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Magnesium in PDB 3t9d: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and 5- (Pp)-IP5 (5-IP7)

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and 5- (Pp)-IP5 (5-IP7)

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and 5- (Pp)-IP5 (5-IP7):
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 5- (Pp)-IP5 (5-IP7), PDB code: 3t9d 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) 41.36 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.204, 110.461, 41.482, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22

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 5- (Pp)-IP5 (5-IP7) (pdb code 3t9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 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 5- (Pp)-IP5 (5-IP7), PDB code: 3t9d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3t9d

Go back to Magnesium Binding Sites List in 3t9d
Magnesium binding site 1 out of 5 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and 5- (Pp)-IP5 (5-IP7)


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 5- (Pp)-IP5 (5-IP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:2.1
occ:1.00
 O3G A:ANP401 1.8 19.8 1.0
O A:HOH587 1.9 18.6 1.0
O2B A:ANP401 2.1 15.7 1.0
ND2 A:ASN323 2.1 12.5 1.0
OD2 A:ASP321 2.2 17.1 1.0
OD1 A:ASP321 2.5 19.2 1.0
CG A:ASP321 2.7 14.6 1.0
PG A:ANP401 3.2 23.6 1.0
CG A:ASN323 3.2 13.1 1.0
PB A:ANP401 3.3 14.4 1.0
OD1 A:ASN323 3.6 17.0 1.0
N3B A:ANP401 3.7 17.8 1.0
O1G A:ANP401 3.7 22.5 1.0
O A:HOH586 3.8 25.7 1.0
MG A:MG602 3.9 13.8 1.0
CB A:ASP321 4.2 12.5 1.0
O A:HOH477 4.3 27.9 1.0
O2G A:ANP401 4.3 23.0 1.0
O1B A:ANP401 4.3 16.9 1.0
O A:ALA191 4.4 14.9 1.0
CE1 A:HIS194 4.5 14.7 1.0
CB A:ASN323 4.5 12.2 1.0
O3A A:ANP401 4.5 14.3 1.0
NH1 A:ARG134 4.5 11.3 0.7
O A:HOH397 4.6 24.9 1.0
NH2 A:ARG134 4.6 7.5 0.3
O2A A:ANP401 4.7 12.4 1.0
ND1 A:HIS194 4.7 14.8 1.0
O A:HOH412 4.9 25.6 1.0
O A:HOH645 4.9 30.6 1.0
CA A:ASN323 4.9 12.0 1.0
O A:VAL322 4.9 11.2 1.0

Magnesium binding site 2 out of 5 in 3t9d

Go back to Magnesium Binding Sites List in 3t9d
Magnesium binding site 2 out of 5 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and 5- (Pp)-IP5 (5-IP7)


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 5- (Pp)-IP5 (5-IP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:13.8
occ:1.00
 OD2 A:ASP309 1.9 20.5 1.0
O1G A:ANP401 1.9 22.5 1.0
O2A A:ANP401 2.0 12.4 1.0
O A:HOH514 2.2 31.5 1.0
OD2 A:ASP321 2.2 17.1 1.0
PG A:ANP401 2.9 23.6 1.0
N3B A:ANP401 3.0 17.8 1.0
CG A:ASP309 3.1 16.8 1.0
CG A:ASP321 3.1 14.6 1.0
PA A:ANP401 3.3 11.7 1.0
CB A:ASP321 3.4 12.5 1.0
O3G A:ANP401 3.6 19.8 1.0
PB A:ANP401 3.7 14.4 1.0
O2B A:ANP401 3.7 15.7 1.0
O3A A:ANP401 3.8 14.3 1.0
OD1 A:ASP309 3.9 22.9 1.0
MG A:MG601 3.9 2.1 1.0
NZ A:LYS248 4.1 25.9 1.0
CB A:ASP309 4.2 11.9 1.0
O1A A:ANP401 4.2 12.0 1.0
OD1 A:ASN323 4.2 17.0 1.0
O2G A:ANP401 4.2 23.0 1.0
O3' A:ANP401 4.2 14.6 1.0
OD1 A:ASP321 4.3 19.2 1.0
O5' A:ANP401 4.4 9.8 1.0
C5' A:ANP401 4.5 12.9 1.0
C3' A:ANP401 4.7 14.5 1.0
ND2 A:ASN323 4.9 12.5 1.0
NH2 A:ARG262 4.9 35.5 1.0
CA A:ASP321 4.9 11.9 1.0
O A:HOH647 4.9 44.3 1.0
CG A:ASN323 5.0 13.1 1.0

Magnesium binding site 3 out of 5 in 3t9d

Go back to Magnesium Binding Sites List in 3t9d
Magnesium binding site 3 out of 5 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and 5- (Pp)-IP5 (5-IP7)


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 5- (Pp)-IP5 (5-IP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:19.8
occ:1.00
 O A:ILE73 2.3 14.2 1.0
O A:SER68 2.3 16.3 1.0
O A:PHE70 2.3 16.8 1.0
O A:HOH537 2.3 40.2 1.0
O A:HOH492 2.4 26.4 1.0
O A:HOH646 2.7 28.5 1.0
C A:SER68 3.3 16.3 1.0
C A:ILE73 3.4 14.8 1.0
C A:PHE70 3.5 17.7 1.0
CA A:SER68 3.9 15.9 1.0
N A:ILE73 4.0 15.8 1.0
O A:LYS71 4.1 18.7 1.0
N A:PHE70 4.2 17.6 1.0
CA A:ILE73 4.2 15.1 1.0
C A:LYS71 4.2 18.6 1.0
NE2 A:GLN43 4.2 28.9 1.0
C A:LEU69 4.4 17.9 1.0
CA A:PHE70 4.4 17.1 1.0
N A:LYS71 4.4 18.4 1.0
N A:LEU69 4.4 16.9 1.0
CA A:LYS71 4.4 19.3 1.0
N A:THR74 4.5 14.5 1.0
CB A:ILE73 4.7 15.2 1.0
O A:ILE67 4.7 14.4 1.0
CB A:SER68 4.7 15.8 1.0
O A:HOH590 4.7 19.6 1.0
CA A:LEU69 4.7 17.6 1.0
N A:TYR72 4.7 18.0 1.0
CA A:THR74 4.8 15.2 1.0
O A:LEU69 4.8 18.0 1.0
O A:HOH581 4.9 33.1 1.0
CB A:PHE70 4.9 16.6 1.0
C A:TYR72 5.0 16.8 1.0

Magnesium binding site 4 out of 5 in 3t9d

Go back to Magnesium Binding Sites List in 3t9d
Magnesium binding site 4 out of 5 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and 5- (Pp)-IP5 (5-IP7)


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 5- (Pp)-IP5 (5-IP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:36.8
occ:1.00
 O44 A:I7P501 2.1 36.5 1.0
O35 A:I7P501 2.1 35.2 1.0
O A:HOH533 2.2 34.5 1.0
O A:HOH672 2.2 36.3 1.0
O A:HOH560 2.3 37.1 1.0
O A:HOH509 2.3 25.7 1.0
PA5 A:I7P501 3.2 36.6 1.0
PA4 A:I7P501 3.3 35.5 1.0
O25 A:I7P501 3.4 33.9 1.0
O14 A:I7P501 3.8 33.7 1.0
O34 A:I7P501 3.9 34.0 1.0
O55 A:I7P501 4.1 41.5 1.0
O15 A:I7P501 4.2 34.0 1.0
O45 A:I7P501 4.4 38.5 1.0
O A:LYS214 4.4 20.8 1.0
O24 A:I7P501 4.7 36.0 1.0
PB5 A:I7P501 4.7 43.0 1.0
O A:HOH623 4.8 42.1 1.0
C4 A:I7P501 4.8 31.8 1.0
O75 A:I7P501 4.9 41.6 1.0
C5 A:I7P501 4.9 33.5 1.0

Magnesium binding site 5 out of 5 in 3t9d

Go back to Magnesium Binding Sites List in 3t9d
Magnesium binding site 5 out of 5 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and 5- (Pp)-IP5 (5-IP7)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and 5- (Pp)-IP5 (5-IP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:27.1
occ:1.00
 O A:HOH404 2.1 22.5 1.0
O A:HOH488 2.2 29.8 1.0
O A:HOH645 2.2 30.6 1.0
O A:HOH463 2.2 23.7 1.0
O A:HOH390 2.2 21.8 1.0
O A:HOH526 2.2 37.6 1.0
O A:ASN323 3.9 13.8 1.0
O A:HOH424 4.0 22.1 1.0
O22 A:I7P501 4.1 27.9 1.0
O33 A:I7P501 4.2 24.1 1.0
O A:HOH586 4.2 25.7 1.0
O A:HOH452 4.2 28.7 1.0
O A:HOH477 4.3 27.9 1.0
O A:HIS101 4.4 14.4 1.0
O A:HOH577 4.4 32.0 1.0
O A:PHE325 4.5 11.6 1.0
O A:HOH387 4.5 20.5 1.0
OE1 A:GLU192 4.6 29.2 1.0
O32 A:I7P501 4.7 30.4 1.0
O31 A:I7P501 4.9 35.5 1.0
C A:ASN323 4.9 12.5 1.0
CB A:ASN323 4.9 12.2 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 11:59:46 2024

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