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Manganese in PDB 8ppj: Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,6,1'- 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-Glucopyranosylmethanol 3,4,6,1'- 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-Glucopyranosylmethanol 3,4,6,1'- 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-Glucopyranosylmethanol 3,4,6,1'- Tetrakisphosphate/Adp/Mn After Reaction, PDB code: 8ppj 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) 95.56 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.53, 97.063, 191.127, 90, 90, 90
R / Rfree (%) 19.7 / 23.4

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-Glucopyranosylmethanol 3,4,6,1'- Tetrakisphosphate/Adp/Mn After Reaction (pdb code 8ppj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 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-Glucopyranosylmethanol 3,4,6,1'- Tetrakisphosphate/Adp/Mn After Reaction, PDB code: 8ppj:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8ppj

Go back to Manganese Binding Sites List in 8ppj
Manganese binding site 1 out of 4 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,6,1'- 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-Glucopyranosylmethanol 3,4,6,1'- Tetrakisphosphate/Adp/Mn After Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:27.8
occ:0.60
 OD2 A:ASP416 2.1 29.1 1.0
O1A A:ADP501 2.1 29.0 1.0
O A:HOH647 2.2 40.7 1.0
O A:HOH687 2.2 30.1 1.0
O1B A:ADP501 2.4 43.2 1.0
O18 A:661502 2.4 44.7 1.0
CG A:ASP416 3.1 29.1 1.0
PB A:ADP501 3.4 41.2 1.0
PA A:ADP501 3.4 31.5 1.0
P6 A:661502 3.5 48.5 1.0
CB A:ASP416 3.6 27.0 1.0
O2B A:ADP501 3.7 43.2 1.0
O3A A:ADP501 3.8 34.0 1.0
O17 A:661502 3.8 47.8 1.0
O A:HOH618 3.9 40.3 1.0
O A:HOH699 4.0 46.8 1.0
O A:GLY397 4.1 28.8 1.0
O16 A:661502 4.2 46.4 1.0
OD1 A:ASP416 4.2 31.1 1.0
O2A A:ADP501 4.3 29.2 1.0
MN A:MN509 4.3 77.0 0.7
MN A:MN508 4.4 113.7 1.0
NZ A:LYS264 4.4 46.4 1.0
OG A:SER399 4.6 28.1 1.0
O5' A:ADP501 4.6 32.3 1.0
O3B A:ADP501 4.8 46.2 1.0
O6 A:661502 4.8 43.1 1.0
C5' A:ADP501 4.9 34.6 1.0

Manganese binding site 2 out of 4 in 8ppj

Go back to Manganese Binding Sites List in 8ppj
Manganese binding site 2 out of 4 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,6,1'- 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-Glucopyranosylmethanol 3,4,6,1'- Tetrakisphosphate/Adp/Mn After Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn508

b:113.7
occ:1.00
 O16 A:661502 2.3 46.4 1.0
O A:HOH699 2.4 46.8 1.0
O A:HOH601 2.6 53.1 1.0
O A:HOH723 2.7 60.9 1.0
O1B A:ADP501 2.9 43.2 1.0
O18 A:661502 3.2 44.7 1.0
P6 A:661502 3.3 48.5 1.0
PB A:ADP501 3.5 41.2 1.0
O3B A:ADP501 3.6 46.2 1.0
O2B A:ADP501 3.7 43.2 1.0
C6 A:661502 3.9 40.4 1.0
C5 A:661502 4.1 42.9 1.0
O6 A:661502 4.1 43.1 1.0
O12 A:661502 4.2 49.0 1.0
MN A:MN509 4.3 77.0 0.7
O09 A:661502 4.3 42.8 1.0
MN A:MN507 4.4 27.8 0.6
O17 A:661502 4.6 47.8 1.0
O A:HOH684 4.8 54.6 1.0
OD2 A:ASP416 4.8 29.1 1.0
C4 A:661502 4.8 41.2 1.0
P4 A:661502 4.9 50.4 1.0

Manganese binding site 3 out of 4 in 8ppj

Go back to Manganese Binding Sites List in 8ppj
Manganese binding site 3 out of 4 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,6,1'- 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-Glucopyranosylmethanol 3,4,6,1'- Tetrakisphosphate/Adp/Mn After Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn509

b:77.0
occ:0.70
 O2B A:ADP501 2.3 43.2 1.0
O A:HOH711 2.3 51.0 0.7
OD1 A:ASP416 2.4 31.1 1.0
O A:HOH699 2.6 46.8 1.0
OD2 A:ASP416 2.7 29.1 1.0
CG A:ASP416 2.9 29.1 1.0
PB A:ADP501 3.6 41.2 1.0
O1B A:ADP501 4.0 43.2 1.0
NZ A:LYS209 4.0 34.9 1.0
MN A:MN508 4.3 113.7 1.0
O12 A:661502 4.3 49.0 1.0
MN A:MN507 4.3 27.8 0.6
CA A:GLY418 4.3 32.4 1.0
CB A:ASP416 4.4 27.0 1.0
N A:GLY418 4.5 30.5 1.0
O18 A:661502 4.5 44.7 1.0
NZ A:LYS419 4.6 40.8 1.0
O A:HOH618 4.6 40.3 1.0
O3B A:ADP501 4.6 46.2 1.0
O3A A:ADP501 4.6 34.0 1.0
CE A:LYS209 4.7 35.2 1.0
CA A:ASP416 4.9 26.5 1.0

Manganese binding site 4 out of 4 in 8ppj

Go back to Manganese Binding Sites List in 8ppj
Manganese binding site 4 out of 4 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,6,1'- 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 4 of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with Beta-D-Glucopyranosylmethanol 3,4,6,1'- Tetrakisphosphate/Adp/Mn After Reaction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn507

b:36.3
occ:0.50
 OD2 B:ASP416 1.9 34.6 1.0
O1A B:ADP501 2.1 39.5 1.0
O1B B:ADP501 2.3 49.3 1.0
O B:HOH648 2.4 33.6 1.0
O16 B:661502 2.6 69.4 1.0
CG B:ASP416 3.0 33.8 1.0
PA B:ADP501 3.4 38.2 1.0
PB B:ADP501 3.5 50.2 1.0
CB B:ASP416 3.5 30.7 1.0
O3A B:ADP501 3.7 47.6 1.0
O B:HOH609 3.8 51.7 1.0
P6 B:661502 3.9 77.5 1.0
O B:HOH605 4.0 52.6 1.0
O B:HOH709 4.0 45.6 1.0
OD1 B:ASP416 4.1 35.3 1.0
O B:GLY397 4.1 32.7 1.0
O2B B:ADP501 4.1 53.6 1.0
O2A B:ADP501 4.2 38.3 1.0
O18 B:661502 4.3 70.8 1.0
O17 B:661502 4.4 65.9 1.0
O5' B:ADP501 4.6 37.0 1.0
OG B:SER399 4.7 29.3 1.0
O3B B:ADP501 4.7 53.7 1.0
C5' B:ADP501 4.9 37.5 1.0
CA B:ASP416 5.0 29.1 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 13:34:25 2024

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