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Manganese in PDB 4gae: Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor

Enzymatic activity of Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor

All present enzymatic activity of Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor:
1.1.1.267;

Protein crystallography data

The structure of Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor, PDB code: 4gae was solved by J.Diao, J.Xue, G.Cai, L.Deng, Y.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.64 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.360, 77.280, 109.410, 90.00, 91.50, 90.00
R / Rfree (%) 23 / 27.3

Other elements in 4gae:

The structure of Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor (pdb code 4gae). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor, PDB code: 4gae:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4gae

Go back to Manganese Binding Sites List in 4gae
Manganese binding site 1 out of 4 in the Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:26.9
occ:1.00
 O2 A:FOB502 2.1 28.9 0.5
OE1 A:GLU233 2.1 29.3 1.0
OE2 A:GLU315 2.1 19.8 1.0
O2 A:FOQ503 2.2 26.7 0.5
OD1 A:ASP231 2.2 30.8 1.0
O1 A:FOQ503 2.2 28.4 0.5
O1 A:FOB502 2.4 30.9 0.5
CD A:GLU233 2.8 26.9 1.0
OE2 A:GLU233 2.8 25.6 1.0
N1 A:FOB502 2.8 31.1 0.5
C1 A:FOB502 3.0 31.5 0.5
N1 A:FOQ503 3.0 28.4 0.5
C1 A:FOQ503 3.0 29.0 0.5
CD A:GLU315 3.0 24.3 1.0
CG A:ASP231 3.2 30.2 1.0
OE1 A:GLU315 3.4 23.6 1.0
OD2 A:ASP231 3.6 26.9 1.0
OG A:SER232 3.9 31.9 1.0
N A:SER232 4.1 28.3 1.0
C3 A:FOB502 4.1 33.6 0.5
C2 A:FOB502 4.1 31.5 0.5
CG A:GLU315 4.2 21.5 1.0
N A:GLU233 4.2 25.0 1.0
CG A:GLU233 4.2 22.7 1.0
ND2 A:ASN311 4.3 29.4 1.0
C5N A:NDP501 4.3 32.7 1.0
CH3 A:FOB502 4.4 30.1 0.5
CB A:ASP231 4.4 27.5 1.0
C2 A:FOQ503 4.4 28.7 0.5
CH3 A:FOQ503 4.4 27.4 0.5
C A:ASP231 4.6 27.8 1.0
NZ A:LYS312 4.6 23.5 1.0
CB A:SER232 4.6 27.7 1.0
NZ A:LYS205 4.6 43.3 1.0
CA A:ASP231 4.7 27.6 1.0
C3 A:FOQ503 4.7 31.2 0.5
CA A:SER232 4.7 27.6 1.0
C4 A:FOQ503 4.7 33.2 0.5
CB A:GLU233 4.7 22.1 1.0
CE1 A:HIS234 4.8 27.3 1.0
ND1 A:HIS234 4.9 26.8 1.0
C A:SER232 5.0 28.2 1.0

Manganese binding site 2 out of 4 in 4gae

Go back to Manganese Binding Sites List in 4gae
Manganese binding site 2 out of 4 in the Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:24.4
occ:1.00
 OE1 B:GLU233 2.1 26.9 1.0
O2 B:FOB502 2.1 30.3 0.5
OE2 B:GLU315 2.1 16.4 1.0
O2 B:FOQ503 2.1 25.3 0.5
OD1 B:ASP231 2.2 19.1 1.0
O1 B:FOQ503 2.3 23.0 0.5
O1 B:FOB502 2.4 27.0 0.5
CD B:GLU233 2.8 25.6 1.0
OE2 B:GLU233 2.9 25.2 1.0
N1 B:FOB502 3.0 29.2 0.5
N1 B:FOQ503 3.0 24.7 0.5
C1 B:FOQ503 3.0 24.9 0.5
CD B:GLU315 3.1 17.0 1.0
C1 B:FOB502 3.1 28.9 0.5
CG B:ASP231 3.1 24.7 1.0
OE1 B:GLU315 3.5 13.8 1.0
OD2 B:ASP231 3.6 24.9 1.0
NZ B:LYS205 3.7 26.0 1.0
OG B:SER232 4.0 22.2 1.0
ND2 B:ASN311 4.1 20.1 1.0
C3 B:FOB502 4.2 30.1 0.5
CG B:GLU233 4.3 24.8 1.0
CG B:GLU315 4.3 16.2 1.0
N B:SER232 4.3 26.0 1.0
C5N B:NDP501 4.3 27.7 1.0
C2 B:FOB502 4.3 29.1 0.5
N B:GLU233 4.3 23.9 1.0
CB B:ASP231 4.3 24.6 1.0
C2 B:FOQ503 4.4 23.9 0.5
CH3 B:FOQ503 4.5 23.1 0.5
CH3 B:FOB502 4.5 26.6 0.5
NZ B:LYS312 4.6 20.0 1.0
C4 B:FOQ503 4.6 25.1 0.5
C B:ASP231 4.6 26.6 1.0
CA B:ASP231 4.7 25.6 1.0
CB B:GLU233 4.7 23.5 1.0
C3 B:FOQ503 4.8 24.0 0.5
CE B:LYS205 4.9 21.9 1.0
CB B:SER232 4.9 21.5 1.0
CA B:SER232 4.9 23.9 1.0

Manganese binding site 3 out of 4 in 4gae

Go back to Manganese Binding Sites List in 4gae
Manganese binding site 3 out of 4 in the Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn505

b:40.8
occ:1.00
 O B:GLN239 2.4 22.8 1.0
O A:HOH1542 2.4 26.8 1.0
O B:LEU241 2.4 31.4 1.0
O B:HOH654 2.5 29.9 1.0
OD1 A:ASP242 2.5 26.3 1.0
O B:HOH623 2.7 30.9 1.0
O A:HOH1514 2.7 24.0 1.0
CG A:ASP242 3.4 28.7 1.0
C B:GLN239 3.4 22.4 1.0
C B:LEU241 3.5 30.1 1.0
OD2 A:ASP242 3.7 31.2 1.0
C B:CYS240 4.1 28.1 1.0
N B:LEU241 4.1 29.1 1.0
CA B:GLN239 4.2 23.2 1.0
O B:CYS240 4.3 31.1 1.0
N B:CYS240 4.4 23.4 1.0
N B:ASN243 4.4 28.0 1.0
N B:ASP242 4.4 29.7 1.0
CA B:LEU241 4.5 29.7 1.0
ND2 B:ASN243 4.5 27.5 1.0
CA B:CYS240 4.5 25.7 1.0
CA B:ASP242 4.5 28.5 1.0
O B:PHE238 4.6 21.9 1.0
CG B:ASN243 4.7 30.7 1.0
CB A:ASP242 4.7 25.3 1.0
OH B:TYR366 4.7 28.9 1.0
O B:HOH605 4.8 20.9 1.0
CA A:ASP242 4.9 25.9 1.0
O A:CYS240 4.9 31.0 1.0
C B:ASP242 4.9 28.6 1.0
N A:ASP242 4.9 27.6 1.0
NH2 B:ARG373 4.9 31.0 1.0
OD1 B:ASN243 5.0 28.1 1.0

Manganese binding site 4 out of 4 in 4gae

Go back to Manganese Binding Sites List in 4gae
Manganese binding site 4 out of 4 in the Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Plasmodium Dxr in Complex with A Pyridine- Containing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn506

b:49.8
occ:1.00
 OD1 B:ASN452 2.5 35.7 1.0
O B:HOH615 2.7 26.5 1.0
CG B:ASN452 3.6 34.6 1.0
ND2 B:ASN452 4.2 33.4 1.0
O B:SER450 4.3 32.9 1.0
O B:GLU449 4.3 34.5 1.0
CB B:ASN452 4.8 32.6 1.0
O B:PHE451 4.9 28.2 1.0
C B:SER450 5.0 32.8 1.0

Reference:

J.Xue, J.Diao, G.Cai, L.Deng, B.Zheng, Y.Yao, Y.Song. Antimalarial and Structural Studies of Pyridine-Containing Inhibitors of 1-Deoxyxylulose-5-Phosphate Reductoisomerase. Acs Med Chem Lett V. 4 278 2013.
ISSN: ISSN 1948-5875
PubMed: 23795240
DOI: 10.1021/ML300419R
Page generated: Sat Oct 5 19:28:38 2024

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