Sodium in PDB 4gnm: Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp

All present enzymatic activity of Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp:
4.1.1.32;

The structure of Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp, PDB code: 4gnm 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)	26.66 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.491, 84.706, 118.775, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.2

The structure of Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp (pdb code 4gnm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp, PDB code: 4gnm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:25.1 occ:1.00 O A:LEU79 2.2 21.6 1.0 O A:ASN208 2.3 24.5 1.0 O A:HOH950 2.3 24.9 1.0 O A:HOH976 2.3 23.9 1.0 O A:HOH1065 2.4 37.7 1.0 C A:LEU79 3.3 20.2 1.0 C A:ASN208 3.4 24.7 1.0 N A:LEU79 3.8 19.9 1.0 CB A:ASN208 3.9 27.2 1.0 CA A:LEU79 3.9 20.6 1.0 O A:VAL65 4.0 24.2 1.0 CB A:LEU79 4.0 20.6 1.0 CA A:ASN208 4.2 23.4 1.0 CB A:ASN209 4.3 27.3 1.0 O A:HOH1279 4.3 38.5 1.0 C A:ASN209 4.4 22.1 1.0 O A:GLY64 4.4 31.2 1.0 N A:ASN209 4.4 24.1 1.0 O A:ASN209 4.4 22.3 1.0 N A:THR80 4.5 21.2 1.0 CA A:ASN209 4.6 24.1 1.0 CB A:TRP210 4.7 21.5 1.0 N A:TRP210 4.7 20.7 1.0 C A:VAL65 4.8 23.8 1.0 CA A:THR80 4.8 19.8 1.0 CE3 A:TRP210 4.9 19.2 1.0 C A:ALA78 5.0 19.8 1.0

Sodium binding site 2 out of 2 in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:22.0 occ:1.00 O A:HOH1372 1.9 34.1 1.0 NE2 A:HIS502 2.1 28.5 1.0 OE2 A:GLU607 2.1 32.8 1.0 O A:HOH1350 2.2 24.4 0.5 O A:HOH872 2.5 24.6 1.0 CD A:GLU607 3.0 32.4 1.0 CE1 A:HIS502 3.1 29.6 1.0 OE1 A:GLU607 3.2 35.0 1.0 CD2 A:HIS502 3.2 31.0 1.0 ND1 A:HIS502 4.3 30.4 1.0 CG A:GLU607 4.3 27.9 1.0 CG A:HIS502 4.4 29.1 1.0 O A:HOH1379 4.4 45.9 1.0 NE2 A:GLN451 4.4 27.1 1.0 O A:LEU498 4.7 21.5 1.0

T.A.Johnson, T.Holyoak. The {Omega}-Loop Lid Domain of Phosphoenolpyruvate Carboxykinase Is Essential For Catalytic Function. Biochemistry V. 51 9547 2012.
ISSN: ISSN 0006-2960
PubMed: 23127136
DOI: 10.1021/BI301278T