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Magnesium in PDB 5d86: Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F Variant

Protein crystallography data

The structure of Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F Variant, PDB code: 5d86 was solved by M.J.Kobylarz, J.C.Grigg, 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) 35.38 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.360, 115.990, 45.450, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F Variant (pdb code 5d86). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F Variant, PDB code: 5d86:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5d86

Go back to Magnesium Binding Sites List in 5d86
Magnesium binding site 1 out of 2 in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F Variant


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 Y152F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:24.8
occ:1.00
O A:HOH1166 2.0 23.6 1.0
O A:HOH1429 2.2 30.3 1.0
O A:HOH1210 2.2 27.5 1.0
O A:HOH1242 4.0 16.4 1.0
O A:HOH1336 4.2 28.9 1.0
O A:ASP144 4.3 22.5 1.0
O A:HOH1231 4.4 26.0 1.0
OD2 A:ASP144 4.4 22.5 1.0
CB A:ASP144 4.6 20.5 1.0
O A:HOH1416 4.7 21.9 1.0
O A:HOH1325 4.8 23.5 1.0
C A:ASP144 4.9 19.2 1.0

Magnesium binding site 2 out of 2 in 5d86

Go back to Magnesium Binding Sites List in 5d86
Magnesium binding site 2 out of 2 in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F Variant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:22.8
occ:1.00
O A:HOH1136 3.0 37.0 1.0
N A:SER232 3.1 14.2 1.0
NH2 A:ARG233 3.4 27.5 0.6
NE A:ARG233 3.7 24.1 0.6
CB A:SER232 3.8 16.0 1.0
CA A:SER232 3.9 14.2 1.0
CA A:ALA231 3.9 12.0 1.0
CB A:ALA231 3.9 10.3 1.0
O A:HOH1132 4.0 37.9 1.0
CD A:ARG233 4.0 21.5 0.4
C A:ALA231 4.0 10.7 1.0
CZ A:ARG233 4.0 23.5 0.6
CZ A:PHE152 4.1 16.1 1.0
C A:SER232 4.3 16.3 1.0
OG A:SER232 4.4 20.7 1.0
CG A:ARG233 4.4 17.2 0.4
N A:ARG233 4.4 14.2 1.0
CD1 A:LEU129 4.5 33.5 1.0
NH2 A:ARG132 4.6 22.2 0.5
CE2 A:PHE152 4.6 14.6 1.0
CE1 A:PHE152 4.8 16.2 1.0
CG A:ARG233 4.9 17.7 0.6
CD A:ARG233 4.9 20.8 0.6
O A:SER232 5.0 18.4 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 20:10:28 2020

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