Atomistry » Magnesium » PDB 3t2d-3tar » 3t9d
Atomistry »
  Magnesium »
    PDB 3t2d-3tar »
      3t9d »

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

Last articles

As in 4NLU
As in 4NLW
As in 4NLV
As in 4NLT
As in 4NLS
As in 4NLR
As in 4NLQ
As in 4NGE
As in 4NLP
As in 4NLO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy