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Manganese in PDB 3mof: The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp

Enzymatic activity of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp

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

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp, PDB code: 3mof 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) 33.24 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.983, 119.601, 87.068, 90.00, 106.87, 90.00
R / Rfree (%) 17.9 / 22.8

Other elements in 3mof:

The structure of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp 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 Oxalate and Gtp (pdb code 3mof). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp, PDB code: 3mof:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 3mof

Go back to Manganese Binding Sites List in 3mof
Manganese binding site 1 out of 5 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp


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 Oxalate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn700

b:16.1
occ:0.70
 MN A:MN700 0.0 16.1 0.7
MN A:MN700 1.3 18.5 0.3
O A:HOH802 1.9 9.4 1.0
O2B A:GTP900 1.9 16.1 0.7
O1G A:GTP900 2.0 18.7 0.3
O A:HOH856 2.1 19.2 1.0
OG1 A:THR291 2.2 8.7 1.0
O1G A:GTP900 2.4 9.6 0.7
O A:HOH794 2.6 7.3 1.0
O1B A:GTP900 2.6 14.0 0.3
O2G A:GTP900 3.0 17.3 0.3
PG A:GTP900 3.0 20.8 0.3
PB A:GTP900 3.1 17.0 0.7
CB A:THR291 3.4 8.6 1.0
O3B A:GTP900 3.4 14.4 0.7
PG A:GTP900 3.4 12.8 0.7
OD2 A:ASP310 3.5 9.4 1.0
PB A:GTP900 3.7 14.8 0.3
O3B A:GTP900 3.9 18.1 0.3
O1A A:GTP900 3.9 21.1 0.7
O A:HOH631 4.0 10.2 1.0
N A:THR291 4.0 10.2 1.0
O3G A:GTP900 4.0 10.0 0.7
O3A A:GTP900 4.2 18.3 0.7
O A:ASP310 4.2 7.5 1.0
CG A:ASP310 4.2 8.6 1.0
CA A:THR291 4.2 9.7 1.0
O3G A:GTP900 4.3 17.6 0.3
O1B A:GTP900 4.3 16.5 0.7
OD1 A:ASP311 4.3 3.6 1.0
PA A:GTP900 4.5 20.0 0.7
O2B A:GTP900 4.5 11.3 0.3
CG2 A:THR291 4.5 8.1 1.0
NH1 A:ARG405 4.5 5.1 1.0
O1A A:GTP900 4.6 9.9 0.3
CA A:GLY334 4.6 6.1 1.0
O A:PHE333 4.7 7.0 1.0
O2G A:GTP900 4.7 11.4 0.7
OD1 A:ASP310 4.7 8.8 1.0
O2A A:GTP900 4.8 18.7 0.7
O3 A:OXL1000 4.8 16.7 1.0
CB A:ASP311 4.9 5.8 1.0
CB A:LYS290 4.9 9.1 1.0
CG A:ASP311 4.9 5.7 1.0
CB A:ASP310 4.9 7.5 1.0
C A:ASP310 5.0 7.4 1.0

Manganese binding site 2 out of 5 in 3mof

Go back to Manganese Binding Sites List in 3mof
Manganese binding site 2 out of 5 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp


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 Oxalate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn700

b:18.5
occ:0.30
 MN A:MN700 0.0 18.5 0.3
MN A:MN700 1.3 16.1 0.7
O A:HOH794 1.4 7.3 1.0
O1G A:GTP900 1.4 18.7 0.3
O1B A:GTP900 2.0 14.0 0.3
O2B A:GTP900 2.0 16.1 0.7
O1G A:GTP900 2.4 9.6 0.7
OG1 A:THR291 2.7 8.7 1.0
PG A:GTP900 2.7 20.8 0.3
O1A A:GTP900 2.8 21.1 0.7
O A:HOH856 2.9 19.2 1.0
PB A:GTP900 2.9 17.0 0.7
O3B A:GTP900 3.0 14.4 0.7
O A:HOH802 3.1 9.4 1.0
PB A:GTP900 3.2 14.8 0.3
O2G A:GTP900 3.3 17.3 0.3
O3B A:GTP900 3.3 18.1 0.3
PG A:GTP900 3.3 12.8 0.7
CB A:THR291 3.4 8.6 1.0
O1A A:GTP900 3.4 9.9 0.3
O3A A:GTP900 3.5 18.3 0.7
PA A:GTP900 3.6 20.0 0.7
O3G A:GTP900 3.9 17.6 0.3
NH1 A:ARG405 4.0 5.1 1.0
N A:VAL335 4.1 4.8 1.0
CA A:GLY334 4.1 6.1 1.0
O A:HOH703 4.2 9.4 1.0
O3A A:GTP900 4.2 11.5 0.3
O2A A:GTP900 4.2 18.7 0.7
O2B A:GTP900 4.3 11.3 0.3
O1B A:GTP900 4.3 16.5 0.7
N A:THR291 4.3 10.2 1.0
O2G A:GTP900 4.3 11.4 0.7
O3G A:GTP900 4.3 10.0 0.7
OD2 A:ASP310 4.4 9.4 1.0
PA A:GTP900 4.4 11.2 0.3
CG2 A:VAL335 4.4 6.6 1.0
CA A:THR291 4.5 9.7 1.0
CG2 A:THR291 4.5 8.1 1.0
O A:PHE333 4.6 7.0 1.0
O A:HOH631 4.7 10.2 1.0
C A:GLY334 4.7 6.1 1.0
CB A:VAL335 4.8 6.3 1.0

Manganese binding site 3 out of 5 in 3mof

Go back to Manganese Binding Sites List in 3mof
Manganese binding site 3 out of 5 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp


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 Oxalate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn800

b:14.9
occ:1.00
 O3 A:OXL1000 2.0 16.7 1.0
O3G A:GTP900 2.1 10.0 0.7
OD1 A:ASP311 2.1 3.6 1.0
O2 A:OXL1000 2.2 11.8 1.0
NE2 A:HIS264 2.3 6.7 1.0
NZ A:LYS244 2.3 5.1 1.0
O2G A:GTP900 2.8 17.3 0.3
C1 A:OXL1000 2.8 16.7 1.0
C2 A:OXL1000 2.9 18.4 1.0
CG A:ASP311 3.0 5.7 1.0
OD2 A:ASP311 3.2 8.1 1.0
PG A:GTP900 3.2 12.8 0.7
CE1 A:HIS264 3.3 6.2 1.0
CD2 A:HIS264 3.3 4.5 1.0
CE A:LYS244 3.3 9.9 1.0
O1G A:GTP900 3.5 9.6 0.7
O3G A:GTP900 3.7 17.6 0.3
PG A:GTP900 3.8 20.8 0.3
O2G A:GTP900 3.9 11.4 0.7
O1 A:OXL1000 4.0 20.0 1.0
NZ A:LYS290 4.0 5.2 1.0
O4 A:OXL1000 4.1 19.9 1.0
O A:HOH802 4.2 9.4 1.0
CE A:LYS290 4.2 5.8 1.0
OG A:SER286 4.3 7.8 0.5
O A:HOH631 4.3 10.2 1.0
ND1 A:HIS264 4.4 4.1 1.0
CB A:ASP311 4.4 5.8 1.0
CG A:HIS264 4.4 5.7 1.0
OG A:SER286 4.4 13.8 0.5
O3B A:GTP900 4.7 14.4 0.7
CD A:LYS244 4.8 8.4 1.0
O1G A:GTP900 4.8 18.7 0.3
CA A:SER286 4.9 10.3 0.5
CA A:SER286 4.9 11.1 0.5
CB A:SER286 4.9 10.1 0.5
O3B A:GTP900 4.9 18.1 0.3

Manganese binding site 4 out of 5 in 3mof

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Manganese binding site 4 out of 5 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp


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 Oxalate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn700

b:14.3
occ:1.00
 O3 B:OXL1200 2.0 21.6 1.0
OD1 B:ASP311 2.1 3.0 1.0
O3G B:GTP1000 2.2 13.2 1.0
O4 B:OXL1200 2.2 12.5 1.0
NE2 B:HIS264 2.3 5.7 1.0
NZ B:LYS244 2.5 2.9 1.0
C1 B:OXL1200 2.8 20.4 1.0
C2 B:OXL1200 2.8 17.4 1.0
CG B:ASP311 3.0 7.1 1.0
CE1 B:HIS264 3.2 8.7 1.0
OD2 B:ASP311 3.3 12.2 1.0
CD2 B:HIS264 3.3 6.0 1.0
PG B:GTP1000 3.3 15.8 1.0
CE B:LYS244 3.4 8.1 1.0
O1G B:GTP1000 3.8 16.7 1.0
O2G B:GTP1000 3.8 18.2 1.0
NZ B:LYS290 3.9 6.0 1.0
O1 B:OXL1200 4.0 22.5 1.0
O2 B:OXL1200 4.0 22.8 1.0
CE B:LYS290 4.2 3.6 1.0
OG B:SER286 4.2 10.8 0.5
O B:HOH667 4.2 10.1 1.0
O B:HOH705 4.3 9.4 1.0
ND1 B:HIS264 4.4 8.3 1.0
CG B:HIS264 4.4 5.5 1.0
CB B:ASP311 4.5 6.4 1.0
O3B B:GTP1000 4.7 17.9 1.0
CD B:LYS244 4.8 10.7 1.0

Manganese binding site 5 out of 5 in 3mof

Go back to Manganese Binding Sites List in 3mof
Manganese binding site 5 out of 5 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:13.7
occ:0.80
 O B:HOH667 2.1 10.1 1.0
O B:HOH716 2.1 7.2 1.0
O2B B:GTP1000 2.2 15.8 1.0
O2G B:GTP1000 2.2 18.2 1.0
OG1 B:THR291 2.2 9.5 1.0
O B:HOH820 2.2 10.6 1.0
PG B:GTP1000 3.3 15.8 1.0
CB B:THR291 3.3 5.7 1.0
PB B:GTP1000 3.3 16.6 1.0
O3B B:GTP1000 3.5 17.9 1.0
OD2 B:ASP310 3.7 9.3 1.0
O3G B:GTP1000 4.0 13.2 1.0
O2A B:GTP1000 4.1 19.1 1.0
N B:THR291 4.1 6.4 1.0
O B:HOH705 4.1 9.4 1.0
CA B:THR291 4.3 7.1 1.0
NH1 B:ARG405 4.3 5.9 1.0
CG2 B:THR291 4.4 8.4 1.0
O3A B:GTP1000 4.4 17.2 1.0
O B:ASP310 4.4 8.5 1.0
O1B B:GTP1000 4.4 14.3 1.0
CA B:GLY334 4.5 8.1 1.0
O1G B:GTP1000 4.5 16.7 1.0
CG B:ASP310 4.5 10.2 1.0
OD1 B:ASP311 4.7 3.0 1.0
O B:HOH704 4.7 8.8 1.0
PA B:GTP1000 4.7 19.4 1.0
O B:PHE333 4.8 7.1 1.0
N B:VAL335 4.8 7.7 1.0
CB B:LYS290 4.9 4.7 1.0
O3 B:OXL1200 4.9 21.6 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 17:09:57 2024

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