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Manganese in PDB 3moh: The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Phosphoglycolate and Gdp

Enzymatic activity of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Phosphoglycolate and Gdp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Phosphoglycolate and Gdp:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Phosphoglycolate and Gdp, PDB code: 3moh was solved by T.A.Johnson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.93 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.078, 119.520, 87.018, 90.00, 107.15, 90.00
R / Rfree (%) 19 / 24.7

Other elements in 3moh:

The structure of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Phosphoglycolate and Gdp 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 Mutant A467G in Complex with Phosphoglycolate and Gdp (pdb code 3moh). 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 Mutant A467G in Complex with Phosphoglycolate and Gdp, PDB code: 3moh:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3moh

Go back to Manganese Binding Sites List in 3moh
Manganese binding site 1 out of 4 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Phosphoglycolate and Gdp


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 Mutant A467G in Complex with Phosphoglycolate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn700

b:18.6
occ:1.00
 O3P A:PGA900 2.0 15.9 1.0
NE2 A:HIS264 2.2 11.1 1.0
O A:HOH623 2.2 9.6 1.0
OD1 A:ASP311 2.2 12.3 1.0
NZ A:LYS244 2.3 11.1 1.0
O A:HOH907 2.5 13.0 1.0
CG A:ASP311 3.1 11.6 1.0
CE1 A:HIS264 3.1 13.6 1.0
OD2 A:ASP311 3.1 13.3 1.0
P A:PGA900 3.2 18.2 1.0
CD2 A:HIS264 3.3 11.2 1.0
O4P A:PGA900 3.5 16.4 1.0
CE A:LYS244 3.6 14.7 1.0
NZ A:LYS290 3.9 18.4 1.0
O A:HOH740 4.2 15.1 1.0
O2P A:PGA900 4.2 18.4 1.0
ND1 A:HIS264 4.3 13.0 1.0
O A:HOH767 4.3 10.2 1.0
O1P A:PGA900 4.3 16.7 1.0
O A:HOH624 4.3 11.4 1.0
CG A:HIS264 4.4 10.9 1.0
O A:HOH991 4.4 11.9 1.0
CB A:ASP311 4.5 12.0 1.0
CZ A:PHE485 4.7 8.0 1.0
CB A:SER286 4.8 14.9 1.0
CD A:LYS244 4.8 15.2 1.0
CE2 A:PHE485 4.9 9.3 1.0
O A:HOH892 5.0 1.0 0.5
O A:ASP311 5.0 12.3 1.0

Manganese binding site 2 out of 4 in 3moh

Go back to Manganese Binding Sites List in 3moh
Manganese binding site 2 out of 4 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Phosphoglycolate and Gdp


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 Mutant A467G in Complex with Phosphoglycolate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:19.5
occ:1.00
 O A:HOH893 1.9 11.8 1.0
O A:HOH625 2.1 9.6 1.0
O1B A:GDP1000 2.1 15.0 1.0
O A:HOH624 2.1 11.4 1.0
OG1 A:THR291 2.2 12.1 1.0
O A:HOH767 2.3 10.2 1.0
PB A:GDP1000 3.3 17.3 1.0
CB A:THR291 3.3 11.5 1.0
O2B A:GDP1000 3.4 18.8 1.0
OD2 A:ASP310 3.7 16.7 1.0
N A:THR291 4.0 11.6 1.0
O A:HOH740 4.1 15.1 1.0
CA A:THR291 4.2 12.2 1.0
O A:HOH623 4.3 9.6 1.0
O3B A:GDP1000 4.3 15.8 1.0
O1A A:GDP1000 4.3 18.3 1.0
CG2 A:THR291 4.4 12.2 1.0
O A:ASP310 4.4 13.6 1.0
O3A A:GDP1000 4.5 16.6 1.0
CG A:ASP310 4.5 15.4 1.0
O A:HOH833 4.6 16.1 1.0
CA A:GLY334 4.6 13.1 1.0
PA A:GDP1000 4.7 16.9 1.0
O2P A:PGA900 4.8 18.4 1.0
O2A A:GDP1000 4.8 15.5 1.0
O A:PHE333 4.9 13.6 1.0
N A:VAL335 4.9 13.5 1.0
CB A:LYS290 5.0 11.4 1.0
OD1 A:ASP311 5.0 12.3 1.0
O3P A:PGA900 5.0 15.9 1.0

Manganese binding site 3 out of 4 in 3moh

Go back to Manganese Binding Sites List in 3moh
Manganese binding site 3 out of 4 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Phosphoglycolate and Gdp


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 Mutant A467G in Complex with Phosphoglycolate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn700

b:19.5
occ:1.00
 O B:HOH639 2.1 10.0 1.0
O4P B:PGA900 2.1 21.1 1.0
OD1 B:ASP311 2.1 13.1 1.0
NE2 B:HIS264 2.2 10.1 1.0
O B:HOH845 2.2 10.3 1.0
NZ B:LYS244 2.3 9.9 1.0
CG B:ASP311 3.0 13.6 1.0
CD2 B:HIS264 3.1 11.7 1.0
CE1 B:HIS264 3.2 12.0 1.0
OD2 B:ASP311 3.2 14.8 1.0
CE B:LYS244 3.5 9.2 1.0
P B:PGA900 3.5 20.0 1.0
O2P B:PGA900 4.0 21.2 1.0
CE B:LYS290 4.1 13.6 1.0
ND1 B:HIS264 4.3 12.1 1.0
NZ B:LYS290 4.3 12.6 1.0
CG B:HIS264 4.3 12.3 1.0
O3P B:PGA900 4.4 21.6 1.0
O B:HOH640 4.4 11.1 1.0
CB B:ASP311 4.4 12.9 1.0
O B:HOH751 4.5 18.2 1.0
O1P B:PGA900 4.5 20.3 1.0
CD B:LYS244 4.7 9.4 1.0
CB B:SER286 4.8 14.1 1.0
O B:ASP311 4.8 12.4 1.0
CZ B:PHE485 4.9 9.5 1.0
CA B:ASP311 5.0 13.1 1.0
CE2 B:PHE485 5.0 7.8 1.0

Manganese binding site 4 out of 4 in 3moh

Go back to Manganese Binding Sites List in 3moh
Manganese binding site 4 out of 4 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Phosphoglycolate and Gdp


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 Mutant A467G in Complex with Phosphoglycolate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:21.0
occ:1.00
 O B:HOH840 1.8 11.1 1.0
O3B B:GDP1000 2.0 19.4 1.0
O B:HOH640 2.1 11.1 1.0
O B:HOH746 2.1 11.2 1.0
O B:HOH841 2.3 17.5 1.0
OG1 B:THR291 2.3 11.9 1.0
PB B:GDP1000 3.3 20.5 1.0
CB B:THR291 3.4 12.4 1.0
O1B B:GDP1000 3.6 19.7 1.0
OD2 B:ASP310 3.9 15.7 1.0
N B:THR291 4.1 12.1 1.0
O2B B:GDP1000 4.1 18.9 1.0
O1A B:GDP1000 4.2 19.6 1.0
O B:HOH639 4.2 10.0 1.0
O B:HOH751 4.3 18.2 1.0
CA B:GLY334 4.3 13.7 1.0
CA B:THR291 4.3 12.5 1.0
O B:ASP310 4.4 12.5 1.0
O3A B:GDP1000 4.5 18.4 1.0
CG2 B:THR291 4.5 11.8 1.0
CG B:ASP310 4.6 12.8 1.0
N B:VAL335 4.6 13.4 1.0
O B:HOH839 4.7 14.7 1.0
PA B:GDP1000 4.7 20.6 1.0
O B:PHE333 4.7 13.4 1.0
O2A B:GDP1000 4.8 22.1 1.0
O3P B:PGA900 4.9 21.6 1.0
OD1 B:ASP311 4.9 13.1 1.0
CB B:LYS290 5.0 11.4 1.0

Reference:

T.A.Johnson, T.Holyoak. Increasing the Conformational Entropy of the Omega-Loop Lid Domain in Phosphoenolpyruvate Carboxykinase Impairs Catalysis and Decreases Catalytic Fidelity . Biochemistry V. 49 5176 2010.
ISSN: ISSN 0006-2960
PubMed: 20476774
DOI: 10.1021/BI100399E
Page generated: Sat Oct 5 17:10:10 2024

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