Magnesium in PDB 1efk: Structure of Human Malic Enzyme in Complex with Ketomalonate

All present enzymatic activity of Structure of Human Malic Enzyme in Complex with Ketomalonate:
1.1.1.39;

The structure of Structure of Human Malic Enzyme in Complex with Ketomalonate, PDB code: 1efk was solved by Z.Yang, D.L.Floyd, G.Loeber, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	229.600, 118.600, 113.100, 90.00, 109.60, 90.00
R / Rfree (%)	21.8 / 30.1

The binding sites of Magnesium atom in the Structure of Human Malic Enzyme in Complex with Ketomalonate (pdb code 1efk). 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 Human Malic Enzyme in Complex with Ketomalonate, PDB code: 1efk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Human Malic Enzyme in Complex with Ketomalonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Malic Enzyme in Complex with Ketomalonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:25.9 occ:1.00 O3 A:MAK603 2.1 35.1 1.0 O1 A:MAK603 2.2 36.7 1.0 OD1 A:ASP256 2.2 32.5 1.0 OD1 A:ASP279 2.3 22.3 1.0 OE1 A:GLU255 2.3 25.8 1.0 O A:HOH4072 2.4 31.0 1.0 C2 A:MAK603 2.7 40.2 1.0 C1 A:MAK603 2.8 39.2 1.0 CG A:ASP279 3.0 22.2 1.0 CG A:ASP256 3.0 28.8 1.0 OD2 A:ASP279 3.1 20.7 1.0 CD A:GLU255 3.1 22.1 1.0 NH2 A:ARG165 3.3 35.0 1.0 OD2 A:ASP256 3.4 26.9 1.0 CG A:GLU255 3.9 21.8 1.0 OE2 A:GLU255 3.9 26.2 1.0 O2 A:MAK603 3.9 35.0 1.0 N A:ASP256 4.1 25.6 1.0 CZ A:ARG165 4.2 29.6 1.0 CB A:ASP256 4.2 26.1 1.0 C3 A:MAK603 4.2 47.5 1.0 NH1 A:ARG165 4.4 31.7 1.0 CA A:ASP256 4.4 25.9 1.0 CB A:ASP279 4.5 22.8 1.0 C5N A:NAD601 4.6 22.0 1.0 CE A:LYS183 4.8 23.4 1.0 CD2 A:LEU167 4.9 21.9 1.0 O5 A:MAK603 4.9 53.8 1.0 C6N A:NAD601 5.0 20.0 1.0

Magnesium binding site 2 out of 4 in the Structure of Human Malic Enzyme in Complex with Ketomalonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Malic Enzyme in Complex with Ketomalonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1604 b:24.8 occ:1.00 OD1 B:ASP256 1.9 24.9 1.0 OD1 B:ASP279 2.0 28.7 1.0 O3 B:MAK1603 2.1 37.7 1.0 OE1 B:GLU255 2.2 18.5 1.0 O1 B:MAK1603 2.3 40.9 1.0 O B:HOH4073 2.6 25.9 1.0 C2 B:MAK1603 2.8 39.0 1.0 C1 B:MAK1603 2.8 37.6 1.0 CG B:ASP279 2.9 29.5 1.0 CG B:ASP256 3.1 29.3 1.0 OD2 B:ASP279 3.2 32.5 1.0 CD B:GLU255 3.3 17.0 1.0 NH2 B:ARG165 3.5 18.0 1.0 OD2 B:ASP256 3.7 26.8 1.0 CG B:GLU255 3.7 16.5 1.0 N B:ASP256 3.9 25.5 1.0 O2 B:MAK1603 4.0 34.2 1.0 NH1 B:ARG165 4.1 6.7 1.0 CZ B:ARG165 4.2 13.8 1.0 CB B:ASP256 4.2 28.7 1.0 C3 B:MAK1603 4.2 45.6 1.0 NZ B:LYS183 4.3 24.6 1.0 CB B:ASP279 4.3 24.7 1.0 CA B:ASP256 4.3 26.1 1.0 OE2 B:GLU255 4.4 13.5 1.0 C5N B:NAD1601 4.6 21.1 1.0 CE B:LYS183 4.7 24.1 1.0 CA B:ASP279 4.8 20.5 1.0 O5 B:MAK1603 4.8 51.0 1.0 C B:GLU255 4.9 26.0 1.0 OD2 B:ASP278 4.9 26.8 1.0 C6N B:NAD1601 4.9 17.2 1.0 CB B:GLU255 5.0 22.6 1.0

Magnesium binding site 3 out of 4 in the Structure of Human Malic Enzyme in Complex with Ketomalonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Malic Enzyme in Complex with Ketomalonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2604 b:25.8 occ:1.00 OD1 C:ASP256 1.9 28.0 1.0 O3 C:MAK2603 2.0 35.5 1.0 OE1 C:GLU255 2.2 20.4 1.0 O1 C:MAK2603 2.2 38.7 1.0 OD1 C:ASP279 2.3 25.9 1.0 O C:HOH4074 2.7 29.0 1.0 C2 C:MAK2603 2.7 39.6 1.0 C1 C:MAK2603 2.7 37.1 1.0 CG C:ASP256 2.9 30.6 1.0 CG C:ASP279 3.1 23.9 1.0 OD2 C:ASP279 3.2 26.8 1.0 CD C:GLU255 3.3 21.6 1.0 OD2 C:ASP256 3.3 25.9 1.0 NH2 C:ARG165 3.4 20.7 1.0 NZ C:LYS183 3.6 21.4 1.0 CG C:GLU255 3.7 18.4 1.0 O2 C:MAK2603 3.9 32.5 1.0 N C:ASP256 4.0 26.9 1.0 CB C:ASP256 4.1 29.8 1.0 C3 C:MAK2603 4.2 49.1 1.0 CZ C:ARG165 4.3 16.4 1.0 CA C:ASP256 4.3 25.4 1.0 OE2 C:GLU255 4.4 23.8 1.0 CB C:ASP279 4.5 21.9 1.0 NH1 C:ARG165 4.6 9.7 1.0 C5N C:NAD2601 4.6 20.9 1.0 O5 C:MAK2603 4.9 55.0 1.0 C C:GLU255 4.9 27.8 1.0 C6N C:NAD2601 4.9 17.1 1.0 OD2 C:ASP278 4.9 23.8 1.0 O4 C:MAK2603 5.0 58.2 1.0 CB C:GLU255 5.0 19.5 1.0 CE C:LYS183 5.0 22.8 1.0

Magnesium binding site 4 out of 4 in the Structure of Human Malic Enzyme in Complex with Ketomalonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Malic Enzyme in Complex with Ketomalonate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg3604 b:20.6 occ:1.00 OD1 D:ASP256 2.0 22.8 1.0 OD1 D:ASP279 2.1 26.8 1.0 O1 D:MAK3603 2.2 38.0 1.0 O3 D:MAK3603 2.3 33.2 1.0 OE1 D:GLU255 2.3 18.6 1.0 O D:HOH4075 2.5 32.9 1.0 C1 D:MAK3603 2.8 40.4 1.0 CG D:ASP256 2.8 21.4 1.0 C2 D:MAK3603 2.8 39.6 1.0 CG D:ASP279 3.0 26.9 1.0 OD2 D:ASP279 3.1 29.2 1.0 OD2 D:ASP256 3.2 20.0 1.0 NH2 D:ARG165 3.2 26.5 1.0 CD D:GLU255 3.3 20.9 1.0 CG D:GLU255 3.7 21.8 1.0 N D:ASP256 3.9 25.3 1.0 O2 D:MAK3603 4.0 36.4 1.0 CZ D:ARG165 4.0 29.0 1.0 CB D:ASP256 4.0 23.2 1.0 NH1 D:ARG165 4.2 18.6 1.0 CA D:ASP256 4.2 24.6 1.0 C3 D:MAK3603 4.3 46.7 1.0 CB D:ASP279 4.4 23.7 1.0 OE2 D:GLU255 4.4 22.6 1.0 C5N D:NAD3601 4.5 18.0 1.0 C6N D:NAD3601 4.8 19.6 1.0 CD2 D:LEU167 4.8 26.2 1.0 C D:GLU255 4.9 25.2 1.0 CB D:GLU255 4.9 21.9 1.0 CE D:LYS183 5.0 22.5 1.0 O5 D:MAK3603 5.0 54.3 1.0

Z.Yang, D.L.Floyd, G.Loeber, L.Tong. Structure of A Closed Form of Human Malic Enzyme and Implications For Catalytic Mechanism. Nat.Struct.Biol. V. 7 251 2000.
ISSN: ISSN 1072-8368
PubMed: 10700286
DOI: 10.1038/73378