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Magnesium in PDB 3t9a: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0:
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 at pH 7.0, PDB code: 3t9a 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) 38.80 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.134, 110.504, 41.437, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.6

Other elements in 3t9a:

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0 also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms

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 at pH 7.0 (pdb code 3t9a). 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 at pH 7.0, PDB code: 3t9a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3t9a

Go back to Magnesium Binding Sites List in 3t9a
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 at pH 7.0


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 at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:7.6
occ:1.00
 O A:HOH591 1.9 16.7 1.0
O3G A:ANP401 2.0 14.6 1.0
O2B A:ANP401 2.1 14.5 1.0
OD1 A:ASN323 2.1 15.5 1.0
OD1 A:ASP321 2.3 12.0 1.0
OD2 A:ASP321 2.3 13.2 1.0
CG A:ASP321 2.7 11.6 1.0
PG A:ANP401 3.1 16.6 1.0
CG A:ASN323 3.2 13.2 1.0
PB A:ANP401 3.2 14.4 1.0
N3B A:ANP401 3.5 15.1 1.0
O1G A:ANP401 3.6 15.5 1.0
ND2 A:ASN323 3.6 14.6 1.0
O A:HOH592 3.7 23.9 1.0
MG A:MG602 3.9 13.4 1.0
CB A:ASP321 4.2 11.7 1.0
O1B A:ANP401 4.2 17.5 1.0
NH1 A:ARG134 4.4 12.2 0.7
O2G A:ANP401 4.4 14.7 1.0
O3A A:ANP401 4.4 14.4 1.0
O A:HOH456 4.5 34.4 1.0
O A:ALA191 4.5 19.1 1.0
CE1 A:HIS194 4.5 21.3 1.0
CB A:ASN323 4.5 14.2 1.0
O2A A:ANP401 4.6 11.4 1.0
NH2 A:ARG134 4.6 15.5 0.3
O A:HOH14 4.7 17.6 1.0
ND1 A:HIS194 4.8 20.0 1.0
O A:HOH402 4.8 30.2 1.0
CA A:ASN323 4.9 13.9 1.0
PA A:ANP401 4.9 14.4 1.0
O A:VAL322 5.0 13.2 1.0

Magnesium binding site 2 out of 4 in 3t9a

Go back to Magnesium Binding Sites List in 3t9a
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 at pH 7.0


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 at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:13.4
occ:1.00
 O1G A:ANP401 2.0 15.5 1.0
OD2 A:ASP309 2.0 18.2 1.0
O2A A:ANP401 2.0 11.4 1.0
O A:HOH380 2.0 19.3 1.0
OD2 A:ASP321 2.1 13.2 1.0
N3B A:ANP401 3.0 15.1 1.0
PG A:ANP401 3.0 16.6 1.0
CG A:ASP321 3.1 11.6 1.0
CG A:ASP309 3.2 16.3 1.0
PA A:ANP401 3.4 14.4 1.0
CB A:ASP321 3.5 11.7 1.0
O3G A:ANP401 3.8 14.6 1.0
PB A:ANP401 3.8 14.4 1.0
O3A A:ANP401 3.9 14.4 1.0
MG A:MG601 3.9 7.6 1.0
OD1 A:ASP309 3.9 19.0 1.0
O A:HOH607 3.9 40.0 1.0
O2B A:ANP401 3.9 14.5 1.0
O A:HOH708 4.0 30.3 1.0
ND2 A:ASN323 4.0 14.6 1.0
O3' A:ANP401 4.2 16.2 1.0
OD1 A:ASP321 4.2 12.0 1.0
O2G A:ANP401 4.2 14.7 1.0
CB A:ASP309 4.2 13.5 1.0
NZ A:LYS248 4.2 25.7 1.0
O1A A:ANP401 4.3 12.8 1.0
O5' A:ANP401 4.4 15.4 1.0
C5' A:ANP401 4.5 14.8 1.0
C3' A:ANP401 4.7 16.5 1.0
OD1 A:ASN323 4.8 15.5 1.0
CG A:ASN323 4.9 13.2 1.0

Magnesium binding site 3 out of 4 in 3t9a

Go back to Magnesium Binding Sites List in 3t9a
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 at pH 7.0


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 at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:43.9
occ:1.00
 O A:ILE73 2.2 25.6 1.0
O A:HOH553 2.3 40.5 1.0
O A:SER68 2.4 27.0 1.0
O A:PHE70 2.5 27.7 1.0
O A:HOH373 2.5 46.7 1.0
O A:HOH489 2.8 51.5 1.0
C A:ILE73 3.4 25.4 1.0
C A:SER68 3.4 26.1 1.0
C A:PHE70 3.6 28.4 1.0
CA A:SER68 3.8 25.5 1.0
N A:ILE73 3.9 26.4 1.0
CA A:ILE73 4.1 25.6 1.0
O A:LYS71 4.1 30.3 1.0
OE1 A:GLN43 4.2 39.1 1.0
C A:LYS71 4.3 29.5 1.0
N A:PHE70 4.3 27.4 1.0
N A:THR74 4.4 25.4 1.0
N A:LEU69 4.5 26.7 1.0
CB A:SER68 4.5 24.8 1.0
N A:LYS71 4.5 28.8 1.0
C A:LEU69 4.6 27.6 1.0
CA A:PHE70 4.6 27.5 1.0
CA A:LYS71 4.6 30.0 1.0
CB A:ILE73 4.6 25.2 1.0
O A:ILE67 4.6 23.2 1.0
CA A:THR74 4.7 25.6 1.0
N A:TYR72 4.8 28.9 1.0
O A:HOH679 4.8 38.2 1.0
O A:HOH388 4.8 33.5 1.0
CA A:LEU69 4.9 27.7 1.0
C A:TYR72 4.9 27.4 1.0
NE2 A:GLN43 4.9 39.5 1.0
CD A:GLN43 5.0 37.3 1.0

Magnesium binding site 4 out of 4 in 3t9a

Go back to Magnesium Binding Sites List in 3t9a
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 at pH 7.0


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 at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:16.4
occ:1.00
 OG1 A:THR251 1.8 18.0 1.0
O A:GLN303 2.3 15.2 1.0
SG A:CYS306 2.4 15.5 0.2
O A:THR304 2.5 16.1 1.0
SG A:CYS298 2.8 19.6 1.0
CB A:CYS306 3.1 16.2 0.8
C A:THR304 3.1 15.5 1.0
CB A:CYS298 3.2 15.9 1.0
CB A:THR251 3.2 16.4 1.0
N A:CYS306 3.2 15.4 1.0
CB A:CYS306 3.4 15.6 0.2
C A:GLN303 3.5 15.2 1.0
CA A:CYS298 3.6 15.9 1.0
CA A:CYS306 3.7 16.1 0.8
C A:VAL305 3.8 15.6 1.0
CA A:THR304 3.8 15.7 1.0
CA A:CYS306 3.8 15.7 0.2
N A:VAL305 3.8 15.3 1.0
CG2 A:THR251 3.9 16.7 1.0
CA A:VAL305 4.1 15.1 1.0
N A:THR304 4.1 15.1 1.0
C A:THR251 4.2 15.9 1.0
O A:THR251 4.2 14.9 1.0
CA A:THR251 4.2 16.1 1.0
N A:GLY253 4.4 16.2 1.0
O A:CYS306 4.4 17.3 1.0
O A:VAL305 4.6 14.8 1.0
C A:CYS306 4.6 15.9 1.0
SG A:CYS306 4.6 19.6 0.8
O A:GLY253 4.6 16.6 1.0
C A:CYS298 4.6 16.2 1.0
N A:CYS298 4.6 14.7 1.0
CA A:GLN303 4.7 14.6 1.0
N A:VAL252 4.7 15.8 1.0
O A:CYS298 4.7 15.8 1.0
CB A:GLN303 4.8 14.5 1.0
C A:GLY253 4.8 17.4 1.0
CA A:GLY253 4.9 16.6 1.0
N A:THR251 4.9 15.7 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 11:57:47 2024

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