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Manganese in PDB 3dt7: The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp

Enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 3dt7 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) 29.15 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.019, 119.503, 87.283, 90.00, 107.07, 90.00
R / Rfree (%) 17.4 / 20.9

Other elements in 3dt7:

The structure of The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate 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 in Complex with Beta- Sulfopyruvate and Gtp (pdb code 3dt7). 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 in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 3dt7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 3dt7

Go back to Manganese Binding Sites List in 3dt7
Manganese binding site 1 out of 5 in the The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate 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 in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn700

b:3.1
occ:1.00
 O1 A:SPV900 2.1 4.3 1.0
OD1 A:ASP311 2.1 4.2 1.0
O1G A:GTP800 2.2 2.0 0.8
O2 A:SPV900 2.2 4.2 1.0
NZ A:LYS244 2.3 2.3 1.0
NE2 A:HIS264 2.3 4.5 1.0
C1 A:SPV900 3.0 6.4 1.0
C2 A:SPV900 3.0 2.8 1.0
CG A:ASP311 3.0 2.3 1.0
CD2 A:HIS264 3.2 2.0 1.0
CE1 A:HIS264 3.3 2.8 1.0
OD2 A:ASP311 3.3 2.0 1.0
PG A:GTP800 3.3 2.4 0.8
CE A:LYS244 3.3 2.4 1.0
O3G A:GTP800 3.8 2.0 0.8
O2G A:GTP800 3.9 2.0 0.8
NZ A:LYS290 4.0 2.2 1.0
O A:HOH3480 4.2 4.9 1.0
CE A:LYS290 4.2 3.3 1.0
O2' A:SPV900 4.2 4.7 1.0
O A:HOH3432 4.3 4.2 1.0
OG A:SER286 4.4 5.8 1.0
ND1 A:HIS264 4.4 2.0 1.0
CG A:HIS264 4.4 2.0 1.0
C3 A:SPV900 4.5 4.0 1.0
CB A:ASP311 4.5 2.0 1.0
CD A:LYS244 4.7 3.1 1.0
O3B A:GTP800 4.7 2.5 0.8
CA A:SER286 4.8 6.2 1.0
CB A:SER286 4.8 4.6 1.0
O A:ASP311 4.9 3.8 1.0
CZ A:PHE485 5.0 2.4 1.0

Manganese binding site 2 out of 5 in 3dt7

Go back to Manganese Binding Sites List in 3dt7
Manganese binding site 2 out of 5 in the The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate 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 in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:2.8
occ:0.80
 MN A:MN703 1.0 2.2 0.2
OG1 A:THR291 2.1 3.4 1.0
O A:HOH3480 2.1 4.9 1.0
O2B A:GTP800 2.2 2.0 0.8
O3G A:GTP800 2.2 2.0 0.8
O A:HOH3557 2.3 8.2 1.0
O A:HOH3477 2.4 6.3 1.0
PB A:GTP800 3.3 2.0 0.8
PG A:GTP800 3.3 2.4 0.8
CB A:THR291 3.4 3.5 1.0
O3B A:GTP800 3.5 2.5 0.8
OD2 A:ASP310 3.6 5.2 1.0
O1G A:GTP800 3.9 2.0 0.8
O A:HOH3432 3.9 4.2 1.0
N A:THR291 4.0 4.4 1.0
O2A A:GTP800 4.2 2.7 0.8
O A:ASP310 4.2 3.9 1.0
CG A:ASP310 4.2 4.2 1.0
CA A:THR291 4.2 3.9 1.0
OD1 A:ASP311 4.3 4.2 1.0
O3A A:GTP800 4.3 2.9 0.8
O1B A:GTP800 4.4 2.0 0.8
CG2 A:THR291 4.4 4.4 1.0
O A:PHE333 4.5 3.2 1.0
O2G A:GTP800 4.5 2.0 0.8
CA A:GLY334 4.5 2.1 1.0
NH1 A:ARG405 4.6 2.1 1.0
PA A:GTP800 4.6 3.6 0.8
O1A A:GTP800 4.9 3.1 0.8
OD1 A:ASP310 4.9 5.4 1.0
CG A:ASP311 4.9 2.3 1.0
CB A:LYS290 4.9 4.4 1.0
CB A:ASP310 4.9 2.8 1.0
CB A:ASP311 4.9 2.0 1.0
O A:HOH3531 5.0 7.7 1.0

Manganese binding site 3 out of 5 in 3dt7

Go back to Manganese Binding Sites List in 3dt7
Manganese binding site 3 out of 5 in the The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate 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 in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:2.2
occ:0.20
 MN A:MN701 1.0 2.8 0.8
O A:HOH3477 1.6 6.3 1.0
O2B A:GTP800 1.9 2.0 0.8
O3G A:GTP800 1.9 2.0 0.8
OG1 A:THR291 2.6 3.4 1.0
PB A:GTP800 2.8 2.0 0.8
O3B A:GTP800 2.8 2.5 0.8
PG A:GTP800 2.9 2.4 0.8
O A:HOH3480 3.0 4.9 1.0
O A:HOH3557 3.0 8.2 1.0
O2A A:GTP800 3.3 2.7 0.8
CB A:THR291 3.5 3.5 1.0
O3A A:GTP800 3.6 2.9 0.8
PA A:GTP800 3.9 3.6 0.8
O1G A:GTP800 3.9 2.0 0.8
O2G A:GTP800 4.0 2.0 0.8
NH1 A:ARG405 4.1 2.1 1.0
O1B A:GTP800 4.1 2.0 0.8
N A:THR291 4.2 4.4 1.0
N A:VAL335 4.3 3.2 1.0
CA A:GLY334 4.3 2.1 1.0
O A:HOH3432 4.4 4.2 1.0
O1A A:GTP800 4.4 3.1 0.8
OD2 A:ASP310 4.4 5.2 1.0
O A:HOH3531 4.5 7.7 1.0
O A:PHE333 4.5 3.2 1.0
CA A:THR291 4.5 3.9 1.0
CG2 A:VAL335 4.6 5.9 1.0
CG2 A:THR291 4.6 4.4 1.0
C A:GLY334 4.9 2.4 1.0
OD1 A:ASP311 4.9 4.2 1.0

Manganese binding site 4 out of 5 in 3dt7

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Manganese binding site 4 out of 5 in the The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate 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 in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn700

b:4.1
occ:1.00
 O1 B:SPV900 2.2 3.5 1.0
OD1 B:ASP311 2.2 3.1 1.0
O2G B:GTP800 2.2 2.3 1.0
O2 B:SPV900 2.3 4.0 1.0
NE2 B:HIS264 2.3 2.5 1.0
NZ B:LYS244 2.3 2.1 1.0
C1 B:SPV900 2.9 3.7 1.0
C2 B:SPV900 3.0 3.8 1.0
CG B:ASP311 3.1 3.1 1.0
CD2 B:HIS264 3.2 3.3 1.0
OD2 B:ASP311 3.3 5.1 1.0
CE1 B:HIS264 3.3 3.6 1.0
PG B:GTP800 3.4 5.0 1.0
CE B:LYS244 3.4 2.0 1.0
O3G B:GTP800 3.9 5.9 1.0
NZ B:LYS290 4.0 3.6 1.0
O1G B:GTP800 4.0 4.5 1.0
CE B:LYS290 4.1 2.1 1.0
O2' B:SPV900 4.2 5.5 1.0
O B:HOH3884 4.2 2.4 1.0
O B:HOH3851 4.3 6.3 1.0
OG B:SER286 4.3 13.0 0.5
CG B:HIS264 4.4 2.0 1.0
ND1 B:HIS264 4.4 3.1 1.0
C3 B:SPV900 4.5 3.0 1.0
CB B:ASP311 4.5 2.0 1.0
O3B B:GTP800 4.7 4.9 1.0
CD B:LYS244 4.7 2.6 1.0
CB B:SER286 4.8 5.4 0.5
CB B:SER286 4.9 6.9 0.5
O B:ASP311 4.9 4.6 1.0

Manganese binding site 5 out of 5 in 3dt7

Go back to Manganese Binding Sites List in 3dt7
Manganese binding site 5 out of 5 in the The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate 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 in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:4.1
occ:1.00
 O1G B:GTP800 2.1 4.5 1.0
O2B B:GTP800 2.1 4.3 1.0
O B:HOH3898 2.2 3.8 1.0
O B:HOH3884 2.2 2.4 1.0
OG1 B:THR291 2.2 2.4 1.0
O B:HOH3887 2.3 5.0 1.0
PG B:GTP800 3.3 5.0 1.0
PB B:GTP800 3.3 4.3 1.0
CB B:THR291 3.4 2.0 1.0
O3B B:GTP800 3.4 4.9 1.0
OD2 B:ASP310 3.8 4.8 1.0
O2G B:GTP800 4.0 2.3 1.0
O1A B:GTP800 4.0 5.6 1.0
O B:HOH3851 4.0 6.3 1.0
N B:THR291 4.0 3.6 1.0
CA B:THR291 4.3 3.2 1.0
CG2 B:THR291 4.3 5.5 1.0
O3A B:GTP800 4.3 3.6 1.0
O1B B:GTP800 4.4 3.4 1.0
NH1 B:ARG405 4.4 2.0 1.0
O B:ASP310 4.4 4.6 1.0
CA B:GLY334 4.5 4.0 1.0
O3G B:GTP800 4.5 5.9 1.0
CG B:ASP310 4.5 2.0 1.0
OD1 B:ASP311 4.6 3.1 1.0
O B:PHE333 4.6 3.2 1.0
O B:HOH3850 4.7 3.5 1.0
N B:VAL335 4.8 3.7 1.0
PA B:GTP800 4.8 5.4 1.0
CB B:LYS290 4.9 3.2 1.0

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 16:06:16 2024

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