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Magnesium in PDB 4g74: Crystal Structure of Ndh with Quinone

Enzymatic activity of Crystal Structure of Ndh with Quinone

All present enzymatic activity of Crystal Structure of Ndh with Quinone:
1.6.5.9;

Protein crystallography data

The structure of Crystal Structure of Ndh with Quinone, PDB code: 4g74 was solved by W.Li, Y.Feng, J.Ge, M.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.61 / 2.48
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 132.909, 230.844, 112.450, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.3

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Ndh with Quinone (pdb code 4g74). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Crystal Structure of Ndh with Quinone, PDB code: 4g74:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 4g74

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Magnesium binding site 1 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:60.9
occ:1.00
 O A:LEU502 3.2 41.3 1.0
O A:PHE505 3.5 41.2 1.0
NZ A:LYS257 3.9 60.0 1.0
C A:PHE505 4.0 34.9 1.0
C A:LEU502 4.4 35.5 1.0
N A:LYS506 4.5 34.8 1.0
N A:PHE505 4.5 35.7 1.0
O A:ALA503 4.6 43.5 1.0
OD1 A:ASP254 4.6 40.5 1.0
CA A:PHE505 4.6 36.5 1.0
C A:ALA503 4.7 43.4 1.0
CA A:LYS506 4.7 39.9 1.0
C A:PHE504 4.7 36.9 1.0
O A:PHE504 5.0 35.6 1.0

Magnesium binding site 2 out of 11 in 4g74

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Magnesium binding site 2 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:32.0
occ:1.00
 O2P A:FAD607 2.7 24.1 1.0
O A:ILE381 2.8 25.6 1.0
N A:ASN384 2.9 28.1 1.0
ND2 A:ASN384 3.0 28.5 1.0
N A:GLY177 3.0 23.2 1.0
CG A:ASN384 3.1 25.9 1.0
N A:ASP383 3.2 21.3 1.0
CA A:ALA175 3.3 25.8 1.0
CA A:GLY177 3.4 24.2 1.0
C A:ALA175 3.4 24.4 1.0
C A:GLY382 3.4 23.1 1.0
CB A:ASN384 3.5 28.3 1.0
OD1 A:ASN384 3.6 23.7 1.0
CA A:GLY382 3.6 15.5 1.0
N A:VAL176 3.6 23.0 1.0
CA A:ASN384 3.7 31.9 1.0
C A:ASP383 3.8 31.2 1.0
C A:ILE381 3.9 27.8 1.0
P A:FAD607 3.9 22.6 1.0
CA A:ASP383 3.9 27.5 1.0
O A:ALA175 4.0 23.9 1.0
CB A:ALA175 4.0 23.4 1.0
O A:GLY382 4.1 27.1 1.0
C A:VAL176 4.2 24.4 1.0
O A:SER174 4.2 27.9 1.0
N A:GLY382 4.2 24.4 1.0
O1P A:FAD607 4.3 20.5 1.0
C A:GLY177 4.3 23.9 1.0
N A:ALA175 4.4 25.5 1.0
O A:GLY177 4.4 28.8 1.0
CA A:VAL176 4.5 25.9 1.0
O3P A:FAD607 4.5 22.9 1.0
N A:ALA385 4.7 32.2 1.0
C A:ASN384 4.7 30.6 1.0
CB A:ASP383 4.7 29.1 1.0
C A:SER174 4.7 28.1 1.0
O A:ASP383 4.9 28.6 1.0

Magnesium binding site 3 out of 11 in 4g74

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Magnesium binding site 3 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:32.4
occ:1.00
 O1P A:FAD607 2.8 20.5 1.0
O A:ALA175 2.8 23.9 1.0
N A:ALA65 2.9 21.8 1.0
N A:GLY62 3.1 24.7 1.0
CB A:ALA175 3.3 23.4 1.0
CB A:ALA65 3.3 22.2 1.0
O5B A:FAD607 3.3 27.1 1.0
C A:GLY62 3.4 22.2 1.0
CA A:GLY62 3.4 22.3 1.0
N A:GLY64 3.6 23.8 1.0
O A:GLY62 3.6 21.8 1.0
CA A:ALA65 3.7 20.1 1.0
C4B A:FAD607 3.8 24.7 1.0
C5B A:FAD607 3.8 23.7 1.0
C A:ALA175 3.8 24.4 1.0
N A:TRP63 3.8 22.6 1.0
C A:GLY64 3.9 22.9 1.0
CA A:GLY64 3.9 20.4 1.0
N A:SER61 4.0 22.1 1.0
P A:FAD607 4.1 22.6 1.0
CA A:ALA175 4.2 25.8 1.0
C A:GLY60 4.2 26.0 1.0
C A:SER61 4.2 25.0 1.0
CA A:GLY60 4.3 23.3 1.0
C A:TRP63 4.3 22.4 1.0
PA A:FAD607 4.4 22.1 1.0
O3P A:FAD607 4.4 22.9 1.0
O4B A:FAD607 4.5 24.9 1.0
O2A A:FAD607 4.5 22.8 1.0
CA A:SER61 4.5 20.8 1.0
O A:LEU59 4.6 26.1 1.0
CA A:TRP63 4.7 21.9 1.0
O A:GLY60 4.8 21.6 1.0
N A:ILE66 4.8 23.3 1.0
C A:ALA65 4.8 24.0 1.0
O2P A:FAD607 4.8 24.1 1.0
C3B A:FAD607 5.0 24.6 1.0
N A:VAL176 5.0 23.0 1.0

Magnesium binding site 4 out of 11 in 4g74

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Magnesium binding site 4 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:33.5
occ:1.00
 O1A A:FAD607 2.7 20.1 1.0
O A:HOH704 2.7 23.3 1.0
O A:HOH716 3.0 25.6 1.0
NH1 A:ARG85 3.1 23.4 1.0
O2A A:FAD607 3.3 22.8 1.0
PA A:FAD607 3.5 22.1 1.0
NH2 A:ARG85 3.5 21.4 1.0
CG2 A:THR91 3.6 21.9 1.0
O A:HOH743 3.7 34.2 1.0
CZ A:ARG85 3.7 23.9 1.0
O A:HOH774 3.7 31.8 1.0
CD2 A:LEU89 3.8 23.4 1.0
O5B A:FAD607 4.1 27.1 1.0
CB A:LEU89 4.2 19.9 1.0
O4' A:FAD607 4.3 26.5 1.0
CG A:LEU89 4.4 24.2 1.0
O A:LEU89 4.5 27.2 1.0
OE2 A:GLU197 4.6 30.0 1.0
OE1 A:GLU197 4.6 27.8 1.0
C3B A:FAD607 4.8 24.6 1.0
O A:LYS196 4.8 27.1 1.0
CA A:GLY62 4.9 22.3 1.0
C5B A:FAD607 4.9 23.7 1.0
CD A:GLU197 4.9 30.1 1.0
O3P A:FAD607 4.9 22.9 1.0

Magnesium binding site 5 out of 11 in 4g74

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Magnesium binding site 5 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:40.2
occ:1.00
 O A:HOH732 2.7 37.1 1.0
O1A A:FAD607 2.7 20.1 1.0
N A:ALA178 3.0 22.0 1.0
NZ A:LYS196 3.0 32.0 1.0
O3P A:FAD607 3.2 22.9 1.0
O A:ALA178 3.3 30.6 1.0
CA A:GLY177 3.4 24.2 1.0
O A:HOH774 3.6 31.8 1.0
PA A:FAD607 3.6 22.1 1.0
O A:HOH743 3.6 34.2 1.0
C A:GLY177 3.7 23.9 1.0
CE A:LYS196 3.7 31.5 1.0
CA A:ALA178 4.0 26.9 1.0
C A:ALA178 4.1 27.7 1.0
O A:HOH841 4.2 36.6 1.0
NH1 A:ARG344 4.3 32.0 1.0
O4' A:FAD607 4.3 26.5 1.0
CB A:ALA178 4.5 26.2 1.0
C5B A:FAD607 4.5 23.7 1.0
O A:HOH716 4.5 25.6 1.0
O5B A:FAD607 4.5 27.1 1.0
OD2 A:ASP383 4.5 34.5 1.0
P A:FAD607 4.6 22.6 1.0
N A:GLY177 4.7 23.2 1.0
CB A:ASP383 4.7 29.1 1.0
O A:VAL176 4.8 25.0 1.0
C5' A:FAD607 4.8 26.4 1.0
O2A A:FAD607 4.8 22.8 1.0
O2P A:FAD607 4.8 24.1 1.0
O A:GLY177 4.9 28.8 1.0

Magnesium binding site 6 out of 11 in 4g74

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Magnesium binding site 6 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:20.2
occ:1.00
 O B:GLY333 2.7 25.0 1.0
O B:HOH722 2.8 34.0 1.0
O B:HOH707 2.9 32.8 1.0
O B:HOH761 2.9 34.8 1.0
O B:HOH757 3.4 31.6 1.0
C B:GLY333 3.8 28.1 1.0
CG2 B:THR207 4.2 23.2 1.0
O B:GLU311 4.4 34.4 1.0
CE1 B:TYR332 4.5 27.7 1.0
CA B:GLY333 4.6 27.5 1.0
O B:TYR191 4.6 29.0 1.0
N B:THR334 4.7 23.5 1.0
ND2 B:ASN211 4.8 19.7 1.0
CA B:THR334 4.8 24.3 1.0
O B:HOH848 4.9 40.9 1.0

Magnesium binding site 7 out of 11 in 4g74

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Magnesium binding site 7 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:52.0
occ:1.00
 O B:HOH805 2.8 39.3 1.0
O B:HOH774 2.9 40.7 1.0
OD1 B:ASP254 3.1 37.9 1.0
O B:PHE505 3.3 36.6 1.0
O B:LEU502 3.5 36.8 1.0
NH1 B:ARG507 3.7 28.1 1.0
CD1 B:LEU502 4.0 33.1 1.0
OE1 B:GLN253 4.0 29.7 1.0
CA B:LYS506 4.0 37.4 1.0
C B:PHE505 4.0 33.3 1.0
CG B:ASP254 4.1 36.5 1.0
OD2 B:ASP254 4.2 37.6 1.0
CG B:LEU502 4.2 34.9 1.0
N B:LYS506 4.4 34.6 1.0
C B:LEU502 4.6 33.5 1.0
N B:ARG507 4.6 29.0 1.0
CB B:GLN253 4.7 24.0 1.0
CZ B:ARG507 4.7 28.2 1.0
C B:LYS506 4.7 38.5 1.0
CG B:LYS506 4.9 35.0 1.0
CA B:LEU502 4.9 33.1 1.0
CB B:LYS506 5.0 29.4 1.0

Magnesium binding site 8 out of 11 in 4g74

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Magnesium binding site 8 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:47.8
occ:1.00
 O2P B:FAD606 2.8 42.3 1.0
O B:ILE381 2.8 40.7 1.0
N B:GLY177 3.0 33.3 1.0
N B:ASN384 3.0 36.2 1.0
ND2 B:ASN384 3.0 36.9 1.0
N B:ASP383 3.2 41.2 1.0
CG B:ASN384 3.2 36.8 1.0
CA B:ALA175 3.2 38.6 1.0
CA B:GLY177 3.3 36.4 1.0
C B:ALA175 3.3 37.6 1.0
C B:GLY382 3.5 43.4 1.0
CB B:ASN384 3.6 38.2 1.0
N B:VAL176 3.6 39.0 1.0
CA B:GLY382 3.8 39.8 1.0
O B:ALA175 3.8 34.9 1.0
OD1 B:ASN384 3.8 39.6 1.0
CA B:ASN384 3.8 46.0 1.0
C B:ASP383 3.9 41.0 1.0
P B:FAD606 3.9 34.1 1.0
C B:ILE381 3.9 40.4 1.0
CA B:ASP383 4.0 41.1 1.0
CB B:ALA175 4.0 33.9 1.0
C B:VAL176 4.2 38.4 1.0
O1P B:FAD606 4.2 37.2 1.0
O B:GLY382 4.3 44.3 1.0
C B:GLY177 4.3 40.4 1.0
N B:GLY382 4.3 38.6 1.0
N B:ALA175 4.3 40.7 1.0
O3P B:FAD606 4.4 37.4 1.0
O B:SER174 4.5 47.9 1.0
CA B:VAL176 4.5 35.0 1.0
O B:GLY177 4.5 38.2 1.0
CB B:ASP383 4.6 42.5 1.0
C B:SER174 4.8 48.0 1.0
C B:ASN384 4.8 47.2 1.0
N B:ALA385 4.9 48.4 1.0

Magnesium binding site 9 out of 11 in 4g74

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Magnesium binding site 9 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:45.0
occ:1.00
 O1P B:FAD606 2.7 37.2 1.0
O B:ALA175 2.7 34.9 1.0
N B:ALA65 2.9 32.1 1.0
N B:GLY62 3.0 33.4 1.0
O5B B:FAD606 3.2 39.0 1.0
CA B:GLY62 3.3 33.5 1.0
C B:GLY62 3.3 33.0 1.0
CB B:ALA65 3.3 38.0 1.0
N B:GLY64 3.5 34.1 1.0
CB B:ALA175 3.6 33.9 1.0
O B:GLY62 3.6 33.3 1.0
CA B:ALA65 3.7 36.5 1.0
C4B B:FAD606 3.8 37.6 1.0
C5B B:FAD606 3.8 36.4 1.0
N B:TRP63 3.8 32.4 1.0
C B:ALA175 3.8 37.6 1.0
CA B:GLY64 3.9 35.5 1.0
C B:GLY64 3.9 35.9 1.0
P B:FAD606 4.1 34.1 1.0
N B:SER61 4.1 35.9 1.0
C B:SER61 4.2 35.7 1.0
C B:GLY60 4.3 37.9 1.0
CA B:ALA175 4.3 38.6 1.0
PA B:FAD606 4.3 34.8 1.0
C B:TRP63 4.4 37.2 1.0
O3P B:FAD606 4.4 37.4 1.0
CA B:GLY60 4.4 38.8 1.0
O4B B:FAD606 4.5 34.2 1.0
CA B:SER61 4.5 36.4 1.0
O2A B:FAD606 4.6 30.8 1.0
O B:LEU59 4.6 37.0 1.0
CA B:TRP63 4.7 31.8 1.0
N B:ILE66 4.8 37.3 1.0
C B:ALA65 4.8 37.5 1.0
O B:GLY60 4.8 39.1 1.0
O2P B:FAD606 4.9 42.3 1.0
C3B B:FAD606 4.9 32.4 1.0

Magnesium binding site 10 out of 11 in 4g74

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Magnesium binding site 10 out of 11 in the Crystal Structure of Ndh with Quinone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Ndh with Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg609

b:40.2
occ:1.00
 O B:HOH708 2.8 36.8 1.0
O B:LEU89 3.0 26.2 1.0
O2A B:FAD606 3.0 30.8 1.0
NH2 B:ARG85 3.1 26.2 1.0
CA B:GLY62 3.5 33.5 1.0
CB B:LEU89 3.7 25.7 1.0
NH1 B:ARG85 3.8 30.1 1.0
N B:LEU89 3.8 26.7 1.0
CZ B:ARG85 3.9 29.3 1.0
C B:LEU89 3.9 28.6 1.0
N B:TRP63 3.9 32.4 1.0
CG2 B:THR91 3.9 26.4 1.0
CA B:LEU89 4.0 27.1 1.0
PA B:FAD606 4.0 34.8 1.0
C B:GLY62 4.1 33.0 1.0
CD1 B:TRP63 4.2 28.8 1.0
CE1 B:PHE88 4.2 29.1 1.0
CD1 B:PHE88 4.3 29.1 1.0
O1A B:FAD606 4.3 33.1 1.0
O5B B:FAD606 4.4 39.0 1.0
CG B:LEU89 4.4 29.8 1.0
CD2 B:LEU89 4.7 29.9 1.0
O4' B:FAD606 4.7 39.2 1.0
N B:GLY62 4.7 33.4 1.0
NE1 B:TRP63 4.7 21.7 1.0
O B:SER61 4.8 35.6 1.0
O B:HOH729 4.9 33.4 1.0
CG B:TRP63 4.9 33.2 1.0
CZ B:PHE88 5.0 27.6 1.0
C B:PHE88 5.0 31.6 1.0

Reference:

Y.Feng, W.Li, J.Li, J.Wang, J.Ge, D.Xu, Y.Liu, K.Wu, Q.Zeng, J.W.Wu, C.Tian, B.Zhou, M.Yang. Structural Insight Into the Type-II Mitochondrial Nadh Dehydrogenases. Nature V. 491 478 2012.
ISSN: ISSN 0028-0836
PubMed: 23086143
DOI: 10.1038/NATURE11541
Page generated: Fri Aug 16 15:25:20 2024

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