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Manganese in PDB 4y6p: Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese

Enzymatic activity of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese

All present enzymatic activity of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese:
1.1.1.267;

Protein crystallography data

The structure of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese, PDB code: 4y6p was solved by S.Sooriyaarachchi, T.Bergfors, T.A.Jones, S.L.Mowbray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.47 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.384, 55.759, 85.433, 103.18, 102.83, 100.91
R / Rfree (%) 16.5 / 19.6

Other elements in 4y6p:

The structure of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese (pdb code 4y6p). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese, PDB code: 4y6p:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4y6p

Go back to Manganese Binding Sites List in 4y6p
Manganese binding site 1 out of 2 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:14.1
occ:1.00
 O10 A:R77501 2.1 16.0 1.0
OE2 A:GLU315 2.1 12.9 1.0
OD1 A:ASP231 2.2 12.3 1.0
OE1 A:GLU233 2.2 13.0 1.0
O12 A:R77501 2.2 16.2 1.0
OE2 A:GLU233 2.6 13.4 1.0
CD A:GLU233 2.7 12.8 1.0
C8 A:R77501 2.9 17.5 1.0
N9 A:R77501 2.9 16.9 1.0
CD A:GLU315 3.1 12.6 1.0
CG A:ASP231 3.1 12.4 1.0
OE1 A:GLU315 3.5 13.1 1.0
NZ A:LYS205 3.5 17.9 1.0
OD2 A:ASP231 3.6 12.0 1.0
OG A:SER232 3.8 14.2 1.0
O A:HOH835 3.9 31.3 1.0
O A:HOH733 3.9 28.2 1.0
N A:SER232 4.1 12.1 1.0
ND2 A:ASN311 4.2 13.7 1.0
CG A:GLU233 4.2 12.4 1.0
CG A:GLU315 4.3 11.8 1.0
C11 A:R77501 4.3 17.2 1.0
C3 A:R77501 4.3 18.4 1.0
CB A:ASP231 4.4 12.2 1.0
N A:GLU233 4.4 11.1 1.0
NZ A:LYS312 4.5 14.2 1.0
C A:ASP231 4.6 12.2 1.0
CA A:ASP231 4.7 12.1 1.0
CB A:SER232 4.8 12.7 1.0
CE A:LYS205 4.8 18.3 1.0
C1 A:R77501 4.8 20.0 1.0
CB A:GLU233 4.8 11.8 1.0
CA A:SER232 4.9 12.1 1.0
C2 A:R77501 4.9 19.4 1.0

Manganese binding site 2 out of 2 in 4y6p

Go back to Manganese Binding Sites List in 4y6p
Manganese binding site 2 out of 2 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, RC177, and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:13.9
occ:1.00
 OE2 B:GLU315 2.1 12.5 1.0
OE1 B:GLU233 2.1 12.8 1.0
OD1 B:ASP231 2.2 13.7 1.0
O10 B:R77501 2.2 15.2 1.0
O12 B:R77501 2.2 14.5 1.0
OE2 B:GLU233 2.6 13.2 1.0
CD B:GLU233 2.7 12.4 1.0
C8 B:R77501 2.9 15.6 1.0
N9 B:R77501 2.9 15.5 1.0
CD B:GLU315 3.0 12.3 1.0
CG B:ASP231 3.1 14.3 1.0
OE1 B:GLU315 3.5 13.3 1.0
OD2 B:ASP231 3.5 16.1 1.0
NZ B:LYS205 3.6 17.8 1.0
OG B:SER232 3.9 12.9 1.0
O B:HOH747 4.1 27.1 1.0
N B:SER232 4.1 11.8 1.0
CG B:GLU233 4.2 11.9 1.0
ND2 B:ASN311 4.2 14.9 1.0
CG B:GLU315 4.2 11.6 1.0
C11 B:R77501 4.3 16.0 1.0
C3 B:R77501 4.3 16.3 1.0
CB B:ASP231 4.4 13.6 1.0
NZ B:LYS312 4.4 14.3 1.0
N B:GLU233 4.5 10.6 1.0
C B:ASP231 4.6 12.2 1.0
CA B:ASP231 4.7 12.9 1.0
CB B:GLU233 4.8 11.3 1.0
CE B:LYS205 4.8 18.3 1.0
C1 B:R77501 4.8 18.1 1.0
CB B:SER232 4.8 11.8 1.0
C2 B:R77501 4.9 17.7 1.0
CA B:SER232 4.9 11.5 1.0
CE1 B:HIS234 5.0 11.8 1.0

Reference:

R.Chofor, S.Sooriyaarachchi, M.D.Risseeuw, T.Bergfors, J.Pouyez, C.Johny, A.Haymond, A.Everaert, C.S.Dowd, L.Maes, T.Coenye, A.Alex, R.D.Couch, T.A.Jones, J.Wouters, S.L.Mowbray, S.Van Calenbergh. Synthesis and Bioactivity of Beta-Substituted Fosmidomycin Analogues Targeting 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase. J.Med.Chem. 2015.
ISSN: ISSN 0022-2623
PubMed: 25781377
DOI: 10.1021/JM5014264
Page generated: Sat Oct 5 23:00:16 2024

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