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Manganese in PDB 8ppg: Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction

Enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction

All present enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction:
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 Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction, PDB code: 8ppg 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) 95.38 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 71.283, 97.102, 190.755, 90, 90, 90
R / Rfree (%) 20.6 / 24.4

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 Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction (pdb code 8ppg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction, PDB code: 8ppg:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 8ppg

Go back to Manganese Binding Sites List in 8ppg
Manganese binding site 1 out of 3 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction


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 Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn706

b:46.7
occ:1.00
 O1A A:ADP704 2.2 35.7 1.0
OD2 A:ASP416 2.2 36.4 1.0
O A:HOH861 2.3 36.0 1.0
O A:HOH897 2.3 47.8 1.0
O1B A:ADP704 2.4 52.5 1.0
O16 A:46I705 2.7 61.1 1.0
CG A:ASP416 3.2 39.7 1.0
PA A:ADP704 3.5 41.2 1.0
PB A:ADP704 3.5 57.4 1.0
CB A:ASP416 3.6 34.6 1.0
P6 A:46I705 3.7 60.9 1.0
O A:HOH882 3.9 53.9 1.0
O3A A:ADP704 3.9 47.6 1.0
O18 A:46I705 3.9 59.0 1.0
O2B A:ADP704 4.0 59.8 1.0
O A:GLY397 4.0 35.2 1.0
MN A:MN707 4.1 91.1 1.0
O17 A:46I705 4.3 55.3 1.0
OD1 A:ASP416 4.4 37.7 1.0
O2A A:ADP704 4.4 38.3 1.0
NZ A:LYS264 4.5 58.5 1.0
OG A:SER399 4.6 33.0 1.0
O5' A:ADP704 4.6 40.5 1.0
OD2 A:ASP262 4.8 52.7 1.0
C5' A:ADP704 4.8 39.0 1.0
O3B A:ADP704 4.8 60.4 1.0

Manganese binding site 2 out of 3 in 8ppg

Go back to Manganese Binding Sites List in 8ppg
Manganese binding site 2 out of 3 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction


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 Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn707

b:91.1
occ:1.00
 O A:HOH882 2.3 53.9 1.0
OD2 A:ASP416 2.5 36.4 1.0
OD1 A:ASP416 2.6 37.7 1.0
O2B A:ADP704 2.7 59.8 1.0
O A:HOH816 2.7 53.5 1.0
CG A:ASP416 2.8 39.7 1.0
O A:HOH923 3.2 59.3 1.0
O1B A:ADP704 3.6 52.5 1.0
PB A:ADP704 3.7 57.4 1.0
NZ A:LYS419 3.9 60.5 1.0
O10 A:46I705 3.9 62.0 1.0
MN A:MN706 4.1 46.7 1.0
CB A:ASP416 4.4 34.6 1.0
O16 A:46I705 4.4 61.1 1.0
CA A:GLY418 4.5 43.2 1.0
O A:HOH876 4.5 60.7 1.0
N A:GLY418 4.6 37.6 1.0
NZ A:LYS209 4.6 42.3 1.0
O3B A:ADP704 4.7 60.4 1.0
O3A A:ADP704 4.9 47.6 1.0
O A:GLY397 4.9 35.2 1.0

Manganese binding site 3 out of 3 in 8ppg

Go back to Manganese Binding Sites List in 8ppg
Manganese binding site 3 out of 3 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosyl 1,3,4,6- Tetrakisphosphate/Adp/Mn After Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn705

b:51.3
occ:1.00
 O B:HOH902 1.9 51.7 1.0
OD2 B:ASP416 2.0 42.0 1.0
O1A B:ADP703 2.2 43.1 1.0
O1B B:ADP703 2.3 48.9 1.0
O B:HOH831 2.4 38.1 1.0
O B:HOH802 2.4 40.0 0.5
CG B:ASP416 3.0 42.0 1.0
PA B:ADP703 3.3 42.6 1.0
PB B:ADP703 3.5 54.8 1.0
CB B:ASP416 3.5 37.8 1.0
O3A B:ADP703 3.6 58.4 1.0
O18 B:46I704 3.9 73.3 1.0
O B:HOH812 4.1 49.6 1.0
O B:HOH896 4.1 54.9 1.0
OD1 B:ASP416 4.1 40.8 1.0
O2A B:ADP703 4.2 42.1 1.0
O B:GLY397 4.2 40.8 1.0
O B:HOH832 4.2 45.4 1.0
O3B B:ADP703 4.5 61.0 1.0
O2B B:ADP703 4.5 67.4 1.0
OG B:SER399 4.6 38.2 1.0
O5' B:ADP703 4.6 41.8 1.0
C5' B:ADP703 4.8 40.0 1.0
CE B:LYS264 4.9 44.4 1.0
P6 B:46I704 4.9 81.3 1.0
O16 B:46I704 4.9 81.5 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 13:34:08 2024

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