Sodium in PDB 1khf: Pepck Complex with Pep

All present enzymatic activity of Pepck Complex with Pep:
4.1.1.32;

The structure of Pepck Complex with Pep, PDB code: 1khf was solved by P.Dunten, C.Belunis, R.Crowther, K.Hollfelder, U.Kammlott, W.Levin, H.Michel, G.B.Ramsey, A.Swain, D.Weber, S.J.Wertheimer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.02
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.251, 60.679, 62.032, 88.69, 70.00, 72.54
R / Rfree (%)	18.3 / 24.4

The structure of Pepck Complex with Pep also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Sodium atom in the Pepck Complex with Pep (pdb code 1khf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Pepck Complex with Pep, PDB code: 1khf:

Sodium binding site 1 out of 1 in the Pepck Complex with Pep


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pepck Complex with Pep within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:20.3 occ:1.00 O A:HOH813 2.7 16.2 1.0 O2 A:PEP703 2.8 15.4 1.0 O1P A:PEP703 2.9 19.2 1.0 O A:HOH861 3.0 15.4 1.0 O1 A:PEP703 3.1 13.8 1.0 P A:PEP703 3.4 19.0 1.0 ND2 A:ASN403 3.7 11.9 1.0 OD1 A:ASN403 3.7 9.3 1.0 C1 A:PEP703 3.8 15.2 1.0 CG A:ASN403 3.9 8.4 1.0 CB A:ALA86 3.9 11.2 1.0 C2 A:PEP703 3.9 12.1 1.0 NH2 A:ARG405 4.1 13.7 1.0 N A:ARG87 4.2 11.3 1.0 CB A:ARG87 4.3 13.3 1.0 NH2 A:ARG87 4.3 3.8 1.0 O2P A:PEP703 4.5 16.6 1.0 O A:ARG87 4.5 10.1 1.0 O A:HOH819 4.6 15.4 1.0 NE A:ARG87 4.6 8.0 1.0 CA A:ALA86 4.6 12.5 1.0 O A:HOH860 4.6 16.6 1.0 CZ A:ARG87 4.7 8.5 1.0 O3P A:PEP703 4.8 18.3 1.0 CA A:ARG87 4.8 10.8 1.0 C A:ALA86 4.9 11.9 1.0 O2' A:PEP703 5.0 15.1 1.0

P.Dunten, C.Belunis, R.Crowther, K.Hollfelder, U.Kammlott, W.Levin, H.Michel, G.B.Ramsey, A.Swain, D.Weber, S.J.Wertheimer. Crystal Structure of Human Cytosolic Phosphoenolpyruvate Carboxykinase Reveals A New Gtp-Binding Site. J.Mol.Biol. V. 316 257 2002.
ISSN: ISSN 0022-2836
PubMed: 11851336
DOI: 10.1006/JMBI.2001.5364