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Magnesium in PDB 5jwc: Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552

Enzymatic activity of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552

All present enzymatic activity of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552:
1.6.99.3;

Protein crystallography data

The structure of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552, PDB code: 5jwc was solved by Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.45 / 2.05
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 192.603, 192.603, 92.025, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.1

Other elements in 5jwc:

The structure of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 also contains other interesting chemical elements:

Fluorine (F) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 (pdb code 5jwc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552, PDB code: 5jwc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5jwc

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Magnesium binding site 1 out of 8 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:39.0
occ:1.00
 O2P A:FAD601 2.7 29.7 1.0
N A:GLY149 2.8 29.4 1.0
O A:ILE352 2.8 32.1 1.0
N A:CYS355 3.1 32.4 1.0
CA A:GLY149 3.2 30.7 1.0
N A:ASP354 3.3 28.1 1.0
SG A:CYS355 3.3 35.3 1.0
C A:ALA147 3.4 28.4 1.0
CB A:CYS355 3.5 31.3 1.0
N A:VAL148 3.5 29.3 1.0
CA A:ALA147 3.6 28.9 1.0
C A:GLY353 3.6 28.3 1.0
CA A:GLY353 3.8 29.3 1.0
P A:FAD601 3.9 26.5 1.0
CA A:CYS355 3.9 36.9 1.0
O A:ALA147 3.9 30.0 1.0
C A:ILE352 3.9 31.0 1.0
C A:VAL148 3.9 28.4 1.0
C A:ASP354 4.0 33.9 1.0
CA A:ASP354 4.1 31.9 1.0
C A:GLY149 4.2 31.4 1.0
O1P A:FAD601 4.2 27.3 1.0
O A:GLY149 4.3 30.3 1.0
CA A:VAL148 4.3 29.9 1.0
O3P A:FAD601 4.3 28.5 1.0
N A:GLY353 4.4 29.4 1.0
O A:GLY353 4.4 29.0 1.0
CB A:ALA147 4.4 23.9 1.0
CB A:ASP354 4.5 28.4 1.0
O A:ILE146 4.6 27.8 1.0
N A:ALA147 4.7 29.5 1.0
C A:CYS355 4.9 38.2 1.0

Magnesium binding site 2 out of 8 in 5jwc

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Magnesium binding site 2 out of 8 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:34.4
occ:1.00
 O A:ALA147 2.7 30.0 1.0
O1P A:FAD601 2.7 27.3 1.0
N A:GLY49 2.9 27.4 1.0
N A:GLY52 2.9 27.8 1.0
CA A:GLY49 3.2 27.7 1.0
O5B A:FAD601 3.3 29.2 1.0
C A:GLY49 3.4 26.6 1.0
CB A:ALA147 3.5 23.9 1.0
CA A:GLY52 3.6 26.9 1.0
N A:GLY51 3.7 24.5 1.0
C5B A:FAD601 3.7 24.5 1.0
O A:GLY49 3.7 23.1 1.0
C4B A:FAD601 3.7 30.0 1.0
C A:GLY47 3.7 26.7 1.0
C A:ALA147 3.8 28.4 1.0
N A:TRP50 3.9 25.1 1.0
C A:GLY51 3.9 27.7 1.0
O A:GLY47 3.9 26.6 1.0
P A:FAD601 3.9 26.5 1.0
CA A:GLY47 4.0 26.1 1.0
N A:SER48 4.0 25.9 1.0
CA A:GLY51 4.0 27.0 1.0
C A:SER48 4.1 29.6 1.0
O3P A:FAD601 4.3 28.5 1.0
CA A:ALA147 4.3 28.9 1.0
PA A:FAD601 4.4 27.4 1.0
O4B A:FAD601 4.4 30.3 1.0
CA A:SER48 4.5 26.8 1.0
C A:TRP50 4.5 26.4 1.0
O2A A:FAD601 4.6 23.2 1.0
O A:LEU46 4.6 29.4 1.0
N A:PHE53 4.6 27.1 1.0
C A:GLY52 4.7 27.7 1.0
O2P A:FAD601 4.8 29.7 1.0
CA A:TRP50 4.9 25.8 1.0
N A:VAL148 4.9 29.3 1.0
C3B A:FAD601 4.9 29.2 1.0

Magnesium binding site 3 out of 8 in 5jwc

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Magnesium binding site 3 out of 8 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:36.2
occ:1.00
 O A:THR76 2.8 26.0 1.0
O A:HOH810 2.9 35.4 1.0
NH2 A:ARG72 2.9 26.4 1.0
O2A A:FAD601 3.0 23.2 1.0
CA A:GLY49 3.4 27.7 1.0
N A:THR76 3.6 25.6 1.0
C A:THR76 3.7 27.1 1.0
CB A:THR76 3.8 26.3 1.0
CZ A:ARG72 3.8 31.3 1.0
N A:TRP50 3.8 25.1 1.0
NH1 A:ARG72 3.8 28.2 1.0
CA A:THR76 3.9 25.6 1.0
CD1 A:TRP50 3.9 26.9 1.0
C A:GLY49 4.0 26.6 1.0
CD1 A:PHE75 4.0 29.1 1.0
CG2 A:THR78 4.0 25.3 1.0
CE1 A:PHE75 4.0 25.5 1.0
PA A:FAD601 4.1 27.4 1.0
NE1 A:TRP50 4.3 24.1 1.0
O5B A:FAD601 4.4 29.2 1.0
O1A A:FAD601 4.4 26.5 1.0
O4' A:FAD601 4.6 28.1 1.0
O A:SER48 4.6 26.7 1.0
OG1 A:THR76 4.6 26.9 1.0
N A:GLY49 4.7 27.4 1.0
CG A:TRP50 4.7 21.3 1.0
C A:PHE75 4.7 29.8 1.0
CG2 A:THR76 4.8 22.9 1.0
CG A:PHE75 4.9 28.9 1.0
CA A:TRP50 4.9 25.8 1.0
CZ A:PHE75 5.0 26.7 1.0
N A:PHE77 5.0 25.8 1.0
O A:GLY49 5.0 23.1 1.0

Magnesium binding site 4 out of 8 in 5jwc

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Magnesium binding site 4 out of 8 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:45.7
occ:1.00
 O1A A:FAD601 2.6 26.5 1.0
NZ A:LYS168 2.7 39.2 1.0
O A:HOH704 2.7 44.7 1.0
N A:ALA150 2.9 29.9 1.0
O A:ALA150 3.3 35.8 1.0
O A:HOH855 3.4 34.5 1.0
O3P A:FAD601 3.5 28.5 1.0
CA A:GLY149 3.5 30.7 1.0
O A:HOH840 3.6 35.8 1.0
PA A:FAD601 3.7 27.4 1.0
C A:GLY149 3.7 31.4 1.0
O A:HOH746 3.8 33.7 1.0
CA A:ALA150 3.8 30.8 1.0
C A:ALA150 3.9 39.6 1.0
CE A:LYS168 4.0 51.3 1.0
OD2 A:ASP354 4.0 34.0 1.0
O A:HOH808 4.1 34.4 1.0
CB A:ALA150 4.2 33.7 1.0
O4' A:FAD601 4.5 28.1 1.0
O A:HOH909 4.6 41.8 1.0
C5B A:FAD601 4.6 24.5 1.0
O5B A:FAD601 4.6 29.2 1.0
CB A:ASP354 4.7 28.4 1.0
O2A A:FAD601 4.8 23.2 1.0
CG A:ASP354 4.8 32.5 1.0
N A:GLY149 4.8 29.4 1.0
C5' A:FAD601 4.8 26.6 1.0
O A:HOH810 4.9 35.4 1.0
CD A:LYS168 4.9 48.6 1.0
O A:GLY149 4.9 30.3 1.0
P A:FAD601 4.9 26.5 1.0
O A:VAL148 4.9 29.7 1.0

Magnesium binding site 5 out of 8 in 5jwc

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Magnesium binding site 5 out of 8 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg602

b:37.2
occ:1.00
 O2P H:FAD601 2.7 29.6 1.0
N H:GLY149 2.8 29.7 1.0
O H:ILE352 2.8 32.6 1.0
N H:CYS355 3.1 32.4 1.0
SG H:CYS355 3.2 35.8 1.0
CA H:GLY149 3.3 29.2 1.0
N H:ASP354 3.3 26.0 1.0
C H:ALA147 3.4 29.6 1.0
N H:VAL148 3.5 27.3 1.0
CB H:CYS355 3.5 30.9 1.0
CA H:ALA147 3.6 28.5 1.0
C H:GLY353 3.6 29.2 1.0
CA H:GLY353 3.8 29.0 1.0
CA H:CYS355 3.9 35.2 1.0
C H:ILE352 3.9 32.2 1.0
P H:FAD601 3.9 25.0 1.0
O H:ALA147 3.9 30.6 1.0
C H:VAL148 4.0 27.0 1.0
C H:ASP354 4.0 33.0 1.0
CA H:ASP354 4.1 32.8 1.0
C H:GLY149 4.2 31.2 1.0
CA H:VAL148 4.3 30.1 1.0
O1P H:FAD601 4.3 26.6 1.0
O H:GLY149 4.3 30.6 1.0
N H:GLY353 4.3 29.1 1.0
O H:GLY353 4.4 29.8 1.0
O3P H:FAD601 4.4 26.6 1.0
CB H:ALA147 4.4 22.9 1.0
CB H:ASP354 4.5 29.5 1.0
O H:ILE146 4.6 26.6 1.0
N H:ALA147 4.6 30.1 1.0
C H:CYS355 4.9 37.6 1.0

Magnesium binding site 6 out of 8 in 5jwc

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Magnesium binding site 6 out of 8 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:35.9
occ:1.00
 O H:ALA147 2.7 30.6 1.0
O1P H:FAD601 2.7 26.6 1.0
N H:GLY49 2.8 28.7 1.0
N H:GLY52 2.9 27.7 1.0
CA H:GLY49 3.2 25.9 1.0
C H:GLY49 3.4 27.2 1.0
O5B H:FAD601 3.4 29.0 1.0
CB H:ALA147 3.5 22.9 1.0
CA H:GLY52 3.6 26.1 1.0
O H:GLY49 3.6 23.7 1.0
N H:GLY51 3.7 25.1 1.0
C5B H:FAD601 3.7 24.0 1.0
C H:GLY47 3.7 27.7 1.0
C4B H:FAD601 3.7 31.4 1.0
C H:ALA147 3.8 29.6 1.0
O H:GLY47 3.9 28.4 1.0
C H:GLY51 3.9 26.5 1.0
N H:TRP50 3.9 25.4 1.0
CA H:GLY47 4.0 27.3 1.0
N H:SER48 4.0 27.6 1.0
CA H:GLY51 4.0 27.0 1.0
P H:FAD601 4.0 25.0 1.0
C H:SER48 4.0 32.3 1.0
CA H:ALA147 4.3 28.5 1.0
O3P H:FAD601 4.3 26.6 1.0
PA H:FAD601 4.4 27.0 1.0
O4B H:FAD601 4.4 28.4 1.0
CA H:SER48 4.5 27.7 1.0
C H:TRP50 4.6 24.9 1.0
O H:LEU46 4.6 29.6 1.0
O2A H:FAD601 4.6 24.5 1.0
N H:PHE53 4.6 24.4 1.0
C H:GLY52 4.7 26.4 1.0
O2P H:FAD601 4.9 29.6 1.0
CA H:TRP50 4.9 25.5 1.0
N H:VAL148 4.9 27.3 1.0
C3B H:FAD601 4.9 29.1 1.0
O3B H:FAD601 5.0 27.7 1.0

Magnesium binding site 7 out of 8 in 5jwc

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Magnesium binding site 7 out of 8 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg604

b:36.3
occ:1.00
 O H:THR76 2.8 27.9 1.0
O H:HOH815 2.8 34.5 1.0
NH2 H:ARG72 3.0 29.4 1.0
O2A H:FAD601 3.1 24.5 1.0
CA H:GLY49 3.4 25.9 1.0
N H:THR76 3.5 26.2 1.0
C H:THR76 3.7 28.6 1.0
CB H:THR76 3.7 26.3 1.0
N H:TRP50 3.8 25.4 1.0
CA H:THR76 3.8 24.3 1.0
CZ H:ARG72 3.8 31.5 1.0
NH1 H:ARG72 3.9 29.3 1.0
CD1 H:PHE75 3.9 28.4 1.0
CE1 H:PHE75 3.9 25.7 1.0
CD1 H:TRP50 3.9 25.4 1.0
C H:GLY49 4.0 27.2 1.0
CG2 H:THR78 4.0 26.6 1.0
PA H:FAD601 4.1 27.0 1.0
NE1 H:TRP50 4.4 22.6 1.0
O5B H:FAD601 4.4 29.0 1.0
O1A H:FAD601 4.5 25.6 1.0
O H:SER48 4.6 27.8 1.0
OG1 H:THR76 4.6 27.9 1.0
O4' H:FAD601 4.6 27.0 1.0
CG H:TRP50 4.7 20.7 1.0
C H:PHE75 4.7 29.8 1.0
N H:GLY49 4.7 28.7 1.0
CG2 H:THR76 4.7 23.0 1.0
CG H:PHE75 4.8 27.1 1.0
CZ H:PHE75 4.8 27.5 1.0
CA H:TRP50 4.9 25.5 1.0
N H:PHE77 4.9 26.7 1.0

Magnesium binding site 8 out of 8 in 5jwc

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Magnesium binding site 8 out of 8 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg605

b:47.3
occ:1.00
 O H:HOH702 2.5 44.1 1.0
O1A H:FAD601 2.6 25.6 1.0
N H:ALA150 2.9 28.9 1.0
NZ H:LYS168 3.3 34.4 1.0
O H:ALA150 3.4 37.9 1.0
O3P H:FAD601 3.4 26.6 1.0
CA H:GLY149 3.4 29.2 1.0
O H:HOH874 3.5 35.7 1.0
PA H:FAD601 3.6 27.0 1.0
C H:GLY149 3.6 31.2 1.0
CE H:LYS168 3.7 45.8 1.0
O H:HOH816 3.7 34.9 1.0
CA H:ALA150 3.8 35.3 1.0
OD2 H:ASP354 3.9 35.3 1.0
O H:HOH749 3.9 33.1 1.0
C H:ALA150 4.0 40.3 1.0
O H:HOH795 4.2 37.2 1.0
CB H:ALA150 4.2 34.8 1.0
O4' H:FAD601 4.3 27.0 1.0
O H:HOH919 4.4 41.0 1.0
CB H:ASP354 4.5 29.5 1.0
CG H:ASP354 4.6 33.5 1.0
C5B H:FAD601 4.6 24.0 1.0
O5B H:FAD601 4.6 29.0 1.0
O2A H:FAD601 4.7 24.5 1.0
N H:GLY149 4.7 29.7 1.0
P H:FAD601 4.8 25.0 1.0
C5' H:FAD601 4.8 26.4 1.0
O H:GLY149 4.8 30.6 1.0
O2P H:FAD601 5.0 29.6 1.0
O H:VAL148 5.0 30.3 1.0

Reference:

Y.Yang, Y.Yu, X.Li, J.Li, Y.Wu, J.Yu, J.Ge, Z.Huang, L.Jiang, Y.Rao, M.Yang. Target Elucidation By Cocrystal Structures of Nadh-Ubiquinone Oxidoreductase of Plasmodium Falciparum (PFNDH2) with Small Molecule to Eliminate Drug-Resistant Malaria J. Med. Chem. V. 60 1994 2017.
ISSN: ISSN 1520-4804
PubMed: 28195463
DOI: 10.1021/ACS.JMEDCHEM.6B01733
Page generated: Sun Sep 29 17:58:59 2024

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