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

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

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

Magnesium

(Mg)

3 atoms

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant, PDB code: 5d87:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K405 b:26.6 occ:1.00 N A:SER232 3.1 10.2 1.0 O A:HOH594 3.2 27.3 1.0 CD A:ARG233 3.5 15.1 0.5 O A:HOH652 3.6 25.4 1.0 O A:HOH628 3.7 27.5 1.0 CA A:ALA231 3.9 8.6 1.0 NE A:ARG233 3.9 21.2 0.5 CB A:ALA231 3.9 8.8 1.0 CB A:SER232 3.9 12.2 1.0 CA A:SER232 3.9 9.7 1.0 CZ A:PHE152 4.0 13.3 1.0 C A:ALA231 4.0 10.1 1.0 NE A:ARG233 4.1 19.1 0.5 CG A:ARG233 4.3 13.8 0.5 C A:SER232 4.3 11.7 1.0 N A:ARG233 4.3 10.5 1.0 O A:HOH863 4.4 37.1 1.0 CD1 A:LEU129 4.5 20.9 1.0 NH2 A:ARG233 4.5 26.9 0.5 CE2 A:PHE152 4.5 11.3 1.0 OG A:SER232 4.5 15.9 1.0 CG A:ARG233 4.6 13.4 0.5 CE1 A:PHE152 4.7 13.0 1.0 CZ A:ARG233 4.7 22.6 0.5 CD A:ARG233 4.7 18.1 0.5 CD2 A:LEU129 4.8 26.1 1.0 O A:HOH830 4.9 37.9 1.0 O A:HOH729 5.0 32.8 1.0

Potassium binding site 2 out of 2 in the Staphyloferrin B Precursor Biosynthetic Enzyme Sbna Y152F/S185G Variant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K406 b:25.9 occ:1.00 O A:HOH587 3.0 30.2 1.0 O A:HOH557 3.0 23.3 1.0 O A:HOH693 3.2 11.0 1.0 O A:HOH640 3.3 16.4 1.0 CZ2 A:TRP148 3.3 19.9 1.0 CG2 A:VAL136 3.8 9.4 1.0 CE2 A:TRP148 4.0 14.4 1.0 NE1 A:TRP148 4.0 16.6 1.0 CB A:VAL136 4.0 6.5 1.0 CA A:ILE133 4.0 10.1 1.0 CB A:SER73 4.1 16.1 1.0 CG1 A:ILE133 4.2 11.7 1.0 CG1 A:VAL136 4.2 11.4 1.0 NH1 A:ARG233 4.2 22.8 0.5 CH2 A:TRP148 4.3 18.1 1.0 NH1 A:ARG233 4.5 23.7 0.5 NH2 A:ARG233 4.5 26.9 0.5 CB A:ILE133 4.5 11.2 1.0 O A:ILE133 4.7 10.1 1.0 OE1 A:GLU72 4.8 15.4 1.0 N A:ILE133 4.8 9.8 1.0 CG2 A:ILE133 4.8 12.5 1.0 O A:ARG132 4.8 9.3 1.0 O A:HOH688 4.8 8.7 1.0 O A:HOH570 4.8 24.1 1.0 O A:HOH654 4.9 22.8 1.0 C A:ILE133 4.9 9.5 1.0 OG A:SER73 4.9 21.5 1.0 CZ A:ARG233 4.9 22.6 0.5

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