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Magnesium in PDB 3t9f: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8)

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8)

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8):
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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8), PDB code: 3t9f 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) 38.82 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.036, 110.009, 41.484, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.4

Other elements in 3t9f:

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8) also contains other interesting chemical elements:

Cadmium (Cd) 1 atom

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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8) (pdb code 3t9f). 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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8), PDB code: 3t9f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3t9f

Go back to Magnesium Binding Sites List in 3t9f
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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8)


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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:7.0
occ:1.00
 OD2 A:ASP309 2.0 11.9 1.0
O3B A:ADP401 2.1 6.4 1.0
O2A A:ADP401 2.1 10.9 1.0
OD2 A:ASP321 2.1 7.1 1.0
O A:HOH22 2.1 9.1 1.0
O61 A:I8P501 2.2 21.1 1.0
CG A:ASP321 3.2 6.2 1.0
CG A:ASP309 3.2 12.0 1.0
PB A:ADP401 3.3 9.1 1.0
PA A:ADP401 3.3 7.3 1.0
PB1 A:I8P501 3.4 27.6 1.0
CB A:ASP321 3.6 6.4 1.0
O3A A:ADP401 3.6 8.6 1.0
O51 A:I8P501 3.8 18.1 1.0
CD A:CD601 3.8 13.4 1.0
O A:HOH447 3.8 19.0 1.0
O71 A:I8P501 3.9 24.6 1.0
OD1 A:ASP309 3.9 13.9 1.0
O2B A:ADP401 3.9 7.2 1.0
NZ A:LYS248 3.9 15.8 1.0
O3' A:ADP401 4.2 10.9 1.0
ND2 A:ASN323 4.2 8.5 1.0
OD1 A:ASP321 4.2 6.1 1.0
C5' A:ADP401 4.3 7.9 1.0
O5' A:ADP401 4.3 10.0 1.0
CB A:ASP309 4.4 8.0 1.0
O1A A:ADP401 4.4 10.1 1.0
O A:HOH698 4.4 26.5 1.0
O1B A:ADP401 4.6 11.4 1.0
C3' A:ADP401 4.6 10.1 1.0
NH2 A:ARG262 4.9 19.3 1.0
O41 A:I8P501 4.9 25.9 1.0
OD1 A:ASN323 4.9 10.5 1.0

Magnesium binding site 2 out of 5 in 3t9f

Go back to Magnesium Binding Sites List in 3t9f
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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8)


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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:19.5
occ:1.00
 O A:ILE73 2.1 14.3 1.0
O A:HOH556 2.3 24.6 1.0
O A:SER68 2.4 15.1 1.0
O A:PHE70 2.4 16.3 1.0
O A:HOH508 2.8 23.0 1.0
C A:ILE73 3.3 14.2 1.0
C A:SER68 3.3 15.0 1.0
C A:PHE70 3.5 17.1 1.0
N A:ILE73 3.9 15.7 1.0
CA A:SER68 3.9 14.3 1.0
CA A:ILE73 4.1 14.5 1.0
N A:PHE70 4.1 16.6 1.0
NE2 A:GLN43 4.2 26.7 1.0
O A:LYS71 4.2 18.8 1.0
C A:LYS71 4.3 18.1 1.0
N A:THR74 4.3 14.1 1.0
C A:LEU69 4.4 17.3 1.0
CA A:PHE70 4.4 16.6 1.0
N A:LEU69 4.4 15.6 1.0
N A:LYS71 4.4 18.3 1.0
CA A:LYS71 4.5 19.0 1.0
CB A:ILE73 4.5 14.1 1.0
O A:ILE67 4.5 12.9 1.0
CA A:THR74 4.6 14.5 1.0
CB A:SER68 4.6 14.5 1.0
CA A:LEU69 4.7 17.3 1.0
N A:TYR72 4.8 17.9 1.0
O A:LEU69 4.8 18.1 1.0
O A:HOH654 4.9 31.4 1.0
C A:TYR72 5.0 17.0 1.0
CB A:PHE70 5.0 15.5 1.0

Magnesium binding site 3 out of 5 in 3t9f

Go back to Magnesium Binding Sites List in 3t9f
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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8)


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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:22.1
occ:1.00
 O A:HOH610 2.0 23.1 1.0
O35 A:I8P501 2.1 18.9 1.0
O A:HOH549 2.1 17.0 1.0
O A:HOH369 2.1 19.3 1.0
O44 A:I8P501 2.1 24.9 1.0
O A:HOH534 2.2 20.6 1.0
PA5 A:I8P501 3.2 21.1 1.0
PA4 A:I8P501 3.3 24.4 1.0
O25 A:I8P501 3.5 18.6 1.0
O14 A:I8P501 3.8 23.4 1.0
O A:HOH674 3.8 35.7 1.0
O34 A:I8P501 4.0 24.8 1.0
O75 A:I8P501 4.1 23.9 1.0
O A:HOH650 4.1 37.4 1.0
O A:HOH631 4.1 33.3 1.0
O15 A:I8P501 4.2 19.6 1.0
O A:HOH692 4.3 27.8 1.0
O A:HOH683 4.3 26.4 1.0
O45 A:I8P501 4.4 21.7 1.0
O A:LYS214 4.4 15.2 1.0
PB5 A:I8P501 4.6 25.1 1.0
O24 A:I8P501 4.7 24.6 1.0
O A:HOH652 4.8 33.8 1.0
C4 A:I8P501 4.8 20.5 1.0
O55 A:I8P501 4.9 25.3 1.0
C5 A:I8P501 4.9 20.6 1.0

Magnesium binding site 4 out of 5 in 3t9f

Go back to Magnesium Binding Sites List in 3t9f
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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8)


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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:34.2
occ:1.00
 O A:HOH517 2.1 25.0 1.0
O A:HOH599 2.2 28.8 1.0
O A:HOH524 2.2 21.1 1.0
O A:HOH483 2.3 20.7 1.0
O A:HOH480 2.4 20.1 1.0
O A:HOH700 2.4 28.2 1.0
O A:ASN323 3.7 10.4 1.0
O A:HOH594 3.8 26.0 1.0
O A:HOH545 4.0 26.7 1.0
O32 A:I8P501 4.1 28.8 1.0
O A:HOH555 4.2 17.4 1.0
O33 A:I8P501 4.3 17.1 1.0
O A:HIS101 4.4 12.3 1.0
O A:HOH608 4.4 20.8 1.0
OE1 A:GLU192 4.5 26.9 1.0
O A:HOH416 4.6 15.7 1.0
O21 A:I8P501 4.6 28.7 1.0
O A:HOH622 4.6 26.8 1.0
O A:PHE325 4.7 10.6 1.0
C A:ASN323 4.8 9.3 1.0
CB A:ASN323 4.9 9.7 1.0
O42 A:I8P501 4.9 27.5 1.0
O A:HOH410 5.0 23.9 1.0

Magnesium binding site 5 out of 5 in 3t9f

Go back to Magnesium Binding Sites List in 3t9f
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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8)


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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:17.7
occ:1.00
 OG1 A:THR251 2.0 8.7 1.0
O A:GLN303 2.2 9.9 1.0
O A:THR304 2.6 6.7 1.0
SG A:CYS298 2.8 15.2 1.0
CB A:CYS306 2.9 10.9 1.0
C A:THR304 3.1 7.6 1.0
CB A:CYS298 3.2 10.6 1.0
CB A:THR251 3.3 8.3 1.0
N A:CYS306 3.3 9.1 1.0
C A:GLN303 3.4 8.7 1.0
CA A:CYS298 3.6 9.9 1.0
CA A:CYS306 3.7 10.1 1.0
CA A:THR304 3.7 7.7 1.0
N A:VAL305 3.8 7.7 1.0
C A:VAL305 3.8 9.1 1.0
N A:THR304 4.0 8.8 1.0
CG2 A:THR251 4.1 8.6 1.0
CA A:VAL305 4.1 7.9 1.0
O A:THR251 4.3 6.0 1.0
C A:THR251 4.3 7.4 1.0
CA A:THR251 4.4 7.9 1.0
SG A:CYS306 4.4 16.2 1.0
O A:CYS306 4.4 10.0 1.0
N A:GLY253 4.4 8.1 1.0
O A:VAL305 4.6 9.6 1.0
CA A:GLN303 4.6 8.8 1.0
C A:CYS306 4.6 9.7 1.0
C A:CYS298 4.6 9.7 1.0
N A:CYS298 4.6 8.6 1.0
CB A:GLN303 4.6 8.3 1.0
O A:CYS298 4.7 10.2 1.0
O A:GLY253 4.7 8.5 1.0
C A:GLY253 4.9 9.5 1.0
CA A:GLY253 4.9 8.8 1.0
N A:VAL252 4.9 6.8 1.0
N A:THR251 4.9 8.2 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 11:59:52 2024

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