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Magnesium in PDB 5d84: Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Bound to Plp

Protein crystallography data

The structure of Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Bound to Plp, PDB code: 5d84 was solved by J.C.Grigg, M.J.Kobylarz, Y.Liu, M.S.F.Lee, D.E.Heinrichs, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.45
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.080, 115.828, 45.138, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 17.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Bound to Plp (pdb code 5d84). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Bound to Plp, PDB code: 5d84:

Magnesium binding site 1 out of 1 in 5d84

Go back to Magnesium Binding Sites List in 5d84
Magnesium binding site 1 out of 1 in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Bound to Plp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Bound to Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:22.8
occ:1.00
O A:HOH1461 2.0 30.1 1.0
O A:HOH1137 2.1 24.5 1.0
O A:HOH1427 2.1 30.5 1.0
O A:HOH1179 2.1 21.3 1.0
O A:HOH1460 2.1 23.1 1.0
O A:HOH1400 2.2 28.1 1.0
O A:HOH1199 4.0 16.2 1.0
O A:ASP144 4.2 18.0 1.0
O A:HOH1313 4.3 28.7 1.0
O A:HOH1217 4.3 30.2 1.0
OD2 A:ASP144 4.4 19.2 1.0
CB A:ASP144 4.5 19.6 1.0
O A:HOH1414 4.7 19.5 1.0
O A:HOH1339 4.8 25.0 1.0
C A:ASP144 4.9 15.3 1.0

Reference:

M.J.Kobylarz, J.C.Grigg, Y.Liu, M.S.Lee, D.E.Heinrichs, M.E.Murphy. Deciphering the Substrate Specificity of Sbna, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis. Biochemistry V. 55 927 2016.
ISSN: ISSN 0006-2960
PubMed: 26794841
DOI: 10.1021/ACS.BIOCHEM.5B01045
Page generated: Mon Dec 14 20:10:25 2020

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