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Magnesium in PDB 1ytm: Crystal Structure of Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions

Enzymatic activity of Crystal Structure of Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions

All present enzymatic activity of Crystal Structure of Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions:
4.1.1.49;

Protein crystallography data

The structure of Crystal Structure of Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions, PDB code: 1ytm was solved by L.T.J.Delbaere, J.J.H.Cotelesage, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 194.871, 123.219, 48.463, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.1

Other elements in 1ytm:

The structure of Crystal Structure of Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions (pdb code 1ytm). 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 Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions, PDB code: 1ytm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1ytm

Go back to Magnesium Binding Sites List in 1ytm
Magnesium binding site 1 out of 2 in the Crystal Structure of Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions


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 Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg998

b:10.1
occ:1.00
 OG1 A:THR249 2.1 16.9 1.0
O A:HOH1002 2.2 18.7 1.0
O2B A:ATP541 2.2 22.2 1.0
O3G A:ATP541 2.3 20.6 1.0
O A:HOH1003 2.3 22.2 1.0
O A:HOH1222 2.4 26.6 1.0
CB A:THR249 3.2 18.4 1.0
PG A:ATP541 3.3 20.8 1.0
PB A:ATP541 3.3 20.5 1.0
O3B A:ATP541 3.6 20.6 1.0
OD1 A:ASP262 3.8 26.3 1.0
O1G A:ATP541 3.8 19.7 1.0
O2A A:ATP541 4.0 19.9 1.0
N A:THR249 4.1 19.3 1.0
O A:ASP262 4.1 21.2 1.0
CA A:THR249 4.2 18.4 1.0
O A:TYR280 4.2 19.6 1.0
O A:HOH1041 4.2 19.5 1.0
CG2 A:THR249 4.3 16.6 1.0
OD2 A:ASP263 4.3 17.5 1.0
O3A A:ATP541 4.3 20.7 1.0
NH1 A:ARG327 4.3 18.5 1.0
CG A:ASP262 4.4 24.2 1.0
O1B A:ATP541 4.5 21.7 1.0
O2G A:ATP541 4.6 20.7 1.0
PA A:ATP541 4.6 23.2 1.0
O6 A:OXD543 4.8 27.0 1.0
CB A:ASP263 4.8 20.1 1.0
CB A:ASP262 4.9 23.8 1.0
CA A:ALA281 4.9 21.2 1.0
C A:ASP262 4.9 22.7 1.0
CG A:ASP263 4.9 18.9 1.0
NZ A:LYS248 5.0 19.5 1.0
CB A:LYS248 5.0 18.8 1.0
C A:TYR280 5.0 19.5 1.0

Magnesium binding site 2 out of 2 in 1ytm

Go back to Magnesium Binding Sites List in 1ytm
Magnesium binding site 2 out of 2 in the Crystal Structure of Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions


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 Phosphoenolpyruvate Carboxykinase of Anaerobiospirillum Succiniciproducens Complexed with Atp, Oxalate, Magnesium and Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1998

b:13.3
occ:1.00
 OG1 B:THR1249 2.2 20.4 1.0
O3G B:ATP1541 2.3 22.8 1.0
O B:HOH351 2.3 24.6 1.0
O2B B:ATP1541 2.3 21.0 1.0
O B:HOH9 2.3 17.3 1.0
O B:HOH229 2.4 33.0 1.0
PG B:ATP1541 3.2 22.6 1.0
PB B:ATP1541 3.3 19.9 1.0
CB B:THR1249 3.3 22.2 1.0
O3B B:ATP1541 3.4 21.8 1.0
OD1 B:ASP1262 3.7 24.1 1.0
O1G B:ATP1541 3.7 24.2 1.0
O2A B:ATP1541 4.0 24.1 1.0
N B:THR1249 4.1 21.6 1.0
O B:TYR1280 4.2 18.0 1.0
O B:ASP1262 4.2 26.9 1.0
O B:HOH143 4.2 20.2 1.0
CA B:THR1249 4.3 21.4 1.0
O3A B:ATP1541 4.3 23.0 1.0
NH1 B:ARG1327 4.4 19.7 1.0
CG2 B:THR1249 4.4 21.7 1.0
CG B:ASP1262 4.4 25.4 1.0
O1B B:ATP1541 4.4 23.6 1.0
OD2 B:ASP1263 4.4 19.7 1.0
O2G B:ATP1541 4.5 25.0 1.0
PA B:ATP1541 4.6 24.3 1.0
CA B:ALA1281 4.8 20.9 1.0
CB B:ASP1263 4.8 22.9 1.0
C B:TYR1280 4.9 19.9 1.0
CB B:LYS1248 4.9 17.8 1.0
C B:ASP1262 5.0 26.8 1.0
O1A B:ATP1541 5.0 26.2 1.0
O3 B:OXD1543 5.0 20.9 1.0
CG B:ASP1263 5.0 21.5 1.0
CB B:ASP1262 5.0 25.4 1.0

Reference:

J.J.H.Cotelesage, L.Prasad, J.G.Zeikus, M.Laivenieks, L.T.J.Delbaere. Crystal Structure of Anaerobiospirillum Succiniciproducens Pep Carboxykinase Reveals An Important Active Site Loop Int.J.Biochem.Cell Biol. V. 37 1829 2005.
ISSN: ISSN 1357-2725
PubMed: 15890557
DOI: 10.1016/J.BIOCEL.2005.03.008
Page generated: Tue Aug 13 19:53:07 2024

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