Magnesium in PDB 2vbv: Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and Fmn

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

The structure of Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and Fmn, PDB code: 2vbv 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 / 2.4
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.482, 73.299, 104.907, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 32.3

The structure of Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and Fmn also contains other interesting chemical elements:

Iodine	(I)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and Fmn (pdb code 2vbv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and Fmn, PDB code: 2vbv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and Fmn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and Fmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1136 b:42.1 occ:1.00 O1A A:CDP1135 2.0 25.7 1.0 O A:THR43 2.0 29.5 1.0 O1P A:FMN1140 2.0 41.7 1.0 OD1 A:ASN45 2.0 28.1 1.0 O2B A:CDP1135 2.1 26.6 1.0 OG1 A:THR43 2.2 28.6 1.0 C A:THR43 3.0 29.1 1.0 CG A:ASN45 3.1 28.6 1.0 PB A:CDP1135 3.3 28.9 1.0 CB A:THR43 3.3 28.3 1.0 PA A:CDP1135 3.4 29.1 1.0 P A:FMN1140 3.5 43.1 1.0 CA A:THR43 3.5 27.8 1.0 ND2 A:ASN45 3.6 25.4 1.0 O3B A:CDP1135 3.6 24.2 1.0 O3A A:CDP1135 3.8 23.6 1.0 N A:THR43 3.8 28.1 1.0 O A:HOH2048 3.8 24.2 1.0 O5' A:FMN1140 4.0 43.8 1.0 OE1 A:GLU107 4.0 41.5 1.0 N A:ASN45 4.1 31.8 1.0 N A:LEU44 4.2 29.8 1.0 O5' A:CDP1135 4.2 32.5 1.0 O2P A:FMN1140 4.3 37.6 1.0 CB A:ASN45 4.3 32.1 1.0 O3P A:FMN1140 4.4 37.4 1.0 CG A:GLU107 4.5 35.0 1.0 CG2 A:THR43 4.5 23.4 1.0 CA A:GLY18 4.5 33.6 1.0 O2A A:CDP1135 4.5 22.7 1.0 O1B A:CDP1135 4.6 24.8 1.0 C A:LEU44 4.6 31.7 1.0 CA A:ASN45 4.6 32.2 1.0 CA A:LEU44 4.6 30.1 1.0 CD A:GLU107 4.6 37.7 1.0 N A:GLY18 4.7 34.8 1.0 C2' A:CDP1135 4.9 33.1 1.0

Magnesium binding site 2 out of 2 in the Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and Fmn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex with Cdp and Fmn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1136 b:35.2 occ:1.00 O1A B:CDP1137 2.0 27.6 1.0 OD1 B:ASN45 2.0 27.8 1.0 O B:THR43 2.2 40.0 1.0 O2B B:CDP1137 2.2 28.8 1.0 OG1 B:THR43 2.2 40.9 1.0 O B:HOH2010 2.4 31.7 1.0 C B:THR43 2.9 40.1 1.0 PB B:CDP1137 3.1 33.7 1.0 CG B:ASN45 3.2 36.4 1.0 PA B:CDP1137 3.2 29.9 1.0 CB B:THR43 3.2 40.8 1.0 O3B B:CDP1137 3.3 26.4 1.0 CA B:THR43 3.3 41.3 1.0 N B:THR43 3.4 43.4 1.0 O3A B:CDP1137 3.5 27.3 1.0 O5' B:CDP1137 3.8 25.6 1.0 ND2 B:ASN45 4.0 36.5 1.0 O B:HOH2003 4.0 28.6 1.0 N B:LEU44 4.0 38.7 1.0 N B:ASN45 4.0 36.9 1.0 CB B:ASN45 4.2 37.2 1.0 N B:GLY18 4.4 57.1 1.0 O1B B:CDP1137 4.4 30.1 1.0 O2A B:CDP1137 4.5 27.7 1.0 CA B:GLY18 4.5 58.5 1.0 CG2 B:THR43 4.5 39.6 1.0 C B:LEU44 4.5 37.0 1.0 CA B:LEU44 4.5 37.1 1.0 CA B:ASN45 4.6 37.4 1.0 C2' B:CDP1137 4.7 31.8 1.0 C B:GLY42 4.7 45.3 1.0 CG B:GLU107 4.8 43.3 1.0 OE2 B:GLU107 4.9 45.5 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