P01 A:4IM501 3.5 44.8 1.0
O12 A:4IM501 3.7 40.3 1.0
PB A:ADP502 3.9 54.2 1.0
O11 A:4IM501 4.0 44.9 1.0
O2B A:ADP502 4.0 58.7 1.0
O A:HOH635 4.2 46.0 1.0
CG A:ASP416 4.2 31.9 1.0
PA A:ADP502 4.3 40.5 1.0
O3A A:ADP502 4.4 45.2 1.0
NZ A:LYS264 4.5 34.9 1.0
CE A:LYS264 4.5 31.8 1.0
O A:GLY397 4.7 27.9 1.0
O A:HOH608 4.7 57.5 1.0
CB A:ASP416 4.8 28.6 1.0
O01 A:4IM501 4.9 39.6 1.0
OG A:SER399 5.0 27.6 1.0

Manganese binding site 2 out of 2 in 8pp9

Go back to Manganese Binding Sites List in 8pp9
Manganese binding site 2 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Scyllo-Inositol 1,2,3,5-Tetrakisphosphate/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 Scyllo-Inositol 1,2,3,5-Tetrakisphosphate/Adp/Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn506

b:68.3
occ:0.50
 O1B B:ADP501 2.5 61.6 1.0
O1A B:ADP501 2.6 47.3 1.0
OD2 B:ASP416 2.7 41.6 1.0
O B:HOH671 2.8 36.0 1.0
O12 B:4IM502 3.0 75.1 1.0
O B:HOH629 3.0 53.7 1.0
O B:HOH624 3.4 54.3 1.0
PB B:ADP501 3.7 61.5 1.0
P01 B:4IM502 3.8 74.5 1.0
PA B:ADP501 3.9 47.3 1.0
CG B:ASP416 3.9 38.8 1.0
O13 B:4IM502 4.0 65.8 1.0
O B:HOH622 4.1 60.6 1.0
O3A B:ADP501 4.1 55.4 1.0
O3B B:ADP501 4.2 63.7 1.0
O11 B:4IM502 4.3 67.8 1.0
CB B:ASP416 4.5 31.9 1.0
O B:GLY397 4.6 28.8 1.0
NZ B:LYS264 4.7 44.6 1.0
CE B:LYS264 4.8 43.4 1.0
OG B:SER399 4.9 31.2 1.0
O5' B:ADP501 4.9 43.4 1.0
OD1 B:ASP416 4.9 40.4 1.0
O2A B:ADP501 4.9 45.6 1.0
C5' B:ADP501 5.0 41.4 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 13:33:03 2024

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