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Manganese in PDB 5fh4: The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Beta-Sulfopyruvate and Gtp

Enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Beta-Sulfopyruvate and Gtp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Beta-Sulfopyruvate and Gtp:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Beta-Sulfopyruvate and Gtp, PDB code: 5fh4 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) 34.34 / 1.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.590, 118.809, 60.508, 90.00, 109.30, 90.00
R / Rfree (%) 20.4 / 22.9

Other elements in 5fh4:

The structure of The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Beta-Sulfopyruvate and Gtp also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Beta-Sulfopyruvate and Gtp (pdb code 5fh4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Beta-Sulfopyruvate and Gtp, PDB code: 5fh4:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5fh4

Go back to Manganese Binding Sites List in 5fh4
Manganese binding site 1 out of 3 in the The Structure of Rat Cytosolic Pepck Variant E89D 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 Variant E89D in Complex with Beta-Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:14.9
occ:1.00
 O2B A:GTP704 2.2 14.6 1.0
O3G A:GTP704 2.2 15.4 1.0
OG1 A:THR291 2.2 15.6 1.0
O A:HOH837 2.2 13.7 1.0
O A:HOH970 2.2 14.5 1.0
O A:HOH817 2.3 14.4 1.0
CB A:THR291 3.3 16.3 1.0
PB A:GTP704 3.3 14.9 1.0
PG A:GTP704 3.3 14.7 1.0
O3B A:GTP704 3.5 14.4 1.0
OD2 A:ASP310 3.8 15.0 1.0
O2A A:GTP704 4.0 16.4 1.0
O2G A:GTP704 4.0 13.1 1.0
O A:HOH1002 4.1 18.1 1.0
N A:THR291 4.1 15.5 1.0
CA A:THR291 4.2 16.1 1.0
CG2 A:THR291 4.4 17.1 1.0
O A:ASP310 4.4 13.9 1.0
NH1 A:ARG405 4.4 17.8 1.0
O1B A:GTP704 4.4 13.8 1.0
O3A A:GTP704 4.4 15.3 1.0
CA A:GLY334 4.4 16.8 1.0
CG A:ASP310 4.5 14.6 1.0
O1G A:GTP704 4.6 15.2 1.0
O A:HOH1063 4.6 14.9 1.0
O A:PHE333 4.7 15.2 1.0
OD1 A:ASP311 4.7 12.3 1.0
N A:VAL335 4.7 17.4 1.0
PA A:GTP704 4.8 15.8 1.0
CB A:LYS290 5.0 14.0 1.0

Manganese binding site 2 out of 3 in 5fh4

Go back to Manganese Binding Sites List in 5fh4
Manganese binding site 2 out of 3 in the The Structure of Rat Cytosolic Pepck Variant E89D 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 Variant E89D in Complex with Beta-Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:13.2
occ:1.00
 OD1 A:ASP311 2.0 12.3 1.0
O1 A:SPV705 2.0 14.3 1.0
O2G A:GTP704 2.1 13.1 1.0
NZ A:LYS244 2.2 13.1 1.0
O2 A:SPV705 2.3 19.8 1.0
NE2 A:HIS264 2.3 12.0 1.0
C1 A:SPV705 2.8 19.6 1.0
C2 A:SPV705 3.0 19.6 1.0
CG A:ASP311 3.0 12.8 1.0
CD2 A:HIS264 3.3 11.6 1.0
CE1 A:HIS264 3.3 12.1 1.0
PG A:GTP704 3.3 14.7 1.0
OD2 A:ASP311 3.3 12.6 1.0
CE A:LYS244 3.4 13.2 1.0
O1G A:GTP704 3.8 15.2 1.0
NZ A:LYS290 3.9 13.4 1.0
O3G A:GTP704 3.9 15.4 1.0
O2' A:SPV705 4.0 23.1 1.0
CE A:LYS290 4.2 13.2 1.0
O A:HOH1002 4.2 18.1 1.0
O A:HOH837 4.3 13.7 1.0
ND1 A:HIS264 4.4 11.9 1.0
CG A:HIS264 4.4 11.6 1.0
CB A:ASP311 4.4 13.0 1.0
C3 A:SPV705 4.5 21.1 1.0
OG A:SER286 4.6 17.4 0.5
O3B A:GTP704 4.6 14.4 1.0
CD A:LYS244 4.7 13.0 1.0
O A:ASP311 5.0 12.6 1.0

Manganese binding site 3 out of 3 in 5fh4

Go back to Manganese Binding Sites List in 5fh4
Manganese binding site 3 out of 3 in the The Structure of Rat Cytosolic Pepck Variant E89D 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 Variant E89D in Complex with Beta-Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:23.9
occ:1.00
 OE1 A:GLU607 2.0 22.2 1.0
NE2 A:HIS502 2.2 23.6 1.0
O A:HOH1193 2.2 28.1 1.0
O A:HOH891 2.6 21.3 1.0
CD A:GLU607 3.0 21.4 1.0
CE1 A:HIS502 3.1 24.9 1.0
CD2 A:HIS502 3.2 23.4 1.0
OE2 A:GLU607 3.3 21.1 1.0
ND1 A:HIS502 4.2 25.2 1.0
CG A:HIS502 4.3 24.2 1.0
CG A:GLU607 4.4 21.0 1.0
O A:HOH1263 4.4 31.9 1.0
O A:HOH1229 4.4 33.2 1.0
NE2 A:GLN451 4.5 17.7 1.0
O A:LEU498 4.8 16.8 1.0

Reference:

T.A.Johnson, M.J.Mcleod, T.Holyoak. Utilization of Substrate Intrinsic Binding Energy For Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase. Biochemistry V. 55 575 2016.
ISSN: ISSN 0006-2960
PubMed: 26709450
DOI: 10.1021/ACS.BIOCHEM.5B01215
Page generated: Sat Aug 16 17:24:13 2025

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