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Magnesium in PDB 5yjw: Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin.

Enzymatic activity of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin.

All present enzymatic activity of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin.:
1.6.5.9;

Protein crystallography data

The structure of Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin., PDB code: 5yjw 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) 29.48 / 1.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 116.670, 128.456, 86.711, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin. (pdb code 5yjw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin., PDB code: 5yjw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5yjw

Go back to Magnesium Binding Sites List in 5yjw
Magnesium binding site 1 out of 4 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin.


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 the Competitive Inhibitor, Stigmatellin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:22.2
occ:1.00
 O2P A:FAD601 2.5 11.2 1.0
O A:ILE381 2.6 12.7 1.0
N A:GLY177 3.1 13.4 1.0
N A:ASN384 3.1 15.7 1.0
OD1 A:ASN384 3.2 15.7 1.0
N A:ASP383 3.2 14.8 1.0
CG A:ASN384 3.3 15.0 1.0
CA A:ALA175 3.3 12.2 1.0
C A:ALA175 3.4 12.2 1.0
CA A:GLY177 3.4 14.0 1.0
C A:GLY382 3.5 14.3 1.0
CA A:GLY382 3.6 13.8 1.0
CB A:ASN384 3.6 15.2 1.0
C A:ILE381 3.6 13.3 1.0
P A:FAD601 3.7 11.7 1.0
N A:VAL176 3.7 12.2 1.0
ND2 A:ASN384 3.9 14.1 1.0
CA A:ASN384 3.9 15.6 1.0
O A:ALA175 3.9 11.8 1.0
CB A:ALA175 4.0 12.1 1.0
C A:ASP383 4.0 15.5 1.0
N A:GLY382 4.1 13.6 1.0
CA A:ASP383 4.1 15.6 1.0
O1P A:FAD601 4.1 11.3 1.0
O A:GLY382 4.2 14.2 1.0
C A:VAL176 4.3 12.9 1.0
O3P A:FAD601 4.4 11.5 1.0
O A:SER174 4.4 12.4 1.0
C A:GLY177 4.5 14.7 1.0
N A:ALA175 4.5 12.1 1.0
CA A:VAL176 4.6 12.6 1.0
CB A:ASP383 4.6 15.8 1.0
O A:GLY177 4.7 14.6 1.0
N A:ALA385 4.8 17.1 1.0
C A:ASN384 4.8 16.3 1.0
C A:SER174 4.9 12.4 1.0
CA A:ILE381 5.0 13.3 1.0
O5' A:FAD601 5.0 11.8 1.0

Magnesium binding site 2 out of 4 in 5yjw

Go back to Magnesium Binding Sites List in 5yjw
Magnesium binding site 2 out of 4 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin.


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 the Competitive Inhibitor, Stigmatellin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:18.3
occ:1.00
 O A:ALA175 2.5 11.8 1.0
O1P A:FAD601 2.6 11.3 1.0
N A:GLY62 3.1 12.0 1.0
N A:ALA65 3.2 11.2 1.0
O5B A:FAD601 3.4 11.6 1.0
CA A:GLY62 3.4 11.9 1.0
CB A:ALA65 3.4 11.2 1.0
C A:GLY62 3.4 11.9 1.0
CB A:ALA175 3.5 12.1 1.0
C A:ALA175 3.6 12.2 1.0
C5B A:FAD601 3.7 11.5 1.0
N A:GLY64 3.7 11.6 1.0
C4B A:FAD601 3.7 11.5 1.0
O A:GLY62 3.8 11.8 1.0
P A:FAD601 3.9 11.7 1.0
CA A:ALA65 3.9 11.2 1.0
N A:TRP63 3.9 11.9 1.0
N A:SER61 4.0 11.7 1.0
CA A:GLY64 4.1 11.5 1.0
C A:GLY64 4.1 11.4 1.0
CA A:ALA175 4.2 12.2 1.0
CA A:GLY60 4.2 11.7 1.0
C A:GLY60 4.2 11.5 1.0
O3P A:FAD601 4.2 11.5 1.0
C A:SER61 4.2 11.8 1.0
PA A:FAD601 4.4 11.7 1.0
O4B A:FAD601 4.5 11.7 1.0
C A:TRP63 4.5 11.7 1.0
O A:LEU59 4.5 11.6 1.0
CA A:SER61 4.6 11.8 1.0
O1A A:FAD601 4.6 11.4 1.0
O2P A:FAD601 4.8 11.2 1.0
N A:VAL176 4.8 12.2 1.0
CA A:TRP63 4.8 12.0 1.0
C3B A:FAD601 4.9 11.5 1.0
O A:GLY60 4.9 11.3 1.0
O3B A:FAD601 4.9 11.1 1.0

Magnesium binding site 3 out of 4 in 5yjw

Go back to Magnesium Binding Sites List in 5yjw
Magnesium binding site 3 out of 4 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin.


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 the Competitive Inhibitor, Stigmatellin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:44.2
occ:1.00
 O A:HOH731 2.6 23.2 1.0
O A:HOH832 2.6 16.8 1.0
O2A A:FAD601 2.9 12.0 1.0
O1A A:FAD601 3.0 11.4 1.0
NH1 A:ARG85 3.2 11.5 1.0
PA A:FAD601 3.3 11.7 1.0
CG2 A:THR91 3.3 12.2 1.0
O A:HOH736 3.4 29.3 1.0
O A:HOH826 3.6 19.8 1.0
NH2 A:ARG85 3.8 11.3 1.0
O5B A:FAD601 3.8 11.6 1.0
CZ A:ARG85 3.9 11.3 1.0
O4' A:FAD601 4.1 12.8 1.0
CD2 A:LEU89 4.4 11.0 1.0
CB A:LEU89 4.5 11.1 1.0
OE2 A:GLU197 4.6 17.1 1.0
O A:LYS196 4.7 14.3 1.0
O A:LEU89 4.7 11.3 1.0
CG A:LEU89 4.8 11.0 1.0
CB A:THR91 4.8 12.2 1.0
C5B A:FAD601 4.8 11.5 1.0
O3P A:FAD601 4.8 11.5 1.0
C3B A:FAD601 4.8 11.5 1.0
CA A:GLY62 4.9 11.9 1.0
OE1 A:GLU197 4.9 16.0 1.0

Magnesium binding site 4 out of 4 in 5yjw

Go back to Magnesium Binding Sites List in 5yjw
Magnesium binding site 4 out of 4 in the Structure of the NDI1 Protein From Saccharomyces Cerevisiae in Complex with the Competitive Inhibitor, Stigmatellin.


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 the Competitive Inhibitor, Stigmatellin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:27.1
occ:1.00
 O2A A:FAD601 2.7 12.0 1.0
O A:HOH703 2.7 30.6 1.0
OD2 A:ASP383 2.9 16.7 1.0
NZ A:LYS196 3.0 18.0 1.0
N A:ALA178 3.2 15.6 1.0
O3P A:FAD601 3.3 11.5 1.0
O A:HOH826 3.4 19.8 1.0
O A:ALA178 3.5 17.0 1.0
CA A:GLY177 3.5 14.0 1.0
CE A:LYS196 3.6 17.3 1.0
PA A:FAD601 3.7 11.7 1.0
CG A:ASP383 3.8 16.3 1.0
C A:GLY177 3.8 14.7 1.0
CB A:ASP383 3.9 15.8 1.0
O4' A:FAD601 4.0 12.8 1.0
CA A:ALA178 4.2 16.3 1.0
C A:ALA178 4.2 17.2 1.0
C5' A:FAD601 4.3 12.3 1.0
O A:HOH803 4.5 25.9 1.0
CB A:ALA178 4.5 16.4 1.0
O A:HOH736 4.5 29.3 1.0
O2P A:FAD601 4.5 11.2 1.0
P A:FAD601 4.6 11.7 1.0
C4' A:FAD601 4.6 12.7 1.0
C3' A:FAD601 4.6 13.2 1.0
O1A A:FAD601 4.7 11.4 1.0
O5B A:FAD601 4.8 11.6 1.0
N A:GLY177 4.8 13.4 1.0
C5B A:FAD601 4.8 11.5 1.0
O5' A:FAD601 4.9 11.8 1.0
OD1 A:ASP383 4.9 16.9 1.0
O A:HOH731 4.9 23.2 1.0
O A:HOH813 5.0 26.7 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: Wed Aug 13 00:59:12 2025

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