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Manganese in PDB 2rka: The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate

Enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate

All present enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate, PDB code: 2rka was solved by S.M.Sullivan, R.M.Stiffin, G.M.Carlson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.92 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.670, 119.660, 90.867, 90.00, 108.90, 90.00
R / Rfree (%) 18.3 / 22.2

Other elements in 2rka:

The structure of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate (pdb code 2rka). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate, PDB code: 2rka:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2rka

Go back to Manganese Binding Sites List in 2rka
Manganese binding site 1 out of 4 in the The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn700

b:10.7
occ:1.00
 O A:HOH1138 1.9 7.5 0.5
O A:HOH704 2.0 12.8 1.0
OD1 A:ASP311 2.2 12.4 1.0
NZ A:LYS244 2.2 16.0 1.0
O A:HOH703 2.2 6.9 1.0
NE2 A:HIS264 2.2 15.9 1.0
O4P A:PGA623 2.3 17.9 0.5
CG A:ASP311 3.0 14.2 1.0
OD2 A:ASP311 3.1 15.3 1.0
CE1 A:HIS264 3.2 15.8 1.0
CD2 A:HIS264 3.3 15.3 1.0
CE A:LYS244 3.3 14.7 1.0
P A:PGA623 3.5 16.9 0.5
O2P A:PGA623 3.8 16.5 0.5
NZ A:LYS290 3.9 24.8 1.0
O3P A:PGA623 3.9 23.3 0.5
O3P A:PGA623 4.2 17.2 0.5
ND1 A:HIS264 4.3 15.9 1.0
O A:HOH1141 4.3 26.9 1.0
CG A:HIS264 4.4 16.9 1.0
O A:HOH1154 4.4 32.8 1.0
O A:HOH1140 4.4 23.4 1.0
O4P A:PGA623 4.4 23.2 0.5
CB A:ASP311 4.5 14.7 1.0
CD A:LYS244 4.6 14.9 1.0
O1P A:PGA623 4.8 16.7 0.5
P A:PGA623 4.9 23.5 0.5
O A:ASP311 4.9 15.8 1.0
CZ A:PHE485 5.0 15.6 1.0
O A:HOH1115 5.0 30.8 1.0
CA A:ASP311 5.0 15.3 1.0

Manganese binding site 2 out of 4 in 2rka

Go back to Manganese Binding Sites List in 2rka
Manganese binding site 2 out of 4 in the The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:19.4
occ:0.40
 O A:HOH1016 2.0 40.0 1.0
O A:HOH753 2.0 25.8 1.0
OE2 A:GLU607 2.1 25.6 1.0
NE2 A:HIS502 2.4 24.5 1.0
CD A:GLU607 2.8 23.5 1.0
O A:HOH1017 2.9 16.8 1.0
OE1 A:GLU607 3.0 26.0 1.0
CE1 A:HIS502 3.2 25.2 1.0
CD2 A:HIS502 3.6 24.1 1.0
O A:HOH1174 3.8 39.2 1.0
CG A:GLU607 4.1 20.3 1.0
O A:HOH1148 4.2 38.4 1.0
NE2 A:GLN451 4.4 21.6 1.0
ND1 A:HIS502 4.4 24.7 1.0
CG A:HIS502 4.6 23.4 1.0
CG A:GLN451 4.9 18.3 1.0
O A:LEU498 5.0 18.4 1.0

Manganese binding site 3 out of 4 in 2rka

Go back to Manganese Binding Sites List in 2rka
Manganese binding site 3 out of 4 in the The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn700

b:10.3
occ:1.00
 O C:HOH1114 2.1 2.0 0.5
O3P C:PGA623 2.1 14.9 0.5
O C:HOH703 2.2 7.8 1.0
OD1 C:ASP311 2.2 12.6 1.0
NZ C:LYS244 2.3 17.5 1.0
NE2 C:HIS264 2.3 15.8 1.0
O C:HOH704 2.5 9.4 1.0
CG C:ASP311 3.1 14.3 1.0
CE1 C:HIS264 3.2 15.6 1.0
CD2 C:HIS264 3.3 14.0 1.0
OD2 C:ASP311 3.3 15.5 1.0
CE C:LYS244 3.3 17.1 1.0
P C:PGA623 3.5 15.1 0.5
O4P C:PGA623 3.6 20.3 0.5
O4P C:PGA623 3.8 15.0 0.5
NZ C:LYS290 4.0 22.9 1.0
O2P C:PGA623 4.1 20.4 0.5
O2P C:PGA623 4.1 15.4 0.5
ND1 C:HIS264 4.3 16.1 1.0
O C:HOH1115 4.4 21.5 1.0
P C:PGA623 4.4 20.2 0.5
CG C:HIS264 4.4 15.1 1.0
O C:HOH1006 4.5 22.4 1.0
CB C:ASP311 4.5 15.6 1.0
O C:HOH887 4.5 17.3 1.0
CD C:LYS244 4.7 17.1 1.0
O1P C:PGA623 4.7 15.0 0.5
O C:HOH987 4.7 41.9 1.0
O C:HOH983 4.7 34.3 1.0
O3P C:PGA623 4.8 20.2 0.5
CZ C:PHE485 4.9 16.0 1.0
C2 C:PGA623 4.9 14.2 0.5
CE2 C:PHE485 4.9 15.7 1.0

Manganese binding site 4 out of 4 in 2rka

Go back to Manganese Binding Sites List in 2rka
Manganese binding site 4 out of 4 in the The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn701

b:30.1
occ:0.40
 NE2 C:HIS502 2.1 24.9 1.0
OE2 C:GLU607 2.4 27.0 1.0
CD C:GLU607 2.9 23.8 1.0
OE1 C:GLU607 2.9 25.5 1.0
O C:HOH1007 2.9 50.1 1.0
CE1 C:HIS502 3.0 25.8 1.0
CD2 C:HIS502 3.1 24.7 1.0
O C:HOH733 3.2 21.4 1.0
O C:HOH1137 3.5 35.1 1.0
CG C:GLU607 4.1 19.8 1.0
ND1 C:HIS502 4.2 25.1 1.0
CG C:HIS502 4.3 24.1 1.0
O C:LEU498 4.9 17.9 1.0
O C:HOH1130 4.9 37.3 1.0
NE2 C:GLN451 4.9 23.6 1.0

Reference:

R.M.Stiffin, S.M.Sullivan, G.M.Carlson, T.Holyoak. Differential Inhibition of Cytosolic Pepck By Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition. Biochemistry V. 47 2099 2008.
ISSN: ISSN 0006-2960
PubMed: 18197707
DOI: 10.1021/BI7020662
Page generated: Tue Dec 15 04:05:25 2020

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