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

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

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

Protein crystallography data

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

Resolution Low / High (Å) 28.83 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.154, 119.683, 86.849, 90.00, 107.05, 90.00
R / Rfree (%) 16.8 / 19.3

Other elements in 3dtb:

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

Manganese binding site 1 out of 4 in 3dtb

Go back to Manganese Binding Sites List in 3dtb
Manganese binding site 1 out of 4 in the The Structure of Rat Cytosolic Pepck 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 in Complex with Phosphoglycolate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn700

b:4.4
occ:0.90
 O2P A:PGA900 2.1 4.2 0.8
OD1 A:ASP311 2.1 6.6 1.0
NZ A:LYS244 2.2 7.5 1.0
O1 A:PGA900 2.2 5.3 0.8
NE2 A:HIS264 2.2 5.7 1.0
O1P A:PGA900 2.4 4.9 0.8
P A:PGA900 2.9 5.2 0.8
C1 A:PGA900 3.0 5.1 0.8
CG A:ASP311 3.1 7.2 1.0
CD2 A:HIS264 3.1 5.2 1.0
C2 A:PGA900 3.2 6.8 0.8
CE1 A:HIS264 3.2 5.4 1.0
CE A:LYS244 3.3 6.1 1.0
OD2 A:ASP311 3.3 7.2 1.0
O4P A:PGA900 3.9 6.0 0.8
O3P A:PGA900 3.9 5.2 0.8
NZ A:LYS290 4.0 6.2 1.0
CE A:LYS290 4.0 6.8 1.0
O2 A:PGA900 4.2 7.0 0.8
OG A:SER286 4.2 9.1 1.0
O A:HOH3430 4.3 7.0 1.0
ND1 A:HIS264 4.3 3.6 1.0
CG A:HIS264 4.3 3.4 1.0
O A:HOH3382 4.4 9.9 1.0
CB A:ASP311 4.5 5.4 1.0
CD A:LYS244 4.6 6.7 1.0
CA A:SER286 4.8 7.7 1.0
CB A:SER286 4.8 7.6 1.0
O A:ASP311 4.8 6.0 1.0
CZ A:PHE485 4.9 5.0 1.0
CE2 A:PHE485 4.9 5.1 1.0

Manganese binding site 2 out of 4 in 3dtb

Go back to Manganese Binding Sites List in 3dtb
Manganese binding site 2 out of 4 in the The Structure of Rat Cytosolic Pepck 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 in Complex with Phosphoglycolate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:5.4
occ:0.80
 O A:HOH3430 2.1 7.0 1.0
O3B A:GDP800 2.1 3.2 0.8
O3P A:PGA900 2.1 5.2 0.8
O A:HOH3507 2.2 9.6 1.0
O A:HOH3427 2.3 7.4 1.0
OG1 A:THR291 2.4 6.8 1.0
PB A:GDP800 3.2 4.5 0.8
O2B A:GDP800 3.2 5.5 0.8
P A:PGA900 3.5 5.2 0.8
CB A:THR291 3.5 5.8 1.0
OD2 A:ASP310 3.8 7.8 1.0
O2P A:PGA900 3.9 4.2 0.8
N A:THR291 4.1 5.7 1.0
O2A A:GDP800 4.1 5.2 0.8
O A:HOH3382 4.1 9.9 1.0
O1B A:GDP800 4.3 4.0 0.8
O3A A:GDP800 4.3 4.7 0.8
O A:ASP310 4.3 7.3 1.0
CA A:THR291 4.4 6.3 1.0
O A:PHE333 4.4 6.9 1.0
CG A:ASP310 4.4 6.6 1.0
O4P A:PGA900 4.4 6.0 0.8
O1P A:PGA900 4.4 4.9 0.8
CA A:GLY334 4.5 6.6 1.0
NH1 A:ARG405 4.5 5.8 1.0
OD1 A:ASP311 4.5 6.6 1.0
CG2 A:THR291 4.6 7.9 1.0
PA A:GDP800 4.7 5.1 0.8
CE A:LYS290 4.8 6.8 1.0
CB A:LYS290 4.8 5.2 1.0
NZ A:LYS290 4.9 6.2 1.0
N A:VAL335 4.9 6.2 1.0

Manganese binding site 3 out of 4 in 3dtb

Go back to Manganese Binding Sites List in 3dtb
Manganese binding site 3 out of 4 in the The Structure of Rat Cytosolic Pepck 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 in Complex with Phosphoglycolate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn700

b:5.1
occ:0.90
 O2P B:PGA900 2.1 6.0 0.8
OD1 B:ASP311 2.2 9.6 1.0
O B:HOH1800 2.2 8.8 1.0
NZ B:LYS244 2.3 5.0 1.0
NE2 B:HIS264 2.3 7.7 1.0
O B:HOH1578 2.3 11.1 1.0
CG B:ASP311 3.1 8.2 1.0
CD2 B:HIS264 3.2 6.5 1.0
CE1 B:HIS264 3.2 7.1 1.0
OD2 B:ASP311 3.2 8.6 1.0
CE B:LYS244 3.3 6.0 1.0
P B:PGA900 3.3 7.7 0.8
O4P B:PGA900 3.6 10.4 0.8
NZ B:LYS290 3.9 8.9 0.4
NZ B:LYS290 4.1 14.8 0.6
O3P B:PGA900 4.2 9.9 0.8
O B:HOH1116 4.3 13.7 1.0
O B:HOH1149 4.3 10.5 1.0
O B:HOH1581 4.3 10.8 1.0
O1P B:PGA900 4.3 11.4 0.8
ND1 B:HIS264 4.3 5.6 1.0
CG B:HIS264 4.4 4.4 1.0
O B:HOH1572 4.4 12.1 1.0
CB B:ASP311 4.5 7.7 1.0
CD B:LYS244 4.6 6.8 1.0
O B:HOH1555 4.8 12.1 1.0
CE B:LYS290 4.8 11.7 0.4
CE2 B:PHE485 4.9 7.4 1.0
CZ B:PHE485 4.9 7.4 1.0
O B:ASP311 4.9 8.2 1.0

Manganese binding site 4 out of 4 in 3dtb

Go back to Manganese Binding Sites List in 3dtb
Manganese binding site 4 out of 4 in the The Structure of Rat Cytosolic Pepck 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 in Complex with Phosphoglycolate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:7.9
occ:0.80
 O2B B:GDP800 2.2 7.0 0.8
O B:HOH1152 2.2 10.9 1.0
O B:HOH1163 2.2 10.8 1.0
OG1 B:THR291 2.2 9.5 1.0
O B:HOH1149 2.2 10.5 1.0
O B:HOH1581 2.3 10.8 1.0
CB B:THR291 3.3 8.2 1.0
PB B:GDP800 3.4 8.2 0.8
O1B B:GDP800 3.6 9.6 0.8
OD2 B:ASP310 3.8 10.8 1.0
N B:THR291 4.0 9.3 1.0
O B:HOH1116 4.1 13.7 1.0
O B:HOH1800 4.2 8.8 1.0
O2A B:GDP800 4.3 8.6 0.8
CA B:THR291 4.3 9.2 1.0
O3A B:GDP800 4.4 8.6 0.8
CG2 B:THR291 4.4 9.3 1.0
O3B B:GDP800 4.4 8.5 0.8
O B:ASP310 4.4 9.3 1.0
O B:HOH1115 4.6 11.9 1.0
CA B:GLY334 4.6 8.5 1.0
CG B:ASP310 4.6 8.8 1.0
O3P B:PGA900 4.7 9.9 0.8
PA B:GDP800 4.7 9.0 0.8
O1A B:GDP800 4.7 9.7 0.8
NZ B:LYS290 4.8 8.9 0.4
O B:PHE333 4.8 9.8 1.0
OD1 B:ASP311 4.9 9.6 1.0
CB B:LYS290 4.9 8.9 0.4
N B:VAL335 4.9 9.2 1.0
CB B:LYS290 5.0 9.0 0.6

Reference:

S.M.Sullivan, T.Holyoak. Enzymes with Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead of Conformational Selection. Proc.Natl.Acad.Sci.Usa V. 105 13829 2008.
ISSN: ISSN 0027-8424
PubMed: 18772387
DOI: 10.1073/PNAS.0805364105
Page generated: Sat Oct 5 16:06:25 2024

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