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Manganese in PDB 5jmp: Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC57 and Manganese

Enzymatic activity of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC57 and Manganese

All present enzymatic activity of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC57 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, LC57 and Manganese, PDB code: 5jmp 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) 35.00 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.718, 56.580, 85.660, 104.13, 103.33, 100.12
R / Rfree (%) 17.8 / 20.8

Other elements in 5jmp:

The structure of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC57 and Manganese also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC57 and Manganese (pdb code 5jmp). 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, LC57 and Manganese, PDB code: 5jmp:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5jmp

Go back to Manganese Binding Sites List in 5jmp
Manganese binding site 1 out of 2 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC57 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, LC57 and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:13.2
occ:1.00
OE1 A:GLU233 2.1 12.7 1.0
OD1 A:ASP231 2.1 12.9 1.0
OE2 A:GLU315 2.1 12.2 1.0
O10 A:LC7501 2.2 14.5 1.0
O12 A:LC7501 2.2 14.7 1.0
OE2 A:GLU233 2.8 12.7 1.0
CD A:GLU233 2.8 12.1 1.0
C4 A:LC7501 2.9 15.7 1.0
N9 A:LC7501 2.9 15.8 1.0
CD A:GLU315 3.1 11.7 1.0
CG A:ASP231 3.1 12.8 1.0
OE1 A:GLU315 3.5 12.6 1.0
OD2 A:ASP231 3.5 13.2 1.0
NZ A:LYS205 3.6 19.6 1.0
OG A:SER232 3.9 12.2 1.0
O A:HOH640 4.0 32.8 1.0
O A:HOH604 4.0 38.7 1.0
N A:SER232 4.0 11.5 1.0
ND2 A:ASN311 4.2 12.8 1.0
CG A:GLU233 4.3 11.8 1.0
C3 A:LC7501 4.3 15.9 1.0
C11 A:LC7501 4.3 16.2 1.0
CG A:GLU315 4.3 11.0 1.0
CB A:ASP231 4.4 12.4 1.0
N A:GLU233 4.4 10.7 1.0
C A:ASP231 4.6 11.7 1.0
C2 A:LC7501 4.6 16.8 1.0
NZ A:LYS312 4.6 12.2 1.0
CA A:ASP231 4.7 11.8 1.0
CB A:SER232 4.8 11.7 1.0
CB A:GLU233 4.8 11.1 1.0
CA A:SER232 4.8 11.4 1.0
CE A:LYS205 4.9 19.8 1.0
CE1 A:HIS234 5.0 11.2 1.0

Manganese binding site 2 out of 2 in 5jmp

Go back to Manganese Binding Sites List in 5jmp
Manganese binding site 2 out of 2 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC57 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, LC57 and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:12.1
occ:1.00
OE1 B:GLU233 2.1 12.3 1.0
OE2 B:GLU315 2.1 10.7 1.0
OD1 B:ASP231 2.1 12.4 1.0
O10 B:LC7502 2.2 13.9 1.0
O12 B:LC7502 2.2 13.4 1.0
CD B:GLU233 2.8 11.6 1.0
OE2 B:GLU233 2.8 12.2 1.0
C4 B:LC7502 2.9 15.1 1.0
N9 B:LC7502 2.9 14.8 1.0
CD B:GLU315 3.0 10.9 1.0
CG B:ASP231 3.1 12.4 1.0
OE1 B:GLU315 3.4 11.4 1.0
OD2 B:ASP231 3.5 12.9 1.0
NZ B:LYS205 3.6 19.7 1.0
O B:HOH760 3.9 29.7 1.0
OG B:SER232 3.9 11.8 1.0
N B:SER232 4.0 11.1 1.0
ND2 B:ASN311 4.2 11.8 1.0
C3 B:LC7502 4.3 15.6 1.0
CG B:GLU315 4.3 10.4 1.0
CG B:GLU233 4.3 11.3 1.0
C11 B:LC7502 4.3 15.0 1.0
CB B:ASP231 4.4 12.1 1.0
N B:GLU233 4.4 10.2 1.0
C B:ASP231 4.6 11.4 1.0
C2 B:LC7502 4.7 16.0 1.0
NZ B:LYS312 4.7 12.3 1.0
CA B:ASP231 4.7 11.6 1.0
CB B:SER232 4.8 11.3 1.0
CA B:SER232 4.8 11.0 1.0
CB B:GLU233 4.9 10.6 1.0
CE B:LYS205 4.9 20.0 1.0

Reference:

S.Sooriyaarachchi, R.Chofor, M.D.Risseeuw, T.Bergfors, J.Pouyez, C.S.Dowd, L.Maes, J.Wouters, T.A.Jones, S.Van Calenbergh, S.L.Mowbray. Targeting An Aromatic Hotspot in Plasmodium Falciparum 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase with Beta-Arylpropyl Analogues of Fosmidomycin. Chemmedchem V. 11 2024 2016.
ISSN: ESSN 1860-7187
PubMed: 27487410
DOI: 10.1002/CMDC.201600249
Page generated: Tue Dec 15 04:42:23 2020

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