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Magnesium in PDB 6fd5: Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated)

Enzymatic activity of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated)

All present enzymatic activity of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated):
2.4.2.7;

Protein crystallography data

The structure of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated), PDB code: 6fd5 was solved by P.Nioche, J.Huyet, M.Ozeir, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.62 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.232, 47.750, 48.039, 77.30, 61.71, 69.47
R / Rfree (%) 17.5 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated) (pdb code 6fd5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated), PDB code: 6fd5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6fd5

Go back to Magnesium Binding Sites List in 6fd5
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated)


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 Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:18.8
occ:0.55
 O21 A:PPV202 1.8 23.2 0.6
O22 A:PPV202 2.1 16.1 0.6
O3' A:AMP201 2.2 16.4 1.0
O A:HOH323 2.3 22.4 1.0
O A:HOH309 2.3 30.2 1.0
O2' A:AMP201 2.7 20.0 1.0
P1 A:PPV202 3.0 18.9 0.6
P2 A:PPV202 3.1 15.4 0.6
OPP A:PPV202 3.3 19.8 0.6
C3' A:AMP201 3.3 12.8 1.0
C2' A:AMP201 3.5 16.3 1.0
O31 A:PPV202 3.8 18.7 0.6
O32 A:PPV202 3.8 17.8 0.6
C1' A:AMP201 4.0 15.1 1.0
O A:ASP65 4.1 17.2 1.0
C4' A:AMP201 4.1 13.2 1.0
O4' A:AMP201 4.2 14.3 1.0
OD1 A:ASP127 4.2 14.2 1.0
N A:SER66 4.2 13.3 1.0
O11 A:PPV202 4.2 21.8 0.6
O A:HOH334 4.3 34.8 1.0
NH2 A:ARG67 4.3 26.4 1.0
OD2 A:ASP127 4.3 14.6 1.0
OD1 A:ASP128 4.3 13.4 1.0
NE A:ARG67 4.3 25.5 1.0
N A:ARG67 4.3 14.3 1.0
CZ A:ARG67 4.4 25.0 1.0
O12 A:PPV202 4.4 18.4 0.6
CB A:ARG67 4.5 14.1 1.0
C A:ASP65 4.6 12.9 1.0
CG A:ASP127 4.7 13.4 1.0
NZ A:LYS88 4.8 38.7 1.0
CG A:ARG67 4.9 17.0 1.0

Magnesium binding site 2 out of 2 in 6fd5

Go back to Magnesium Binding Sites List in 6fd5
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated)


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 Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Days Post Crystallization (with Amp and Ppi Products Partially Generated) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:27.4
occ:1.00
 O12 B:PPV203 1.9 30.2 0.3
O B:HOH304 2.0 40.1 1.0
O2B B:PRP200 2.2 20.3 0.7
O21 B:PPV203 2.2 35.7 0.3
O1 B:PRP200 2.3 17.7 0.7
O B:HOH305 2.3 22.8 1.0
O3 B:PRP200 2.4 14.1 0.7
O2 B:PRP200 2.4 15.0 0.7
O3' B:AMP201 2.4 16.7 0.3
C2 B:PRP200 3.0 15.1 0.7
C1 B:PRP200 3.2 13.8 0.7
C3 B:PRP200 3.2 14.7 0.7
P2 B:PPV203 3.2 27.1 0.3
O3A B:PRP200 3.2 21.7 0.7
P1 B:PPV203 3.3 30.8 0.3
PB B:PRP200 3.3 17.8 0.7
PA B:PRP200 3.4 19.0 0.7
O B:ASP65 3.5 18.6 1.0
OPP B:PPV203 3.5 30.8 0.3
O11 B:PPV203 3.6 30.6 0.3
N B:SER66 3.8 14.9 1.0
C3' B:AMP201 3.8 14.5 0.3
O2' B:AMP201 3.8 14.6 0.3
O32 B:PPV203 4.0 27.6 0.3
O2A B:PRP200 4.0 20.7 0.7
C4 B:PRP200 4.0 14.0 0.7
C B:ASP65 4.1 15.3 1.0
OD1 B:ASP127 4.1 16.6 1.0
O4 B:PRP200 4.1 14.7 0.7
O3B B:PRP200 4.1 18.5 0.7
OD2 B:ASP127 4.2 17.3 1.0
N B:ARG67 4.2 12.2 1.0
O B:HOH309 4.4 31.0 1.0
C2' B:AMP201 4.4 13.0 0.3
C4' B:AMP201 4.4 14.0 0.3
O22 B:PPV203 4.4 29.4 0.3
O1B B:PRP200 4.4 21.4 0.7
NZ B:LYS88 4.4 37.4 1.0
CG B:ASP127 4.6 17.7 1.0
O1A B:PRP200 4.6 24.1 0.7
O31 B:PPV203 4.7 29.4 0.3
O4' B:AMP201 4.7 12.6 0.3
OD1 B:ASP128 4.7 15.3 1.0
CB B:ARG67 4.8 15.8 1.0
NE B:ARG67 4.8 30.9 1.0
C1' B:AMP201 4.8 11.8 0.3
CA B:SER66 4.9 14.7 1.0
NH2 B:ARG67 4.9 27.0 1.0
CZ B:ARG67 5.0 24.6 1.0

Reference:

J.Huyet, M.Ozeir, M.C.Burgevin, B.Pinson, F.Chesney, J.M.Remy, A.R.Siddiqi, R.Lupoli, G.Pinon, C.Saint-Marc, J.F.Gibert, R.Morales, I.Ceballos-Picot, R.Barouki, B.Daignan-Fornier, A.Olivier-Bandini, F.Auge, P.Nioche. Structural Insights Into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Cell Chem Biol V. 25 666 2018.
ISSN: ESSN 2451-9448
PubMed: 29576532
DOI: 10.1016/J.CHEMBIOL.2018.02.011
Page generated: Tue Oct 1 00:24:23 2024

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