Magnesium in PDB 5yjy: Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.

Enzymatic activity of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.

All present enzymatic activity of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.:
1.6.5.9;

Protein crystallography data

The structure of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12., PDB code: 5yjy was solved by T.Yamasita, D.K.Inaoka, T.Shiba, T.Oohashi, S.Iwata, T.Yagi, H.Kosaka, S.Harada, K.Kita, K.Hirano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.854, 115.795, 166.499, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 29.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12. (pdb code 5yjy). 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 the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12., PDB code: 5yjy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5yjy

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Magnesium binding site 1 out of 8 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:59.2
occ:1.00
 O2P A:FAD601 2.0 21.1 1.0
O A:ILE381 2.9 52.7 1.0
P A:FAD601 3.0 20.9 1.0
N A:GLY177 3.0 24.6 1.0
N A:ASP383 3.0 46.7 1.0
CA A:GLY177 3.1 25.9 1.0
OD1 A:ASN384 3.2 44.5 1.0
C A:ALA175 3.3 31.4 1.0
O A:ALA175 3.4 32.5 1.0
O1P A:FAD601 3.4 20.0 1.0
CA A:ALA175 3.4 33.7 1.0
O3P A:FAD601 3.4 20.9 1.0
CA A:GLY382 3.7 49.5 1.0
N A:ASN384 3.7 41.9 1.0
N A:VAL176 3.8 28.5 1.0
C A:GLY382 3.8 49.7 1.0
CG A:ASN384 3.9 44.4 1.0
C A:VAL176 3.9 25.4 1.0
C A:ILE381 3.9 50.7 1.0
CA A:ASP383 4.0 47.3 1.0
MG A:MG603 4.0 36.8 1.0
CB A:ALA175 4.0 34.6 1.0
CB A:ASP383 4.1 48.9 1.0
N A:GLY382 4.3 50.7 1.0
C A:ASP383 4.4 44.4 1.0
O5' A:FAD601 4.4 22.6 1.0
ND2 A:ASN384 4.5 43.9 1.0
CA A:VAL176 4.5 26.8 1.0
C A:GLY177 4.5 27.1 1.0
CB A:ASN384 4.7 44.4 1.0
MG A:MG605 4.7 18.8 1.0
N A:ALA175 4.7 34.4 1.0
O A:VAL176 4.7 24.8 1.0
CA A:ASN384 4.8 43.5 1.0
O A:SER174 4.8 34.3 1.0
C5' A:FAD601 4.9 25.3 1.0
PA A:FAD601 5.0 20.0 1.0
C5B A:FAD601 5.0 19.1 1.0

Magnesium binding site 2 out of 8 in 5yjy

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Magnesium binding site 2 out of 8 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:36.8
occ:1.00
 O A:ALA175 2.3 32.5 1.0
O1P A:FAD601 2.4 20.0 1.0
O5B A:FAD601 3.2 19.5 1.0
CB A:ALA175 3.4 34.6 1.0
C A:ALA175 3.4 31.4 1.0
P A:FAD601 3.4 20.9 1.0
N A:GLY62 3.4 33.4 1.0
O3P A:FAD601 3.5 20.9 1.0
C5B A:FAD601 3.5 19.1 1.0
N A:ALA65 3.5 44.6 1.0
C A:GLY62 3.5 30.6 1.0
CA A:GLY62 3.5 31.1 1.0
N A:GLY64 3.5 42.4 1.0
C4B A:FAD601 3.6 19.3 1.0
N A:TRP63 3.8 34.3 1.0
O A:GLY62 3.8 27.7 1.0
PA A:FAD601 3.9 20.0 1.0
O1A A:FAD601 3.9 20.3 1.0
CB A:ALA65 3.9 44.5 1.0
CA A:ALA175 4.0 33.7 1.0
MG A:MG602 4.0 59.2 1.0
CA A:GLY64 4.1 44.4 1.0
O2P A:FAD601 4.3 21.1 1.0
CA A:ALA65 4.3 43.0 1.0
C A:GLY64 4.3 45.4 1.0
CA A:GLY60 4.4 29.5 1.0
N A:SER61 4.4 28.9 1.0
O4B A:FAD601 4.5 19.2 1.0
N A:VAL176 4.5 28.5 1.0
O A:LEU59 4.5 28.0 1.0
C A:TRP63 4.5 40.1 1.0
C A:GLY60 4.6 28.3 1.0
O5' A:FAD601 4.6 22.6 1.0
CA A:TRP63 4.7 39.0 1.0
C A:SER61 4.7 33.7 1.0
C3B A:FAD601 4.8 19.6 1.0
CA A:VAL176 4.8 26.8 1.0
C A:VAL176 4.9 25.4 1.0
N A:GLY177 5.0 24.6 1.0

Magnesium binding site 3 out of 8 in 5yjy

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Magnesium binding site 3 out of 8 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:31.2
occ:1.00
 O A:LEU89 2.6 34.4 1.0
NH2 A:ARG85 3.1 20.2 1.0
O1A A:FAD601 3.2 20.3 1.0
CA A:GLY62 3.5 31.1 1.0
C A:LEU89 3.5 34.8 1.0
N A:LEU89 3.6 30.3 1.0
CB A:LEU89 3.6 33.7 1.0
CA A:LEU89 3.7 32.3 1.0
N A:TRP63 3.8 34.3 1.0
CE1 A:PHE88 3.8 33.0 1.0
NH1 A:ARG85 3.8 19.9 1.0
CZ A:ARG85 3.9 20.4 1.0
CD1 A:PHE88 4.0 32.6 1.0
C A:GLY62 4.1 30.6 1.0
PA A:FAD601 4.1 20.0 1.0
CG2 A:THR91 4.1 40.6 1.0
CD1 A:TRP63 4.1 40.4 1.0
O5B A:FAD601 4.4 19.5 1.0
CZ A:PHE88 4.4 32.5 1.0
O2A A:FAD601 4.4 19.4 1.0
CG A:TRP63 4.5 41.3 1.0
CG A:LEU89 4.6 35.2 1.0
NE1 A:TRP63 4.6 40.4 1.0
N A:GLY62 4.7 33.4 1.0
O4' A:FAD601 4.7 26.5 1.0
CG A:PHE88 4.8 31.8 1.0
N A:PHE90 4.8 37.7 1.0
C A:PHE88 4.8 29.6 1.0
CA A:TRP63 4.8 39.0 1.0
O A:SER61 4.9 34.5 1.0
CB A:TRP63 4.9 41.1 1.0
N A:THR91 4.9 36.2 1.0

Magnesium binding site 4 out of 8 in 5yjy

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Magnesium binding site 4 out of 8 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:18.8
occ:1.00
 O2A A:FAD601 2.5 19.4 1.0
O3P A:FAD601 2.6 20.9 1.0
NZ A:LYS196 3.1 39.5 1.0
PA A:FAD601 3.1 20.0 1.0
CA A:GLY177 3.2 25.9 1.0
N A:ALA178 3.3 29.6 1.0
OD2 A:ASP383 3.4 46.5 1.0
C5' A:FAD601 3.6 25.3 1.0
O2P A:FAD601 3.6 21.1 1.0
CB A:ASP383 3.7 48.9 1.0
P A:FAD601 3.7 20.9 1.0
C A:GLY177 3.7 27.1 1.0
CG A:ASP383 3.8 50.3 1.0
O A:ALA178 3.9 33.1 1.0
O5' A:FAD601 3.9 22.6 1.0
O5B A:FAD601 4.1 19.5 1.0
C5B A:FAD601 4.2 19.1 1.0
O4' A:FAD601 4.2 26.5 1.0
CE A:LYS196 4.2 39.5 1.0
O A:VAL176 4.3 24.8 1.0
O1A A:FAD601 4.3 20.3 1.0
N A:GLY177 4.3 24.6 1.0
C4' A:FAD601 4.4 26.6 1.0
NH2 A:ARG344 4.4 44.4 1.0
CA A:ALA178 4.5 31.6 1.0
C A:ALA178 4.6 33.1 1.0
MG A:MG602 4.7 59.2 1.0
C A:VAL176 4.7 25.4 1.0
C3' A:FAD601 4.7 27.8 1.0
OD1 A:ASP383 4.9 55.2 1.0
O A:GLY177 4.9 26.9 1.0
O3' A:FAD601 5.0 26.9 1.0

Magnesium binding site 5 out of 8 in 5yjy

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Magnesium binding site 5 out of 8 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:25.4
occ:1.00
 O2P B:FAD601 2.3 26.5 1.0
P B:FAD601 2.8 27.1 1.0
N B:GLY177 2.9 41.6 1.0
O3P B:FAD601 3.0 27.2 1.0
C B:ALA175 3.1 53.9 1.0
O1P B:FAD601 3.2 26.6 1.0
CA B:GLY177 3.2 38.1 1.0
O B:ALA175 3.3 57.4 1.0
OD1 B:ASN384 3.3 51.8 1.0
CA B:ALA175 3.4 54.8 1.0
N B:VAL176 3.5 50.4 1.0
N B:ASP383 3.6 44.7 1.0
O B:ILE381 3.6 43.4 1.0
C B:VAL176 3.8 46.4 1.0
N B:ASN384 3.8 43.5 1.0
MG B:MG603 3.8 46.3 1.0
CB B:ALA175 3.9 55.0 1.0
CG B:ASN384 4.0 50.6 1.0
CA B:VAL176 4.2 48.2 1.0
CB B:ASN384 4.2 50.2 1.0
CB B:ASP383 4.3 48.4 1.0
C B:GLY382 4.3 44.4 1.0
CA B:ASP383 4.3 45.6 1.0
O5B B:FAD601 4.3 25.9 1.0
O5' B:FAD601 4.4 28.6 1.0
C5B B:FAD601 4.4 26.2 1.0
PA B:FAD601 4.4 26.6 1.0
C B:GLY177 4.4 37.7 1.0
CA B:GLY382 4.4 43.2 1.0
C B:ILE381 4.5 44.7 1.0
C B:ASP383 4.5 43.6 1.0
O B:VAL176 4.6 50.6 1.0
CA B:ASN384 4.6 47.3 1.0
N B:ALA175 4.7 56.1 1.0
N B:GLY382 4.8 43.0 1.0
C5' B:FAD601 4.9 30.9 1.0
O B:GLY177 4.9 34.5 1.0
MG B:MG605 4.9 33.6 1.0

Magnesium binding site 6 out of 8 in 5yjy

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Magnesium binding site 6 out of 8 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:46.3
occ:1.00
 O B:ALA175 2.3 57.4 1.0
O1P B:FAD601 2.4 26.6 1.0
O5B B:FAD601 2.8 25.9 1.0
N B:ALA65 3.2 40.0 1.0
CB B:ALA175 3.2 55.0 1.0
C B:ALA175 3.3 53.9 1.0
N B:GLY62 3.4 40.1 1.0
C5B B:FAD601 3.4 26.2 1.0
CA B:GLY62 3.5 37.9 1.0
C4B B:FAD601 3.6 27.8 1.0
P B:FAD601 3.6 27.1 1.0
N B:GLY64 3.6 36.5 1.0
CB B:ALA65 3.7 40.8 1.0
O3P B:FAD601 3.7 27.2 1.0
C B:GLY62 3.7 36.5 1.0
CA B:GLY64 3.8 37.7 1.0
MG B:MG602 3.8 25.4 1.0
PA B:FAD601 3.9 26.6 1.0
CA B:ALA175 3.9 54.8 1.0
C B:GLY64 4.0 39.2 1.0
N B:TRP63 4.0 37.2 1.0
CA B:ALA65 4.1 39.5 1.0
O1A B:FAD601 4.2 25.1 1.0
O B:GLY62 4.3 33.7 1.0
CA B:GLY60 4.3 44.3 1.0
C B:TRP63 4.3 36.1 1.0
O4B B:FAD601 4.4 29.5 1.0
N B:SER61 4.5 45.8 1.0
N B:VAL176 4.5 50.4 1.0
C B:GLY60 4.5 44.6 1.0
O2P B:FAD601 4.6 26.5 1.0
O B:LEU59 4.6 44.0 1.0
C B:SER61 4.6 43.8 1.0
C3B B:FAD601 4.7 28.9 1.0
O5' B:FAD601 4.8 28.6 1.0
CA B:TRP63 4.8 36.4 1.0
CA B:VAL176 4.9 48.2 1.0
C B:VAL176 4.9 46.4 1.0
O3B B:FAD601 5.0 28.4 1.0

Magnesium binding site 7 out of 8 in 5yjy

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Magnesium binding site 7 out of 8 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:42.0
occ:1.00
 O1A B:FAD601 2.4 25.1 1.0
CA B:GLY62 3.3 37.9 1.0
O B:LEU89 3.4 28.0 1.0
PA B:FAD601 3.5 26.6 1.0
N B:TRP63 3.5 37.2 1.0
NH2 B:ARG85 3.5 37.7 1.0
O4' B:FAD601 3.6 31.9 1.0
CG2 B:THR91 3.6 29.6 1.0
CD1 B:TRP63 3.8 31.3 1.0
C B:GLY62 3.8 36.5 1.0
O2A B:FAD601 3.9 25.9 1.0
NH1 B:ARG85 3.9 37.6 1.0
O5B B:FAD601 4.0 25.9 1.0
CZ B:ARG85 4.2 36.9 1.0
NE1 B:TRP63 4.3 31.9 1.0
CG B:TRP63 4.3 33.0 1.0
CB B:LEU89 4.4 32.7 1.0
C B:LEU89 4.4 30.6 1.0
N B:LEU89 4.4 30.4 1.0
N B:GLY62 4.6 40.1 1.0
CA B:TRP63 4.6 36.4 1.0
CA B:LEU89 4.6 30.8 1.0
CB B:TRP63 4.7 35.4 1.0
CE1 B:PHE88 4.8 35.3 1.0
O5' B:FAD601 4.8 28.6 1.0
O3P B:FAD601 4.8 27.2 1.0
CD1 B:PHE88 4.9 35.6 1.0
O B:GLY62 4.9 33.7 1.0
C4' B:FAD601 4.9 32.6 1.0
C3B B:FAD601 5.0 28.9 1.0

Magnesium binding site 8 out of 8 in 5yjy

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Magnesium binding site 8 out of 8 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with AC0-12. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:33.6
occ:1.00
 O2A B:FAD601 2.2 25.9 1.0
O3P B:FAD601 2.7 27.2 1.0
PA B:FAD601 2.9 26.6 1.0
NZ B:LYS196 3.0 41.3 1.0
OD2 B:ASP383 3.2 46.0 1.0
CA B:GLY177 3.3 38.1 1.0
N B:ALA178 3.6 40.6 1.0
O4' B:FAD601 3.7 31.9 1.0
C5' B:FAD601 3.8 30.9 1.0
O B:ALA178 3.8 46.5 1.0
CG B:ASP383 3.9 48.8 1.0
O1A B:FAD601 3.9 25.1 1.0
C B:GLY177 4.0 37.7 1.0
P B:FAD601 4.0 27.1 1.0
CB B:ASP383 4.1 48.4 1.0
C4' B:FAD601 4.1 32.6 1.0
O5B B:FAD601 4.1 25.9 1.0
O5' B:FAD601 4.2 28.6 1.0
C5B B:FAD601 4.3 26.2 1.0
CE B:LYS196 4.3 42.3 1.0
O2P B:FAD601 4.3 26.5 1.0
C3' B:FAD601 4.4 34.0 1.0
NH2 B:ARG344 4.5 40.7 1.0
N B:GLY177 4.6 41.6 1.0
CA B:ALA178 4.7 43.2 1.0
C B:ALA178 4.7 47.3 1.0
O B:VAL176 4.8 50.6 1.0
OD1 B:ASP383 4.9 52.4 1.0
MG B:MG602 4.9 25.4 1.0

Reference:

T.Yamashita, D.K.Inaoka, T.Shiba, T.Oohashi, S.Iwata, T.Yagi, H.Kosaka, H.Miyoshi, S.Harada, K.Kita, K.Hirano. Ubiquinone Binding Site of Yeast Nadh Dehydrogenase Revealed By Structures Binding Novel Competitive- and Mixed-Type Inhibitors Sci Rep V. 8 2427 2018.
ISSN: ESSN 2045-2322
PubMed: 29402945
DOI: 10.1038/S41598-018-20775-6
Page generated: Mon Dec 14 22:13:50 2020

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