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Magnesium in PDB 6n5c: Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5

Enzymatic activity of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-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-PCF2AM-INSP5, PDB code: 6n5c was solved by H.Wang, S.B.Shears, A.Riley, B.Potter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.17 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.604, 111.032, 41.429, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.4

Other elements in 6n5c:

The structure of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

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-PCF2AM-INSP5 (pdb code 6n5c). 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-PCF2AM-INSP5, PDB code: 6n5c:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6n5c

Go back to Magnesium Binding Sites List in 6n5c
Magnesium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-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-PCF2AM-INSP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:27.9
occ:1.00
 O3G A:ANP401 2.0 29.1 1.0
O A:HOH600 2.0 26.9 1.0
ND2 A:ASN323 2.1 26.2 1.0
OD2 A:ASP321 2.1 28.5 1.0
O1B A:ANP401 2.1 29.5 1.0
OD1 A:ASP321 2.2 27.9 1.0
CG A:ASP321 2.4 26.0 1.0
PG A:ANP401 3.1 31.2 1.0
CG A:ASN323 3.2 26.2 1.0
PB A:ANP401 3.2 29.1 1.0
N3B A:ANP401 3.4 30.2 1.0
O1G A:ANP401 3.5 29.1 1.0
OD1 A:ASN323 3.6 29.1 1.0
MG A:MG403 3.7 32.2 1.0
O A:HOH569 3.9 40.6 1.0
CB A:ASP321 3.9 24.7 1.0
NH1 A:ARG134 4.3 32.5 1.0
O3A A:ANP401 4.3 30.2 1.0
O2G A:ANP401 4.3 30.6 1.0
O2B A:ANP401 4.3 28.2 1.0
O A:HOH758 4.3 44.6 1.0
O A:ALA191 4.4 27.6 1.0
CE1 A:HIS194 4.5 27.2 1.0
CB A:ASN323 4.5 24.7 1.0
O2A A:ANP401 4.5 31.8 1.0
O A:HOH636 4.7 26.5 1.0
ND1 A:HIS194 4.7 24.6 1.0
PA A:ANP401 4.8 32.6 1.0
O A:HOH505 4.8 31.9 1.0
CA A:ASN323 4.8 23.4 1.0
O1A A:ANP401 4.9 31.7 1.0
CA A:ASP321 4.9 23.3 1.0
OD2 A:ASP309 5.0 31.4 1.0
O A:VAL322 5.0 24.0 1.0

Magnesium binding site 2 out of 4 in 6n5c

Go back to Magnesium Binding Sites List in 6n5c
Magnesium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-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-PCF2AM-INSP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:32.2
occ:1.00
 O1G A:ANP401 1.9 29.1 1.0
OD2 A:ASP309 2.0 31.4 1.0
O2A A:ANP401 2.0 31.8 1.0
OD2 A:ASP321 2.1 28.5 1.0
O A:HOH565 2.1 30.0 1.0
PG A:ANP401 2.8 31.2 1.0
N3B A:ANP401 2.9 30.2 1.0
CG A:ASP321 3.1 26.0 1.0
CG A:ASP309 3.2 29.2 1.0
PA A:ANP401 3.3 32.6 1.0
CB A:ASP321 3.5 24.7 1.0
O3G A:ANP401 3.6 29.1 1.0
O3A A:ANP401 3.7 30.2 1.0
PB A:ANP401 3.7 29.1 1.0
O1B A:ANP401 3.7 29.5 1.0
MG A:MG402 3.7 27.9 1.0
OD1 A:ASP309 4.0 32.6 1.0
O2G A:ANP401 4.0 30.6 1.0
OD1 A:ASN323 4.1 29.1 1.0
CB A:ASP309 4.1 26.3 1.0
O1A A:ANP401 4.2 31.7 1.0
OD1 A:ASP321 4.2 27.9 1.0
O3' A:ANP401 4.3 32.9 1.0
O5' A:ANP401 4.4 31.0 1.0
NZ A:LYS248 4.5 41.5 1.0
C5' A:ANP401 4.5 32.6 1.0
ND2 A:ASN323 4.6 26.2 1.0
C3' A:ANP401 4.8 33.2 1.0
CG A:ASN323 4.8 26.2 1.0

Magnesium binding site 3 out of 4 in 6n5c

Go back to Magnesium Binding Sites List in 6n5c
Magnesium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-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-PCF2AM-INSP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:32.4
occ:1.00
 O A:PHE70 2.2 30.7 1.0
O A:ILE73 2.2 30.1 1.0
O A:SER68 2.3 29.6 1.0
O A:HOH543 2.3 52.9 1.0
O A:HOH699 2.5 43.2 1.0
O A:HOH740 2.6 38.3 1.0
C A:SER68 3.3 29.1 1.0
C A:PHE70 3.4 31.6 1.0
C A:ILE73 3.5 29.5 1.0
CA A:SER68 3.8 28.3 1.0
N A:ILE73 4.0 30.0 1.0
O A:LYS71 4.1 34.0 1.0
N A:PHE70 4.1 30.1 1.0
C A:LYS71 4.2 33.8 1.0
CA A:ILE73 4.2 29.8 1.0
OE1 A:GLN43 4.2 48.5 1.0
N A:LYS71 4.3 33.9 1.0
C A:LEU69 4.3 31.1 1.0
CA A:PHE70 4.3 29.8 1.0
N A:LEU69 4.3 30.2 1.0
CA A:LYS71 4.4 35.8 1.0
N A:THR74 4.5 29.3 1.0
CB A:SER68 4.6 29.1 1.0
O A:ILE67 4.7 25.7 1.0
CA A:LEU69 4.7 31.1 1.0
CB A:ILE73 4.7 29.2 1.0
O A:LEU69 4.8 30.5 1.0
N A:TYR72 4.8 32.5 1.0
CA A:THR74 4.9 30.2 1.0
CB A:PHE70 4.9 28.8 1.0

Magnesium binding site 4 out of 4 in 6n5c

Go back to Magnesium Binding Sites List in 6n5c
Magnesium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-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-PCF2AM-INSP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:55.9
occ:1.00
 O A:HOH524 1.8 57.4 1.0
O A:HOH690 2.1 39.8 1.0
O A:HOH753 2.1 31.5 1.0
O A:HOH747 2.2 35.7 1.0
O A:HOH559 2.3 49.2 1.0
O A:HOH562 2.4 29.7 1.0
O33 A:KDJ406 3.9 40.2 1.0
O A:HOH605 3.9 27.4 1.0
O A:ASN323 4.0 25.1 1.0
O32 A:KDJ406 4.1 36.9 1.0
O22 A:KDJ406 4.3 37.4 1.0
O A:HOH569 4.3 40.6 1.0
O A:HOH525 4.4 34.4 1.0
O43 A:KDJ406 4.5 43.3 1.0
O A:HIS101 4.5 25.9 1.0
O A:PHE325 4.6 19.4 1.0
O A:HOH616 4.7 34.8 1.0
O31 A:KDJ406 4.7 54.6 1.0
PA3 A:KDJ406 4.7 45.2 1.0
O A:HOH601 4.7 40.1 1.0
O A:HOH758 4.7 44.6 1.0
PA2 A:KDJ406 4.8 34.6 1.0

Reference:

A.M.Riley, H.Wang, S.B.Shears, B.V.L.Potter. Synthesis of An Alpha-Phosphono-Alpha , Alpha-Difluoroacetamide Analogue of the Diphosphoinositol Pentakisphosphate 5-INSP7. Medchemcomm V. 10 1165 2019.
ISSN: ESSN 2040-2511
PubMed: 31391889
DOI: 10.1039/C9MD00163H
Page generated: Wed Aug 13 12:38:49 2025

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