Atomistry » Magnesium » PDB 3t2c-3taq » 3t9d
Atomistry »
  Magnesium »
    PDB 3t2c-3taq »
      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: Mon Dec 14 08:53:51 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy