Magnesium in PDB 4g6h: Crystal Structure of Ndh with Nadh

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

The structure of Crystal Structure of Ndh with Nadh, PDB code: 4g6h 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)	43.15 / 2.26
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	126.187, 229.588, 111.870, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of Ndh with Nadh (pdb code 4g6h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Ndh with Nadh, PDB code: 4g6h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Ndh with Nadh


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 Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:34.5 occ:1.00 O A:HOH765 2.6 30.2 1.0 O A:HOH757 2.8 37.2 1.0 O A:GLY192 2.8 26.6 1.0 O A:THR189 2.9 36.2 1.0 C A:THR189 3.8 37.0 1.0 C A:GLY192 3.8 31.3 1.0 O A:HOH702 3.9 41.0 1.0 CA A:THR189 4.1 33.2 1.0 CA A:HIS193 4.2 25.1 1.0 O A:VAL188 4.2 38.4 1.0 CE2 A:PHE194 4.4 27.3 1.0 CD2 A:PHE194 4.4 28.5 1.0 N A:HIS193 4.4 22.1 1.0 N A:PHE194 4.5 21.1 1.0 O A:HOH779 4.7 36.9 1.0 C A:HIS193 4.7 25.8 1.0 N A:GLY192 4.8 27.4 1.0 CG2 A:THR189 4.9 37.1 1.0 CA A:GLY192 4.9 30.2 1.0 CZ A:PHE194 5.0 34.6 1.0 OE2 A:GLU203 5.0 45.3 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Ndh with Nadh


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 Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:46.5 occ:1.00 O A:HOH856 2.5 43.1 1.0 O A:VAL266 2.7 33.9 1.0 OG A:SER297 2.8 34.1 1.0 O A:HOH736 3.0 30.6 1.0 O A:HOH714 3.0 53.8 1.0 CB A:SER297 3.5 29.4 1.0 O A:HOH745 3.7 46.8 1.0 O A:HOH892 3.7 54.8 1.0 C A:VAL266 3.9 26.9 1.0 O A:SER297 4.0 29.7 1.0 OE1 A:GLN267 4.1 37.2 1.0 O A:GLU264 4.2 41.2 1.0 CA A:GLN267 4.4 25.4 1.0 OE1 A:GLN248 4.5 33.1 1.0 CD A:GLN267 4.6 30.9 1.0 C A:SER297 4.6 27.5 1.0 NE2 A:GLN248 4.6 24.5 1.0 N A:GLN267 4.6 25.9 1.0 CA A:SER297 4.7 26.6 1.0 NE2 A:GLN267 4.7 27.7 1.0 O A:ALA263 4.9 34.9 1.0 CD A:GLN248 5.0 28.2 1.0 CA A:VAL266 5.0 30.8 1.0 N A:VAL266 5.0 27.3 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Ndh with Nadh


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 Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:71.3 occ:1.00 O A:LYS53 2.8 48.0 1.0 O A:PRO48 3.0 84.9 1.0 O A:SER51 3.1 68.7 1.0 OD1 A:ASN55 3.1 53.4 1.0 ND2 A:ASN55 3.5 61.3 1.0 CG A:ASN55 3.6 53.1 1.0 OE1 A:GLN49 3.6 89.5 1.0 C A:SER51 3.8 70.3 1.0 CB A:SER51 4.0 71.6 1.0 CD A:GLN49 4.0 91.2 1.0 C A:LYS53 4.1 44.6 1.0 C A:PRO48 4.1 88.4 1.0 NE2 A:GLN49 4.1 85.3 1.0 CA A:SER51 4.2 73.7 1.0 N A:SER51 4.2 85.8 1.0 CA A:GLN49 4.3 90.0 1.0 N A:LYS53 4.6 61.1 1.0 N A:ASN55 4.6 34.4 1.0 N A:GLN49 4.7 89.6 1.0 OD2 A:ASP170 4.7 44.3 1.0 N A:ASP52 4.7 68.9 1.0 C A:PRO54 4.8 40.5 1.0 C A:ASP52 4.8 68.7 1.0 C A:GLN49 4.8 83.1 1.0 CB A:ASN55 4.9 36.8 1.0 O A:HOH916 4.9 59.0 1.0 CA A:LYS53 4.9 53.1 1.0 CA A:PRO54 4.9 41.0 1.0 OG A:SER51 5.0 66.2 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Ndh with Nadh


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 Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:81.8 occ:1.00 O B:HOH702 3.2 10.4 1.0 O B:HOH761 3.2 37.6 1.0 O B:HOH922 3.2 48.4 1.0 OE2 B:GLU203 3.7 39.2 1.0 O B:HOH945 3.7 64.0 1.0 O B:HOH737 3.8 23.4 1.0 O B:HOH836 3.8 42.4 1.0 CD B:GLU203 4.1 57.5 1.0 OE1 B:GLU203 4.2 53.2 1.0 O B:GLY192 4.2 23.7 1.0 O B:THR189 4.5 34.4 1.0 ND1 B:HIS193 4.5 34.8 1.0 CE1 B:HIS193 4.9 39.1 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Ndh with Nadh


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 Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:20.3 occ:1.00 O B:GLY333 2.7 25.9 1.0 O B:HOH818 2.9 35.5 1.0 O B:HOH728 2.9 19.2 1.0 O B:HOH727 3.0 27.9 1.0 O B:HOH736 3.4 26.8 1.0 O B:HOH909 3.6 55.8 1.0 C B:GLY333 3.8 28.7 1.0 O B:HOH964 3.8 55.4 1.0 CE1 B:TYR332 4.2 29.9 1.0 CG2 B:THR207 4.2 22.4 1.0 O B:GLU311 4.4 29.9 1.0 O B:TYR191 4.5 26.9 1.0 CA B:GLY333 4.6 22.5 1.0 N B:THR334 4.7 27.5 1.0 CA B:THR334 4.7 28.0 1.0 CD1 B:TYR332 4.8 26.1 1.0 ND2 B:ASN211 4.9 26.9 1.0

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


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 Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:50.4 occ:1.00 OD1 B:ASN377 2.7 32.5 1.0 O B:PRO134 2.7 40.3 1.0 OH B:TYR169 2.8 36.5 1.0 OD1 B:ASN137 2.8 43.1 1.0 O B:HOH908 2.9 46.0 1.0 CA B:PRO134 3.4 38.8 1.0 C B:PRO134 3.4 46.3 1.0 CZ B:TYR169 3.6 31.6 1.0 CE1 B:TYR169 3.6 27.8 1.0 CG B:ASN377 3.6 35.6 1.0 CG1 B:ILE378 3.7 27.7 1.0 CD1 B:ILE378 3.8 30.4 1.0 CB B:PRO134 3.9 31.6 1.0 ND2 B:ASN377 3.9 39.5 1.0 CG B:ASN137 3.9 44.0 1.0 CA B:ASN137 4.3 38.5 1.0 O B:HOH920 4.4 52.3 1.0 N B:ASN137 4.6 41.7 1.0 CB B:ASN137 4.6 38.2 1.0 OG B:SER375 4.7 45.6 1.0 N B:PRO134 4.7 34.8 1.0 N B:ASP135 4.7 40.8 1.0 O B:ASN133 4.9 40.6 1.0 CE2 B:TYR169 4.9 27.7 1.0 ND2 B:ASN137 4.9 52.9 1.0 CD1 B:TYR169 4.9 34.0 1.0

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