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Magnesium in PDB 5jwb: Structure of NDH2 From Plasmodium Falciparum in Complex with Nadh

Enzymatic activity of Structure of NDH2 From Plasmodium Falciparum in Complex with Nadh

All present enzymatic activity of Structure of NDH2 From Plasmodium Falciparum in Complex with Nadh:
1.6.5.3;

Protein crystallography data

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

Resolution Low / High (Å) 45.91 / 2.70
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 191.530, 191.530, 91.258, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of NDH2 From Plasmodium Falciparum in Complex with Nadh (pdb code 5jwb). 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 Nadh, PDB code: 5jwb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5jwb

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


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 Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:45.1
occ:1.00
 O A:ILE352 2.6 39.4 1.0
O2P A:FAD601 2.7 33.7 1.0
N A:GLY149 2.9 37.9 1.0
N A:CYS355 3.2 33.7 1.0
N A:ASP354 3.2 35.4 1.0
SG A:CYS355 3.3 36.6 1.0
CA A:GLY149 3.3 34.8 1.0
C A:GLY353 3.4 33.4 1.0
C A:ALA147 3.4 37.8 1.0
CA A:GLY353 3.5 32.6 1.0
CB A:CYS355 3.6 35.2 1.0
CA A:ALA147 3.6 35.2 1.0
N A:VAL148 3.6 35.2 1.0
C A:ILE352 3.7 35.7 1.0
P A:FAD601 3.9 27.0 1.0
O A:ALA147 3.9 34.0 1.0
CA A:CYS355 4.0 38.4 1.0
N A:GLY353 4.0 32.8 1.0
C A:VAL148 4.1 37.8 1.0
CA A:ASP354 4.1 30.3 1.0
C A:ASP354 4.1 35.2 1.0
O A:GLY353 4.1 35.5 1.0
O1P A:FAD601 4.3 31.4 1.0
CB A:ALA147 4.3 33.8 1.0
O3P A:FAD601 4.4 36.5 1.0
C A:GLY149 4.4 33.7 1.0
CA A:VAL148 4.5 34.4 1.0
CB A:ASP354 4.6 30.1 1.0
O A:GLY149 4.7 39.7 1.0
N A:ALA147 4.7 30.6 1.0
O A:ILE146 4.7 35.2 1.0

Magnesium binding site 2 out of 8 in 5jwb

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


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 Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:37.9
occ:1.00
 O A:ALA147 2.7 34.0 1.0
O1P A:FAD601 2.7 31.4 1.0
N A:GLY49 2.9 32.8 1.0
N A:GLY52 2.9 29.9 1.0
CA A:GLY49 3.2 34.7 1.0
CB A:ALA147 3.4 33.8 1.0
C A:GLY49 3.4 34.1 1.0
O5B A:FAD601 3.5 31.2 1.0
CA A:GLY52 3.6 31.3 1.0
C A:GLY47 3.7 35.0 1.0
O A:GLY49 3.7 30.8 1.0
N A:GLY51 3.8 27.1 1.0
C A:ALA147 3.8 37.8 1.0
C5B A:FAD601 3.8 28.9 1.0
C4B A:FAD601 3.9 33.0 1.0
O A:GLY47 3.9 35.4 1.0
C A:GLY51 3.9 32.9 1.0
N A:SER48 4.0 34.1 1.0
CA A:GLY47 4.0 33.1 1.0
C A:SER48 4.0 33.6 1.0
CA A:GLY51 4.0 31.5 1.0
P A:FAD601 4.0 27.0 1.0
N A:TRP50 4.0 33.4 1.0
CA A:ALA147 4.2 35.2 1.0
O3P A:FAD601 4.4 36.5 1.0
CA A:SER48 4.4 30.7 1.0
O4B A:FAD601 4.5 37.0 1.0
PA A:FAD601 4.5 30.3 1.0
O A:LEU46 4.6 36.9 1.0
N A:PHE53 4.6 30.7 1.0
C A:TRP50 4.6 31.1 1.0
C A:GLY52 4.7 32.6 1.0
O2A A:FAD601 4.8 25.4 1.0
O2P A:FAD601 4.8 33.7 1.0
N A:VAL148 4.9 35.2 1.0
CA A:TRP50 5.0 29.5 1.0

Magnesium binding site 3 out of 8 in 5jwb

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


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 Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:45.5
occ:1.00
 O2A A:FAD601 2.9 25.4 1.0
O A:THR76 3.0 33.7 1.0
NH2 A:ARG72 3.1 33.3 1.0
CA A:GLY49 3.5 34.7 1.0
NH1 A:ARG72 3.6 43.3 1.0
CG2 A:THR78 3.8 27.3 1.0
CZ A:ARG72 3.8 40.5 1.0
PA A:FAD601 3.9 30.3 1.0
CB A:THR76 3.9 36.3 1.0
N A:THR76 4.0 33.8 1.0
C A:THR76 4.0 30.8 1.0
N A:TRP50 4.0 33.4 1.0
CA A:THR76 4.1 36.4 1.0
CD1 A:TRP50 4.1 27.2 1.0
C A:GLY49 4.2 34.1 1.0
O5B A:FAD601 4.2 31.2 1.0
O1A A:FAD601 4.3 29.8 1.0
CE1 A:PHE75 4.4 29.4 1.0
O4' A:FAD601 4.4 32.9 1.0
CD1 A:PHE75 4.5 31.9 1.0
OG1 A:THR76 4.6 40.3 1.0
N A:GLY49 4.7 32.8 1.0
NE1 A:TRP50 4.7 28.4 1.0
O A:SER48 4.7 34.5 1.0

Magnesium binding site 4 out of 8 in 5jwb

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


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 Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:47.8
occ:1.00
 N A:ALA150 2.8 30.9 1.0
O1A A:FAD601 2.8 29.8 1.0
OD2 A:ASP354 3.1 35.8 1.0
O A:ALA150 3.1 40.7 1.0
NZ A:LYS168 3.3 48.6 1.0
O3P A:FAD601 3.4 36.5 1.0
CA A:GLY149 3.5 34.8 1.0
C A:GLY149 3.7 33.7 1.0
CE A:LYS168 3.7 51.9 1.0
CA A:ALA150 3.7 37.8 1.0
PA A:FAD601 3.8 30.3 1.0
C A:ALA150 3.8 40.0 1.0
CG A:ASP354 3.9 38.5 1.0
CB A:ASP354 3.9 30.1 1.0
CB A:ALA150 4.1 41.0 1.0
O4' A:FAD601 4.2 32.9 1.0
C5' A:FAD601 4.6 30.2 1.0
P A:FAD601 4.6 27.0 1.0
O A:HOH714 4.7 40.2 1.0
O2A A:FAD601 4.7 25.4 1.0
O2P A:FAD601 4.8 33.7 1.0
C4' A:FAD601 4.8 34.1 1.0
O A:GLY149 4.8 39.7 1.0
C3' A:FAD601 4.9 35.6 1.0
N A:GLY149 4.9 37.9 1.0
O5B A:FAD601 4.9 31.2 1.0
CD A:LYS168 4.9 49.6 1.0
C5B A:FAD601 4.9 28.9 1.0
O5' A:FAD601 5.0 34.3 1.0
O A:HOH709 5.0 34.9 1.0

Magnesium binding site 5 out of 8 in 5jwb

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


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 Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:43.4
occ:1.00
 O H:ILE352 2.6 38.6 1.0
O2P H:FAD602 2.7 33.0 1.0
N H:GLY149 2.9 34.2 1.0
CA H:GLY149 3.3 33.1 1.0
N H:CYS355 3.3 36.0 1.0
N H:ASP354 3.3 33.2 1.0
C H:ALA147 3.4 35.7 1.0
SG H:CYS355 3.4 38.5 1.0
N H:VAL148 3.5 32.8 1.0
C H:GLY353 3.5 35.0 1.0
CA H:ALA147 3.5 37.5 1.0
CA H:GLY353 3.5 32.1 1.0
C H:ILE352 3.7 36.5 1.0
CB H:CYS355 3.7 40.4 1.0
P H:FAD602 3.8 29.6 1.0
O H:ALA147 3.8 33.4 1.0
C H:VAL148 4.0 35.1 1.0
N H:GLY353 4.1 34.7 1.0
CA H:CYS355 4.1 39.4 1.0
CA H:ASP354 4.2 27.7 1.0
C H:ASP354 4.2 35.6 1.0
O1P H:FAD602 4.2 31.6 1.0
O H:GLY353 4.2 36.7 1.0
O3P H:FAD602 4.3 36.8 1.0
CB H:ALA147 4.3 34.9 1.0
C H:GLY149 4.4 34.2 1.0
CA H:VAL148 4.4 34.7 1.0
CB H:ASP354 4.6 33.5 1.0
O H:ILE146 4.6 36.3 1.0
O H:GLY149 4.6 34.8 1.0
N H:ALA147 4.6 32.1 1.0

Magnesium binding site 6 out of 8 in 5jwb

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


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 Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg604

b:39.6
occ:1.00
 O1P H:FAD602 2.6 31.6 1.0
O H:ALA147 2.7 33.4 1.0
N H:GLY52 2.8 30.0 1.0
N H:GLY49 2.9 32.2 1.0
CA H:GLY49 3.2 36.4 1.0
CB H:ALA147 3.4 34.9 1.0
C H:GLY49 3.4 35.2 1.0
O5B H:FAD602 3.5 29.8 1.0
CA H:GLY52 3.6 33.0 1.0
N H:GLY51 3.7 28.5 1.0
C H:ALA147 3.7 35.7 1.0
O H:GLY49 3.7 29.7 1.0
C H:GLY47 3.8 39.2 1.0
C H:GLY51 3.8 33.5 1.0
C5B H:FAD602 3.9 26.4 1.0
CA H:GLY51 3.9 29.4 1.0
O H:GLY47 3.9 34.6 1.0
C4B H:FAD602 3.9 33.8 1.0
P H:FAD602 3.9 29.6 1.0
N H:TRP50 4.0 33.2 1.0
C H:SER48 4.1 35.7 1.0
N H:SER48 4.1 36.8 1.0
CA H:GLY47 4.2 32.9 1.0
CA H:ALA147 4.2 37.5 1.0
O3P H:FAD602 4.3 36.8 1.0
PA H:FAD602 4.4 33.3 1.0
CA H:SER48 4.5 31.5 1.0
C H:TRP50 4.5 32.9 1.0
O4B H:FAD602 4.6 37.0 1.0
N H:PHE53 4.7 31.2 1.0
O H:LEU46 4.7 36.4 1.0
C H:GLY52 4.7 35.8 1.0
O2A H:FAD602 4.7 28.1 1.0
O2P H:FAD602 4.7 33.0 1.0
CA H:TRP50 4.9 29.0 1.0
N H:VAL148 4.9 32.8 1.0
O H:GLY51 5.0 34.8 1.0

Magnesium binding site 7 out of 8 in 5jwb

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


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 Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg605

b:45.9
occ:1.00
 O2A H:FAD602 2.8 28.1 1.0
NH2 H:ARG72 3.0 31.3 1.0
O H:THR76 3.2 35.8 1.0
CA H:GLY49 3.3 36.4 1.0
NH1 H:ARG72 3.7 40.2 1.0
CZ H:ARG72 3.8 37.5 1.0
PA H:FAD602 3.8 33.3 1.0
N H:TRP50 3.9 33.2 1.0
N H:THR76 3.9 33.5 1.0
CB H:THR76 3.9 34.0 1.0
C H:GLY49 3.9 35.2 1.0
C H:THR76 4.0 31.1 1.0
CG2 H:THR78 4.1 25.3 1.0
O5B H:FAD602 4.1 29.8 1.0
CA H:THR76 4.2 34.6 1.0
CD1 H:TRP50 4.2 26.3 1.0
CE1 H:PHE75 4.3 28.1 1.0
CD1 H:PHE75 4.3 32.0 1.0
O4' H:FAD602 4.4 33.5 1.0
O1A H:FAD602 4.4 31.3 1.0
N H:GLY49 4.4 32.2 1.0
O H:SER48 4.5 33.4 1.0
OG1 H:THR76 4.7 41.1 1.0
NE1 H:TRP50 4.8 28.9 1.0
C H:SER48 4.9 35.7 1.0
O H:GLY49 5.0 29.7 1.0
CG H:TRP50 5.0 29.9 1.0

Magnesium binding site 8 out of 8 in 5jwb

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Magnesium binding site 8 out of 8 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Nadh


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 Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg606

b:50.8
occ:1.00
 O1A H:FAD602 2.8 31.3 1.0
N H:ALA150 2.9 29.9 1.0
NZ H:LYS168 2.9 50.9 1.0
O H:ALA150 3.2 42.0 1.0
OD2 H:ASP354 3.2 36.7 1.0
O3P H:FAD602 3.5 36.8 1.0
CE H:LYS168 3.6 50.1 1.0
CA H:GLY149 3.6 33.1 1.0
C H:GLY149 3.7 34.2 1.0
CA H:ALA150 3.7 37.9 1.0
PA H:FAD602 3.8 33.3 1.0
C H:ALA150 3.8 39.1 1.0
CB H:ASP354 4.0 33.5 1.0
CG H:ASP354 4.0 40.4 1.0
CB H:ALA150 4.1 42.3 1.0
O4' H:FAD602 4.3 33.5 1.0
C5' H:FAD602 4.5 31.0 1.0
O H:HOH709 4.6 40.6 1.0
P H:FAD602 4.7 29.6 1.0
O2A H:FAD602 4.7 28.1 1.0
C3' H:FAD602 4.8 33.5 1.0
C4' H:FAD602 4.8 34.7 1.0
O2P H:FAD602 4.8 33.0 1.0
O H:HOH707 4.9 33.6 1.0
CD H:LYS168 4.9 53.4 1.0
O H:GLY149 4.9 34.8 1.0
O5' H:FAD602 5.0 36.1 1.0
N H:GLY149 5.0 34.2 1.0
O5B H:FAD602 5.0 29.8 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 17:58:55 2024

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