Magnesium in PDB 3f5m: Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei

All present enzymatic activity of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei:
2.7.1.11;

The structure of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei, PDB code: 3f5m was solved by I.W.Mcnae, J.Martinez-Oyanedel, J.W.Keillor, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.88 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.578, 117.570, 176.587, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 28.6

The structure of Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei (pdb code 3f5m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei, PDB code: 3f5m:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei


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 Atp-Bound Phosphofructokinase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:49.8 occ:1.00 OD1 A:ASN343 2.5 55.0 1.0 O1B A:ATP1001 2.6 40.0 1.0 O2A A:ATP1001 2.8 28.8 1.0 CG A:ASN343 3.0 46.0 1.0 O1G A:ATP1001 3.1 62.4 1.0 ND2 A:ASN343 3.1 47.3 1.0 PB A:ATP1001 3.9 21.3 1.0 PA A:ATP1001 4.1 24.7 1.0 CB A:ASN343 4.3 29.7 1.0 PG A:ATP1001 4.3 31.9 1.0 O3A A:ATP1001 4.4 19.2 1.0 N A:GLY200 4.5 15.9 1.0 O2G A:ATP1001 4.6 73.3 1.0 O3B A:ATP1001 4.6 56.4 1.0 CA A:GLY200 4.9 21.0 1.0 O1A A:ATP1001 5.0 27.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei


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 Atp-Bound Phosphofructokinase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:51.8 occ:1.00 O1B B:ATP1001 2.4 17.4 1.0 O2A B:ATP1001 2.5 38.5 1.0 OD1 B:ASN343 2.9 49.8 1.0 O B:HOH588 3.0 34.8 1.0 O3G B:ATP1001 3.4 35.1 1.0 CG B:ASN343 3.5 46.6 1.0 PB B:ATP1001 3.6 14.7 1.0 ND2 B:ASN343 3.7 45.8 1.0 O2G B:ATP1001 3.7 66.9 1.0 PA B:ATP1001 3.8 26.3 1.0 O3A B:ATP1001 3.9 30.5 1.0 N B:GLY200 4.0 15.9 1.0 PG B:ATP1001 4.0 41.2 1.0 O3B B:ATP1001 4.3 26.0 1.0 O B:HOH557 4.3 20.8 1.0 CA B:GLY200 4.4 20.7 1.0 CB B:ASP199 4.6 27.8 1.0 O1A B:ATP1001 4.7 36.4 1.0 CB B:ASN343 4.8 36.2 1.0 O5' B:ATP1001 4.9 21.0 1.0 O2B B:ATP1001 4.9 14.9 1.0 OD2 B:ASP199 5.0 74.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei


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 Atp-Bound Phosphofructokinase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:45.5 occ:1.00 O1B D:ATP1001 2.4 21.1 1.0 OD1 D:ASN343 2.8 47.4 1.0 O2A D:ATP1001 3.0 39.6 1.0 O2G D:ATP1001 3.1 36.4 1.0 CG D:ASN343 3.4 48.2 1.0 PB D:ATP1001 3.5 17.3 1.0 ND2 D:ASN343 3.5 48.1 1.0 O3A D:ATP1001 3.8 28.2 1.0 O D:HOH488 4.0 23.7 1.0 PG D:ATP1001 4.0 33.5 1.0 PA D:ATP1001 4.0 38.5 1.0 O1G D:ATP1001 4.1 71.2 1.0 O3B D:ATP1001 4.2 29.8 1.0 N D:GLY200 4.3 18.9 1.0 CB D:ASN343 4.6 39.3 1.0 CA D:GLY200 4.7 21.6 1.0 CB D:ASP199 4.8 29.2 1.0 O2B D:ATP1001 4.9 16.5 1.0 O1A D:ATP1001 5.0 39.1 1.0

I.W.Mcnae, J.Martinez-Oyanedel, J.W.Keillor, P.A.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw. The Crystal Structure of Atp-Bound Phosphofructokinase From Trypanosoma Brucei Reveals Conformational Transitions Different From Those of Other Phosphofructokinases. J.Mol.Biol. V. 385 1519 2009.
ISSN: ISSN 0022-2836
PubMed: 19084537
DOI: 10.1016/J.JMB.2008.11.047