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Sodium in PDB 2x0i: 2.9 A Resolution Structure of Malate Dehydrogenase From Archaeoglobus Fulgidus in Complex with Nadh

Enzymatic activity of 2.9 A Resolution Structure of Malate Dehydrogenase From Archaeoglobus Fulgidus in Complex with Nadh

All present enzymatic activity of 2.9 A Resolution Structure of Malate Dehydrogenase From Archaeoglobus Fulgidus in Complex with Nadh:
1.1.1.37;

Protein crystallography data

The structure of 2.9 A Resolution Structure of Malate Dehydrogenase From Archaeoglobus Fulgidus in Complex with Nadh, PDB code: 2x0i was solved by A.Irimia, D.Madern, G.Zaccai, F.M.D.Vellieux, A.Karshikoff, G.Tibbelin, R.Ladenstein, T.Lien, N.-K.Birkeland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.48 / 2.91
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 112.964, 112.964, 71.294, 90.00, 90.00, 90.00
R / Rfree (%) 15.19 / 21.86

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.9 A Resolution Structure of Malate Dehydrogenase From Archaeoglobus Fulgidus in Complex with Nadh (pdb code 2x0i). 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 2.9 A Resolution Structure of Malate Dehydrogenase From Archaeoglobus Fulgidus in Complex with Nadh, PDB code: 2x0i:

Sodium binding site 1 out of 1 in 2x0i

Go back to Sodium Binding Sites List in 2x0i
Sodium binding site 1 out of 1 in the 2.9 A Resolution Structure of Malate Dehydrogenase From Archaeoglobus Fulgidus in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.9 A Resolution Structure of Malate Dehydrogenase From Archaeoglobus Fulgidus in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3000

b:52.0
occ:1.00
 CA A:GLY294 3.6 62.1 1.0
N A:GLY294 3.7 57.1 1.0
OE2 A:GLU301 3.8 0.4 1.0
O A:GLY297 4.0 65.6 1.0
C A:GLY294 4.1 65.4 1.0
O A:LYS292 4.1 49.0 1.0
CB A:ASN296 4.1 64.7 1.0
C A:LEU293 4.1 49.7 1.0
CD A:GLU301 4.2 93.4 1.0
N A:ASN296 4.2 61.6 1.0
CA A:ASN296 4.5 62.3 1.0
N A:LYS295 4.5 66.7 1.0
O A:GLY294 4.5 58.6 1.0
O A:LEU293 4.6 40.6 1.0
OE1 A:GLU301 4.6 85.4 1.0
N A:GLY297 4.6 63.9 1.0
C A:ASN296 4.6 66.0 1.0
C A:GLY297 4.7 55.7 1.0
CD A:LYS292 4.7 54.4 1.0
CG A:GLU301 4.7 80.5 1.0
C A:LYS292 4.8 47.6 1.0
CA A:LEU293 4.8 52.7 1.0
OD1 A:ASN296 4.9 90.7 1.0
OD1 A:ASP264 5.0 83.3 1.0

Reference:

A.Irimia, F.M.D.Vellieux, D.Madern, G.Zaccai, A.Karshikoff, G.Tibbelin, R.Ladenstein, T.Lien, N.-K.Birkeland. The 2.9A Resolution Crystal Structure of Malate Dehydrogenase From Archaeoglobus Fulgidus: Mechanisms of Oligomerisation and Thermal Stabilisation. J.Mol.Biol. V. 335 343 2004.
ISSN: ISSN 0022-2836
PubMed: 14659762
DOI: 10.1016/J.JMB.2003.10.054
Page generated: Mon Oct 7 05:02:40 2024

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