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Magnesium in PDB 5d87: Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant

Protein crystallography data

The structure of Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant, PDB code: 5d87 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) 34.92 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.980, 115.170, 44.670, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 17.8

Other elements in 5d87:

The structure of Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant (pdb code 5d87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant, PDB code: 5d87:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5d87

Go back to Magnesium Binding Sites List in 5d87
Magnesium binding site 1 out of 3 in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G 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/S185G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:6.9
occ:0.62
O A:HOH608 2.1 15.2 1.0
O A:HOH874 2.1 16.9 1.0
O A:HOH615 2.1 16.1 1.0
O A:HOH823 2.2 17.2 1.0
O A:HOH639 4.0 11.2 1.0
O A:ASP144 4.1 14.7 1.0
O A:HOH725 4.2 20.8 1.0
O A:HOH624 4.4 19.8 1.0
OD2 A:ASP144 4.5 15.4 1.0
CB A:ASP144 4.6 13.2 1.0
O A:HOH845 4.7 13.2 1.0
O A:HOH742 4.7 18.9 1.0
C A:ASP144 4.9 13.4 1.0

Magnesium binding site 2 out of 3 in 5d87

Go back to Magnesium Binding Sites List in 5d87
Magnesium binding site 2 out of 3 in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G 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/S185G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:12.3
occ:1.00
O A:HOH850 3.0 32.2 1.0
O A:HOH700 3.1 12.4 1.0
NH1 A:ARG49 3.1 12.1 1.0
O A:HOH717 3.2 21.9 1.0
O A:HOH663 3.2 14.6 1.0
CD A:ARG49 3.5 12.8 1.0
CG1 A:VAL16 4.1 12.1 1.0
CZ A:ARG49 4.1 12.1 1.0
O A:HOH880 4.1 16.9 1.0
CA A:GLY164 4.1 8.0 1.0
O A:HOH780 4.1 13.5 1.0
NE A:ARG49 4.2 11.1 1.0
CA A:GLY17 4.5 9.9 1.0
O A:HOH781 4.5 32.2 1.0
O A:VAL16 4.6 12.2 1.0
CG A:ARG49 4.7 13.5 1.0
O A:HOH686 4.7 13.9 1.0
CB A:ARG49 4.7 11.3 1.0
N A:GLY17 4.8 10.1 1.0
C A:VAL16 4.8 13.2 1.0
O A:HOH855 4.8 45.5 1.0
CA A:ARG49 4.8 7.8 1.0
OE2 A:GLU168 5.0 11.9 1.0

Magnesium binding site 3 out of 3 in 5d87

Go back to Magnesium Binding Sites List in 5d87
Magnesium binding site 3 out of 3 in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:45.5
occ:1.00
O A:HOH534 2.1 33.0 1.0
O A:HOH899 2.1 59.5 1.0
O A:HOH564 2.2 42.1 1.0
O A:HOH579 2.3 22.5 1.0
O A:HOH690 4.1 19.1 1.0
ND1 A:HIS25 4.2 15.9 1.0
OE2 A:GLU32 4.2 26.2 1.0
CE1 A:HIS25 4.5 15.1 1.0
OE1 A:GLU32 4.5 20.7 1.0
O A:HOH621 4.5 27.9 1.0
O A:HOH646 4.6 27.5 1.0
O A:HOH849 4.7 39.1 1.0
CD A:GLU32 4.8 20.5 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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