Atomistry » Magnesium » PDB 4nxn-4o5e » 4nzm
Atomistry »
  Magnesium »
    PDB 4nxn-4o5e »
      4nzm »

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

Go back to Magnesium Binding Sites List in 4nzm
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy