Sodium in PDB 2vbt: Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and PO4

All present enzymatic activity of Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and PO4:
2.7.1.161;

The structure of Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and PO4, PDB code: 2vbt was solved by M.D.Hartmann, M.Ammelburg, S.Djuranovic, J.Martin, A.N.Lupas, K.Zeth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.7
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.720, 77.720, 106.868, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26.6

The binding sites of Sodium atom in the Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and PO4 (pdb code 2vbt). 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 Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and PO4, PDB code: 2vbt:

Sodium binding site 1 out of 1 in the Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and PO4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and PO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1138 b:73.6 occ:1.00 OG1 A:THR43 2.3 57.8 1.0 O2B A:CDP1137 2.4 75.6 1.0 OD1 A:ASN45 2.6 58.3 1.0 O3A A:CDP1137 2.7 76.4 1.0 O1 A:PO41139 2.8 90.6 1.0 O1A A:CDP1137 3.0 73.4 1.0 PB A:CDP1137 3.1 74.7 1.0 O A:THR43 3.1 56.6 1.0 CG A:ASN45 3.4 54.7 1.0 PA A:CDP1137 3.5 74.0 1.0 ND2 A:ASN45 3.5 50.8 1.0 O1B A:CDP1137 3.5 73.4 1.0 CB A:THR43 3.7 57.1 1.0 C A:THR43 3.9 56.2 1.0 O3 A:PO41139 3.9 92.9 1.0 OE1 A:GLU107 4.0 62.4 1.0 P A:PO41139 4.0 93.3 1.0 N A:GLY18 4.2 91.1 1.0 CA A:THR43 4.2 57.3 1.0 N A:THR43 4.3 58.5 1.0 O3B A:CDP1137 4.4 75.3 1.0 N A:GLU17 4.4 85.2 1.0 O2A A:CDP1137 4.5 75.1 1.0 O5' A:CDP1137 4.6 73.2 1.0 CD A:GLU107 4.7 59.2 1.0 CG2 A:THR43 4.7 56.3 1.0 CA A:GLY18 4.7 92.5 1.0 N A:GLY16 4.7 77.5 1.0 O A:HOH2030 4.8 54.8 1.0 CB A:ASN45 4.8 54.6 1.0 CA A:GLY16 4.8 79.9 1.0 O4 A:PO41139 4.9 93.9 1.0 N A:ASN45 4.9 54.1 1.0 CG A:GLU107 4.9 57.4 1.0 C A:GLY16 5.0 82.3 1.0

M.Ammelburg, M.D.Hartmann, S.Djuranovic, V.Alva, K.K.Koretke, J.Martin, G.Sauer, V.Truffault, K.Zeth, A.N.Lupas, M.Coles. A Ctp-Dependent Archaeal Riboflavin Kinase Forms A Bridge in the Evolution of Cradle-Loop Barrels. Structure V. 15 1577 2007.
ISSN: ISSN 0969-2126
PubMed: 18073108
DOI: 10.1016/J.STR.2007.09.027