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Magnesium in PDB 3t9c: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6)

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6)

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6):
2.7.4.24;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6), PDB code: 3t9c was solved by H.Wang, J.Falck, T.M.T.Hall, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.55 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.037, 110.489, 41.339, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6) (pdb code 3t9c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6), PDB code: 3t9c:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3t9c

Go back to Magnesium Binding Sites List in 3t9c
Magnesium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:14.6
occ:1.00
 O A:HOH13 1.9 15.4 1.0
O3G A:ANP401 1.9 13.8 1.0
ND2 A:ASN323 2.0 9.6 1.0
O2B A:ANP401 2.1 12.6 1.0
OD2 A:ASP321 2.1 14.7 1.0
OD1 A:ASP321 2.4 13.9 1.0
CG A:ASP321 2.6 12.4 1.0
PG A:ANP401 3.2 18.2 1.0
CG A:ASN323 3.2 11.9 1.0
PB A:ANP401 3.3 13.1 1.0
OD1 A:ASN323 3.6 14.9 1.0
N3B A:ANP401 3.6 15.0 1.0
O1G A:ANP401 3.7 15.9 1.0
O A:HOH609 3.9 18.4 1.0
MG A:MG602 3.9 20.0 1.0
CB A:ASP321 4.1 9.7 1.0
O1B A:ANP401 4.3 12.9 1.0
O A:HOH477 4.3 21.4 1.0
NH1 A:ARG134 4.4 11.4 0.9
O A:ALA191 4.4 13.2 1.0
O2G A:ANP401 4.4 17.5 1.0
CB A:ASN323 4.4 11.0 1.0
CE1 A:HIS194 4.4 12.6 1.0
O3A A:ANP401 4.5 12.7 1.0
O2A A:ANP401 4.5 13.6 1.0
O A:HOH496 4.6 21.8 1.0
NH2 A:ARG134 4.6 9.6 0.1
O A:HOH520 4.7 20.7 1.0
ND1 A:HIS194 4.7 12.7 1.0
CA A:ASN323 4.8 11.3 1.0
PA A:ANP401 4.9 12.7 1.0
O A:HOH531 4.9 18.8 1.0

Magnesium binding site 2 out of 4 in 3t9c

Go back to Magnesium Binding Sites List in 3t9c
Magnesium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:20.0
occ:1.00
 OD2 A:ASP309 1.9 17.3 1.0
O1G A:ANP401 1.9 15.9 1.0
O2A A:ANP401 2.0 13.6 1.0
O A:HOH484 2.2 21.6 1.0
OD2 A:ASP321 2.3 14.7 1.0
PG A:ANP401 2.9 18.2 1.0
N3B A:ANP401 3.0 15.0 1.0
CG A:ASP309 3.2 14.1 1.0
CG A:ASP321 3.2 12.4 1.0
PA A:ANP401 3.4 12.7 1.0
CB A:ASP321 3.4 9.7 1.0
O3G A:ANP401 3.7 13.8 1.0
PB A:ANP401 3.8 13.1 1.0
O2B A:ANP401 3.8 12.6 1.0
O3A A:ANP401 3.9 12.7 1.0
MG A:MG601 3.9 14.6 1.0
OD1 A:ASP309 3.9 17.1 1.0
OD1 A:ASN323 4.1 14.9 1.0
CB A:ASP309 4.1 10.8 1.0
O2G A:ANP401 4.2 17.5 1.0
NZ A:LYS248 4.2 23.4 1.0
O3' A:ANP401 4.3 13.6 1.0
OD1 A:ASP321 4.3 13.9 1.0
O1A A:ANP401 4.4 12.5 1.0
NH2 A:ARG262 4.4 19.9 0.5
O5' A:ANP401 4.4 11.5 1.0
C5' A:ANP401 4.5 12.3 1.0
ND2 A:ASN323 4.7 9.6 1.0
C3' A:ANP401 4.8 13.4 1.0
CG A:ASN323 4.8 11.9 1.0
O A:HOH728 4.9 21.1 1.0
CA A:ASP321 5.0 9.5 1.0

Magnesium binding site 3 out of 4 in 3t9c

Go back to Magnesium Binding Sites List in 3t9c
Magnesium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:19.5
occ:1.00
 O A:ILE73 2.3 13.4 1.0
O A:SER68 2.3 15.2 1.0
O A:HOH513 2.3 21.6 1.0
O A:HOH749 2.4 42.8 1.0
O A:PHE70 2.4 16.0 1.0
O A:HOH535 2.6 22.9 1.0
C A:SER68 3.3 15.2 1.0
C A:ILE73 3.4 13.7 1.0
O A:HOH663 3.5 41.9 1.0
C A:PHE70 3.5 16.1 1.0
CA A:SER68 3.9 14.3 1.0
N A:ILE73 4.0 14.4 1.0
OE1 A:GLN43 4.0 31.6 1.0
O A:LYS71 4.1 17.4 1.0
CA A:ILE73 4.2 14.1 1.0
N A:PHE70 4.2 15.8 1.0
C A:LYS71 4.2 16.7 1.0
N A:LEU69 4.4 16.1 1.0
C A:LEU69 4.4 16.6 1.0
N A:LYS71 4.4 16.6 1.0
CA A:LYS71 4.4 17.8 1.0
CA A:PHE70 4.4 15.7 1.0
N A:THR74 4.5 13.8 1.0
O A:HOH18 4.5 15.9 1.0
O A:HOH658 4.6 39.3 1.0
O A:HOH577 4.6 33.1 1.0
CB A:SER68 4.6 14.7 1.0
CB A:ILE73 4.6 13.4 1.0
O A:ILE67 4.7 13.9 1.0
CA A:LEU69 4.7 16.5 1.0
CA A:THR74 4.8 13.9 1.0
N A:TYR72 4.8 16.4 1.0
O A:LEU69 4.9 17.0 1.0

Magnesium binding site 4 out of 4 in 3t9c

Go back to Magnesium Binding Sites List in 3t9c
Magnesium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and Inositol Hexakisphosphate (IP6) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:25.4
occ:1.00
 O A:HOH430 2.1 21.5 1.0
O A:HOH488 2.1 18.0 1.0
O A:HOH462 2.1 20.1 1.0
O A:HOH478 2.2 18.1 1.0
O A:HOH476 2.2 18.3 1.0
O A:HOH531 2.2 18.8 1.0
O A:ASN323 3.9 13.1 1.0
O A:HOH30 4.0 14.1 1.0
O33 A:IHP501 4.3 22.2 1.0
O A:HOH609 4.3 18.4 1.0
O A:HOH727 4.3 16.3 1.0
O A:HOH477 4.3 21.4 1.0
O42 A:IHP501 4.3 28.3 1.0
O A:HIS101 4.3 12.2 1.0
OE1 A:GLU192 4.5 23.1 1.0
O A:HOH446 4.5 19.7 1.0
O A:PHE325 4.6 11.1 1.0
O A:HOH532 4.7 22.2 1.0
O31 A:IHP501 4.7 41.4 1.0
CB A:ASN323 4.9 11.0 1.0
C A:ASN323 4.9 11.8 1.0
CB A:SER102 5.0 13.1 1.0

Reference:

H.Wang, J.R.Falck, T.M.Hall, S.B.Shears. Structural Basis For An Inositol Pyrophosphate Kinase Surmounting Phosphate Crowding. Nat.Chem.Biol. V. 8 111 2011.
ISSN: ISSN 1552-4450
PubMed: 22119861
DOI: 10.1038/NCHEMBIO.733
Page generated: Thu Aug 15 11:58:48 2024

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