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Manganese in PDB 2rk8: The Structure of Rat Cytosolic Pepck in Complex with Phosphonoformate

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

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

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck in Complex with Phosphonoformate, PDB code: 2rk8 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) 30.06 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.251, 119.470, 86.870, 90.00, 107.06, 90.00
R / Rfree (%) 19.5 / 24.9

Other elements in 2rk8:

The structure of The Structure of Rat Cytosolic Pepck in Complex with Phosphonoformate 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 Phosphonoformate (pdb code 2rk8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Structure of Rat Cytosolic Pepck in Complex with Phosphonoformate, PDB code: 2rk8:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2rk8

Go back to Manganese Binding Sites List in 2rk8
Manganese binding site 1 out of 2 in the The Structure of Rat Cytosolic Pepck in Complex with Phosphonoformate


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 Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn700

b:17.4
occ:1.00
O4 A:PPF3969 2.1 17.1 1.0
OD1 A:ASP311 2.1 12.3 1.0
O A:HOH5803 2.1 13.2 1.0
O3 A:PPF3969 2.2 12.8 1.0
NE2 A:HIS264 2.3 7.9 1.0
NZ A:LYS244 2.4 6.8 1.0
C1 A:PPF3969 2.9 16.3 1.0
CG A:ASP311 3.0 13.2 1.0
P1 A:PPF3969 3.2 16.9 1.0
CD2 A:HIS264 3.2 10.1 1.0
CE1 A:HIS264 3.3 8.2 1.0
OD2 A:ASP311 3.3 12.6 1.0
CE A:LYS244 3.4 8.8 1.0
O5 A:PPF3969 4.1 17.2 1.0
NZ A:LYS290 4.1 16.7 0.5
O2 A:PPF3969 4.1 17.3 1.0
O A:HOH6055 4.2 19.3 1.0
NZ A:LYS290 4.2 11.2 0.5
O1 A:PPF3969 4.3 17.5 1.0
O A:HOH5810 4.3 15.2 1.0
ND1 A:HIS264 4.4 9.1 1.0
CG A:HIS264 4.4 10.4 1.0
OG A:SER286 4.4 15.8 1.0
CB A:ASP311 4.4 12.9 1.0
CE A:LYS290 4.5 15.5 0.5
O A:HOH5786 4.6 17.0 1.0
CD A:LYS244 4.7 7.6 1.0
CZ A:PHE485 4.9 11.4 1.0
CA A:ASP311 4.9 13.2 1.0
CB A:SER286 4.9 15.2 1.0
CA A:SER286 5.0 15.3 1.0
CE2 A:PHE485 5.0 11.8 1.0
O A:ASP311 5.0 12.5 1.0

Manganese binding site 2 out of 2 in 2rk8

Go back to Manganese Binding Sites List in 2rk8
Manganese binding site 2 out of 2 in the The Structure of Rat Cytosolic Pepck in Complex with Phosphonoformate


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 Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn700

b:18.9
occ:1.00
O3 B:PPF3969 2.1 24.6 1.0
OD1 B:ASP311 2.2 15.2 1.0
O4 B:PPF3969 2.2 23.8 1.0
O B:HOH4040 2.2 18.2 1.0
NZ B:LYS244 2.2 10.3 1.0
NE2 B:HIS264 2.3 8.2 1.0
C1 B:PPF3969 3.0 24.4 1.0
CG B:ASP311 3.0 16.8 1.0
P1 B:PPF3969 3.1 25.7 1.0
CD2 B:HIS264 3.2 9.0 1.0
OD2 B:ASP311 3.2 18.6 1.0
CE B:LYS244 3.3 9.7 1.0
CE1 B:HIS264 3.3 9.4 1.0
O B:HOH4203 4.1 22.1 1.0
O2 B:PPF3969 4.1 25.5 1.0
O5 B:PPF3969 4.2 24.5 1.0
O1 B:PPF3969 4.2 26.2 1.0
NZ B:LYS290 4.2 21.6 0.5
NZ B:LYS290 4.3 16.9 0.5
OG B:SER286 4.3 24.4 1.0
CG B:HIS264 4.4 8.8 1.0
ND1 B:HIS264 4.4 9.5 1.0
CB B:ASP311 4.4 16.1 1.0
O B:HOH4055 4.5 18.7 1.0
O B:HOH4161 4.5 22.5 1.0
CE B:LYS290 4.6 21.8 0.5
CD B:LYS244 4.6 9.8 1.0
CE2 B:PHE485 4.8 10.1 1.0
CZ B:PHE485 4.9 9.7 1.0
CB B:SER286 4.9 23.9 1.0
CA B:SER286 4.9 23.8 1.0
CA B:ASP311 5.0 15.9 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 04:05:24 2020

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