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Magnesium in PDB 2vkf: Complexes of Dodecin with Flavin and Flavin-Like Ligands

Protein crystallography data

The structure of Complexes of Dodecin with Flavin and Flavin-Like Ligands, PDB code: 2vkf was solved by M.Grininger, G.Noell, S.Trawoeger, E.Sinner, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.03 / 1.7
Space group F 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 141.704, 141.704, 141.704, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.3

Other elements in 2vkf:

The structure of Complexes of Dodecin with Flavin and Flavin-Like Ligands also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complexes of Dodecin with Flavin and Flavin-Like Ligands (pdb code 2vkf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Complexes of Dodecin with Flavin and Flavin-Like Ligands, PDB code: 2vkf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2vkf

Go back to Magnesium Binding Sites List in 2vkf
Magnesium binding site 1 out of 2 in the Complexes of Dodecin with Flavin and Flavin-Like Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complexes of Dodecin with Flavin and Flavin-Like Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1061

b:33.3
occ:1.00
O A:HOH2053 2.2 25.8 1.0
O A:HOH2054 2.2 28.8 1.0
O A:HOH2086 4.0 53.0 0.5
OE2 A:GLU38 4.0 18.9 1.0
OE1 A:GLU38 4.1 22.6 1.0
NZ A:LYS5 4.2 20.8 1.0
O4 A:CF21066 4.4 20.3 1.0
CD A:GLU38 4.5 19.9 1.0

Magnesium binding site 2 out of 2 in 2vkf

Go back to Magnesium Binding Sites List in 2vkf
Magnesium binding site 2 out of 2 in the Complexes of Dodecin with Flavin and Flavin-Like Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complexes of Dodecin with Flavin and Flavin-Like Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1062

b:20.9
occ:1.00
OE2 A:GLU14 2.1 17.8 1.0
O A:HOH2023 2.1 19.4 1.0
O A:HOH2019 2.2 19.6 1.0
O A:HOH2022 2.2 19.4 1.0
CD A:GLU14 3.1 17.1 1.0
OE1 A:GLU14 3.4 17.1 1.0
O A:HOH2020 4.1 27.5 1.0
O A:GLU13 4.4 13.1 1.0
CG A:GLU14 4.4 15.5 1.0
CB A:GLU13 4.5 13.5 1.0
OE1 A:GLU13 4.6 25.4 1.0
C A:GLU13 4.9 12.8 1.0

Reference:

M.Grininger, G.Noell, S.Trawoeger, E.Sinner, D.Oesterhelt. Electrochemical Switching of the Flavoprotein Dodecin at Gold Surfaces Modified By Flavin-Dna Hybrid Linkers Biointerphases V. 3 51 2008.
ISSN: ISSN 1934-8630
PubMed: 20408700
DOI: 10.1116/1.2965134
Page generated: Mon Dec 14 07:42:18 2020

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