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Magnesium in PDB 4nzm: Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5

Enzymatic activity of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5:
2.7.4.21; 2.7.4.24;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5, PDB code: 4nzm 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) 34.28 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.623, 111.226, 41.443, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5 (pdb code 4nzm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5, PDB code: 4nzm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4nzm

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5


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 PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:21.8
occ:1.00
 O A:HOH745 1.8 28.9 1.0
O3G A:ANP401 2.0 26.1 1.0
OD2 A:ASP321 2.1 21.9 1.0
O1B A:ANP401 2.1 24.3 1.0
ND2 A:ASN323 2.1 18.7 1.0
OD1 A:ASP321 2.5 20.4 1.0
CG A:ASP321 2.6 18.2 1.0
PG A:ANP401 3.2 29.2 1.0
CG A:ASN323 3.3 18.6 1.0
PB A:ANP401 3.4 24.3 1.0
N3B A:ANP401 3.7 26.3 1.0
O1G A:ANP401 3.7 29.4 1.0
OD1 A:ASN323 3.8 23.2 1.0
MG A:MG404 4.0 28.2 1.0
O A:HOH744 4.1 39.0 1.0
CB A:ASP321 4.2 16.9 1.0
O A:HOH644 4.3 44.9 1.0
O A:ALA191 4.3 18.1 1.0
O2B A:ANP401 4.4 24.9 1.0
CE1 A:HIS194 4.4 17.7 1.0
NH1 A:ARG134 4.4 17.7 0.7
O2G A:ANP401 4.5 28.9 1.0
O3A A:ANP401 4.5 23.1 1.0
CB A:ASN323 4.5 16.9 1.0
O A:HOH794 4.7 60.6 1.0
O2A A:ANP401 4.7 21.8 1.0
ND1 A:HIS194 4.7 17.0 1.0
O A:HOH567 4.7 31.8 1.0
O A:HOH581 4.8 23.8 1.0
O A:VAL322 4.8 16.4 1.0
CA A:ASN323 4.8 16.3 1.0
NH2 A:ARG134 4.9 13.5 0.3

Magnesium binding site 2 out of 4 in 4nzm

Go back to Magnesium Binding Sites List in 4nzm
Magnesium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5


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 PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:28.2
occ:1.00
 O1G A:ANP401 2.0 29.4 1.0
OD2 A:ASP309 2.0 22.0 1.0
O2A A:ANP401 2.0 21.8 1.0
O A:HOH680 2.1 34.4 1.0
OD2 A:ASP321 2.4 21.9 1.0
N3B A:ANP401 2.8 26.3 1.0
PG A:ANP401 2.9 29.2 1.0
CG A:ASP309 3.2 19.6 1.0
CG A:ASP321 3.3 18.2 1.0
PA A:ANP401 3.4 20.3 1.0
CB A:ASP321 3.5 16.9 1.0
PB A:ANP401 3.6 24.3 1.0
O3G A:ANP401 3.7 26.1 1.0
O1B A:ANP401 3.7 24.3 1.0
O3A A:ANP401 3.9 23.1 1.0
MG A:MG403 4.0 21.8 1.0
OD1 A:ASP309 4.0 25.1 1.0
O A:HOH796 4.1 38.4 1.0
O2G A:ANP401 4.1 28.9 1.0
CB A:ASP309 4.2 16.9 1.0
OD1 A:ASN323 4.2 23.2 1.0
O3' A:ANP401 4.2 20.4 1.0
O1A A:ANP401 4.4 20.4 1.0
NZ A:LYS248 4.4 30.9 1.0
OD1 A:ASP321 4.4 20.4 1.0
O5' A:ANP401 4.5 19.6 1.0
C5' A:ANP401 4.6 19.6 1.0
C3' A:ANP401 4.7 20.4 1.0
ND2 A:ASN323 4.7 18.7 1.0
CG A:ASN323 4.9 18.6 1.0

Magnesium binding site 3 out of 4 in 4nzm

Go back to Magnesium Binding Sites List in 4nzm
Magnesium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5


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 PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:24.1
occ:1.00
 O A:ILE73 2.2 18.9 1.0
O A:SER68 2.3 21.9 1.0
O A:PHE70 2.3 22.7 1.0
O A:HOH701 2.4 39.5 1.0
O A:HOH659 2.4 27.4 1.0
O A:HOH795 2.7 32.2 1.0
C A:SER68 3.3 21.3 1.0
C A:ILE73 3.4 19.1 1.0
C A:PHE70 3.5 23.1 1.0
CA A:SER68 3.9 20.6 1.0
N A:ILE73 3.9 20.8 1.0
O A:LYS71 4.1 23.6 1.0
CA A:ILE73 4.1 19.5 1.0
O A:HOH817 4.2 54.4 1.0
N A:PHE70 4.2 22.7 1.0
O A:HOH739 4.2 55.5 1.0
NE2 A:GLN43 4.2 31.7 1.0
C A:LYS71 4.2 23.5 1.0
N A:LEU69 4.4 22.4 1.0
N A:LYS71 4.4 23.6 1.0
C A:LEU69 4.4 23.2 1.0
CA A:PHE70 4.4 22.7 1.0
CA A:LYS71 4.4 24.1 1.0
N A:THR74 4.4 18.8 1.0
O A:HOH748 4.5 23.7 1.0
CB A:ILE73 4.5 19.5 1.0
O A:ILE67 4.6 18.3 1.0
CB A:SER68 4.6 20.7 1.0
CA A:LEU69 4.7 23.1 1.0
N A:TYR72 4.7 23.1 1.0
CA A:THR74 4.7 19.2 1.0
O A:LEU69 4.9 23.4 1.0
CB A:PHE70 5.0 22.3 1.0
C A:TYR72 5.0 21.6 1.0

Magnesium binding site 4 out of 4 in 4nzm

Go back to Magnesium Binding Sites List in 4nzm
Magnesium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5


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 PPIP5K2 in Complex with Amppnp and 5-Pa-INSP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:68.9
occ:1.00
 O A:HOH630 2.0 55.8 1.0
O A:HOH560 2.3 30.0 1.0
O A:HOH573 2.4 47.3 1.0
O A:HOH655 2.4 34.2 1.0
O A:HOH691 2.4 45.0 1.0
O A:HOH794 2.6 60.6 1.0
O A:HOH557 3.1 66.9 1.0
O A:ASN323 3.5 16.8 1.0
O45 A:0EJ402 3.6 17.5 0.4
O A:HOH593 4.0 36.8 1.0
O A:HOH619 4.1 36.2 1.0
O A:HIS101 4.3 17.5 1.0
O A:HOH744 4.3 39.0 1.0
O A:PHE325 4.4 14.7 1.0
O55 A:0EJ402 4.4 17.0 0.4
O21 A:0EJ402 4.5 36.5 0.6
O A:HOH737 4.5 52.4 1.0
O32 A:0EJ402 4.5 33.9 0.6
O22 A:0EJ402 4.6 34.1 0.6
C A:ASN323 4.6 16.2 1.0
O A:HOH644 4.7 44.9 1.0
PB5 A:0EJ402 4.7 17.2 0.4
CB A:ASN323 4.9 16.9 1.0
O A:HOH625 4.9 31.1 1.0
OE1 A:GLU192 4.9 34.9 1.0

Reference:

H.Wang, H.Y.Godage, A.M.Riley, J.D.Weaver, S.B.Shears, B.V.Potter. Synthetic Inositol Phosphate Analogs Reveal That PPIP5K2 Has A Surface-Mounted Substrate Capture Site That Is A Target For Drug Discovery. Chem.Biol. V. 21 689 2014.
ISSN: ISSN 1074-5521
PubMed: 24768307
DOI: 10.1016/J.CHEMBIOL.2014.03.009
Page generated: Tue Aug 20 00:12:58 2024

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