Atomistry » Manganese » PDB 8kfj-8q1k » 8ppe
Atomistry »
  Manganese »
    PDB 8kfj-8q1k »
      8ppe »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy