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Magnesium in PDB 5dgh: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (Pcp)-IP5

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (Pcp)-IP5

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (Pcp)-IP5:
2.7.4.21; 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 Amp-Pnp and 5- (Pcp)-IP5, PDB code: 5dgh was solved by H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.04 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.900, 110.340, 41.253, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.1

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 Amp-Pnp and 5- (Pcp)-IP5 (pdb code 5dgh). 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 Amp-Pnp and 5- (Pcp)-IP5, PDB code: 5dgh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5dgh

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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 Amp-Pnp and 5- (Pcp)-IP5


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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:16.4
occ:1.00
 O A:HOH563 1.9 21.5 1.0
O1B A:ANP401 2.0 16.7 1.0
O3G A:ANP401 2.1 19.4 1.0
OD1 A:ASN323 2.2 14.6 1.0
OD2 A:ASP321 2.2 15.2 1.0
OD1 A:ASP321 2.2 14.9 1.0
CG A:ASP321 2.5 14.0 1.0
PG A:ANP401 3.2 20.4 1.0
CG A:ASN323 3.2 13.6 1.0
PB A:ANP401 3.3 18.2 1.0
N3B A:ANP401 3.6 18.1 1.0
ND2 A:ASN323 3.7 12.9 1.0
O1G A:ANP401 3.8 18.7 1.0
MG A:MG404 3.9 16.3 1.0
O A:HOH533 3.9 28.5 1.0
CB A:ASP321 4.0 13.2 1.0
NH1 A:ARG134 4.2 17.8 1.0
O A:ALA191 4.3 17.5 1.0
O2B A:ANP401 4.3 17.2 1.0
CE1 A:HIS194 4.3 15.0 1.0
O A:HOH740 4.4 28.9 1.0
O3A A:ANP401 4.4 18.7 1.0
O2A A:ANP401 4.5 18.1 1.0
O2G A:ANP401 4.5 19.2 1.0
O A:HOH613 4.5 13.4 1.0
CB A:ASN323 4.5 12.3 1.0
O A:HOH510 4.6 19.2 1.0
ND1 A:HIS194 4.7 14.1 1.0
PA A:ANP401 4.8 18.5 1.0
CA A:ASN323 4.8 12.2 1.0
NH2 A:ARG134 4.9 15.8 1.0
CA A:ASP321 5.0 12.3 1.0
CZ A:ARG134 5.0 16.6 1.0

Magnesium binding site 2 out of 5 in 5dgh

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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 Amp-Pnp and 5- (Pcp)-IP5


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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:16.3
occ:1.00
 O2A A:ANP401 2.0 18.1 1.0
O1G A:ANP401 2.0 18.7 1.0
O A:HOH574 2.0 22.9 1.0
OD2 A:ASP309 2.1 16.3 1.0
OD2 A:ASP321 2.2 15.2 1.0
N3B A:ANP401 2.8 18.1 1.0
PG A:ANP401 2.9 20.4 1.0
CG A:ASP321 3.2 14.0 1.0
CG A:ASP309 3.3 14.6 1.0
PA A:ANP401 3.3 18.5 1.0
CB A:ASP321 3.5 13.2 1.0
O3G A:ANP401 3.7 19.4 1.0
PB A:ANP401 3.7 18.2 1.0
O1B A:ANP401 3.8 16.7 1.0
O3A A:ANP401 3.9 18.7 1.0
MG A:MG403 3.9 16.4 1.0
OD1 A:ASP309 4.0 14.5 1.0
ND2 A:ASN323 4.1 12.9 1.0
O A:HOH501 4.1 30.5 1.0
O2G A:ANP401 4.2 19.2 1.0
O3' A:ANP401 4.2 18.2 1.0
CB A:ASP309 4.2 13.5 1.0
OD1 A:ASP321 4.3 14.9 1.0
O1A A:ANP401 4.3 18.7 1.0
O5' A:ANP401 4.4 18.8 1.0
C5' A:ANP401 4.5 18.7 1.0
NZ A:LYS248 4.5 24.9 1.0
OD1 A:ASN323 4.7 14.6 1.0
C3' A:ANP401 4.8 18.0 1.0
CG A:ASN323 4.9 13.6 1.0
O A:HOH708 5.0 29.2 1.0

Magnesium binding site 3 out of 5 in 5dgh

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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 Amp-Pnp and 5- (Pcp)-IP5


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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:23.9
occ:1.00
 O A:SER68 2.2 23.0 1.0
O A:PHE70 2.2 21.7 1.0
O A:ILE73 2.2 21.0 1.0
O A:HOH540 2.3 46.6 1.0
O A:HOH654 2.5 26.3 1.0
O A:HOH701 2.5 22.6 1.0
C A:SER68 3.2 22.5 1.0
C A:ILE73 3.4 20.4 1.0
C A:PHE70 3.4 23.6 1.0
CA A:SER68 3.8 21.1 1.0
N A:ILE73 3.9 21.4 1.0
O A:HOH635 4.0 35.0 1.0
O A:LYS71 4.1 26.0 1.0
N A:PHE70 4.1 22.3 1.0
CA A:ILE73 4.1 20.2 1.0
C A:LEU69 4.2 23.5 1.0
N A:LEU69 4.2 21.6 1.0
C A:LYS71 4.2 25.5 1.0
CA A:PHE70 4.3 22.3 1.0
N A:LYS71 4.3 24.6 1.0
N A:THR74 4.5 20.5 1.0
CA A:LYS71 4.5 27.0 1.0
CA A:LEU69 4.5 23.6 1.0
CB A:SER68 4.5 21.3 1.0
CB A:ILE73 4.5 19.4 1.0
O A:LEU69 4.6 23.4 1.0
OE1 A:GLN43 4.6 38.0 1.0
O A:ILE67 4.6 19.4 1.0
O A:HOH558 4.8 31.0 1.0
N A:TYR72 4.8 25.2 1.0
CA A:THR74 4.8 22.5 1.0
NE2 A:GLN43 4.8 37.9 1.0
CB A:PHE70 4.9 21.0 1.0

Magnesium binding site 4 out of 5 in 5dgh

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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 Amp-Pnp and 5- (Pcp)-IP5


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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:49.9
occ:1.00
 O A:HOH731 2.1 30.1 1.0
O A:HOH520 2.2 32.0 1.0
O A:HOH697 2.3 32.7 1.0
O A:HOH571 2.3 33.7 1.0
O A:HOH587 2.4 32.6 1.0
O A:HOH506 2.4 33.6 1.0
O A:ASN323 3.7 12.9 1.0
O A:HOH605 4.1 16.9 1.0
O A:HIS101 4.2 14.8 1.0
O A:HOH557 4.2 35.1 1.0
O A:HOH593 4.3 21.6 1.0
OE2 A:GLU192 4.4 33.7 1.0
O33 A:5A3402 4.4 29.2 1.0
O A:HOH533 4.5 28.5 1.0
O A:HOH740 4.5 28.9 1.0
O A:PHE325 4.5 12.1 1.0
O A:HOH580 4.7 23.1 1.0
O22 A:5A3402 4.7 30.6 1.0
C A:ASN323 4.7 12.2 1.0
O A:HOH579 4.7 25.1 1.0
O A:HOH712 4.9 21.3 1.0
CB A:ASN323 4.9 12.3 1.0

Magnesium binding site 5 out of 5 in 5dgh

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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 Amp-Pnp and 5- (Pcp)-IP5


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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:48.4
occ:1.00
 O A:HOH651 2.0 47.9 1.0
O A:HOH559 2.1 28.3 1.0
O35 A:5A3402 2.1 36.5 1.0
O44 A:5A3402 2.2 32.4 1.0
O A:HOH728 2.3 35.8 1.0
O A:HOH568 2.8 53.3 1.0
PA5 A:5A3402 3.4 35.9 1.0
O25 A:5A3402 3.6 31.4 1.0
PA4 A:5A3402 3.6 33.6 1.0
O75 A:5A3402 4.0 45.0 1.0
O14 A:5A3402 4.1 32.1 1.0
O34 A:5A3402 4.1 31.9 1.0
O A:LYS214 4.2 22.5 1.0
O65 A:5A3402 4.3 43.4 1.0
O A:HOH608 4.3 37.5 1.0
O15 A:5A3402 4.4 32.1 1.0
PB5 A:5A3402 4.5 42.5 1.0
CB5 A:5A3402 4.7 38.6 1.0
O24 A:5A3402 4.7 33.0 1.0

Reference:

A.Hager, M.Wu, H.Wang, N.W.Brown, S.B.Shears, N.Veiga, D.Fiedler. Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues. Chemistry V. 22 12406 2016.
ISSN: ISSN 0947-6539
PubMed: 27460418
DOI: 10.1002/CHEM.201601754
Page generated: Sun Sep 29 02:46:11 2024

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