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Magnesium in PDB 1efl: Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate

Enzymatic activity of Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate

All present enzymatic activity of Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate:
1.1.1.39;

Protein crystallography data

The structure of Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate, PDB code: 1efl 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 (°) 228.800, 117.000, 114.300, 90.00, 109.20, 90.00
R / Rfree (%) 20.6 / 28.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate (pdb code 1efl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate, PDB code: 1efl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1efl

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Magnesium binding site 1 out of 4 in the Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:25.5
occ:1.00
OD1 A:ASP256 2.1 31.2 1.0
OE1 A:GLU255 2.2 24.4 1.0
O3 A:TTN603 2.2 35.7 1.0
OD1 A:ASP279 2.3 15.0 1.0
O5 A:TTN603 2.5 52.5 1.0
O1 A:TTN603 2.6 29.5 1.0
C2 A:TTN603 2.9 41.5 1.0
CG A:ASP256 2.9 27.5 1.0
C3 A:TTN603 3.1 49.0 1.0
C1 A:TTN603 3.1 35.1 1.0
OD2 A:ASP256 3.2 23.8 1.0
CD A:GLU255 3.3 22.8 1.0
CG A:ASP279 3.3 17.1 1.0
NH2 A:ARG165 3.4 21.6 1.0
OD2 A:ASP279 3.6 14.2 1.0
CG A:GLU255 3.7 19.4 1.0
NZ A:LYS183 4.1 15.6 1.0
N A:ASP256 4.3 16.2 1.0
O2 A:TTN603 4.3 29.0 1.0
O4 A:TTN603 4.3 52.9 1.0
CB A:ASP256 4.3 24.3 1.0
OE2 A:GLU255 4.3 26.9 1.0
CZ A:ARG165 4.5 16.8 1.0
CE A:LYS183 4.6 15.4 1.0
CA A:ASP256 4.6 20.4 1.0
C5N A:NAD601 4.6 21.6 1.0
CB A:ASP279 4.7 18.7 1.0
NH1 A:ARG165 4.8 13.7 1.0
CD2 A:LEU167 4.9 18.2 1.0

Magnesium binding site 2 out of 4 in 1efl

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Magnesium binding site 2 out of 4 in the Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1604

b:22.5
occ:1.00
O3 B:TTN1603 2.2 35.4 1.0
OD1 B:ASP256 2.3 29.9 1.0
O5 B:TTN1603 2.3 52.9 1.0
OE1 B:GLU255 2.3 17.9 1.0
OD1 B:ASP279 2.4 22.9 1.0
O1 B:TTN1603 2.4 32.1 1.0
C2 B:TTN1603 2.8 41.9 1.0
C3 B:TTN1603 2.9 49.8 1.0
C1 B:TTN1603 2.9 35.1 1.0
CG B:ASP256 3.1 26.2 1.0
OD2 B:ASP256 3.3 25.9 1.0
CD B:GLU255 3.4 12.0 1.0
NH2 B:ARG165 3.4 30.5 1.0
NZ B:LYS183 3.6 18.8 1.0
CG B:ASP279 3.6 20.9 1.0
CG B:GLU255 3.9 20.1 1.0
O4 B:TTN1603 4.1 53.1 1.0
O2 B:TTN1603 4.1 29.2 1.0
OD2 B:ASP279 4.3 22.8 1.0
CB B:ASP256 4.4 23.7 1.0
N B:ASP256 4.4 19.5 1.0
CD2 B:LEU167 4.5 8.5 1.0
OE2 B:GLU255 4.5 12.5 1.0
CZ B:ARG165 4.5 27.1 1.0
C5N B:NAD1601 4.6 21.6 1.0
CB B:ASP279 4.7 18.2 1.0
CA B:ASP256 4.7 23.0 1.0
NH1 B:ARG165 4.8 25.5 1.0
CG2 B:ILE179 4.8 8.3 1.0
OD2 B:ASP278 4.9 34.5 1.0

Magnesium binding site 3 out of 4 in 1efl

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Magnesium binding site 3 out of 4 in the Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2604

b:21.3
occ:1.00
OE1 C:GLU255 2.1 13.9 1.0
OD1 C:ASP279 2.2 15.5 1.0
O3 C:TTN2603 2.2 37.2 1.0
O5 C:TTN2603 2.4 51.0 1.0
O1 C:TTN2603 2.4 34.5 1.0
OD1 C:ASP256 2.5 29.6 1.0
C2 C:TTN2603 2.8 40.6 1.0
C3 C:TTN2603 2.9 47.4 1.0
C1 C:TTN2603 3.0 35.6 1.0
CG C:ASP256 3.0 25.6 1.0
OD2 C:ASP256 3.0 24.3 1.0
CD C:GLU255 3.1 15.5 1.0
CG C:ASP279 3.3 18.9 1.0
NH2 C:ARG165 3.6 19.8 1.0
CG C:GLU255 3.6 18.5 1.0
NZ C:LYS183 3.7 11.2 1.0
OD2 C:ASP279 3.9 21.6 1.0
O4 C:TTN2603 4.1 52.2 1.0
O2 C:TTN2603 4.2 29.8 1.0
N C:ASP256 4.2 18.1 1.0
OE2 C:GLU255 4.2 17.0 1.0
CB C:ASP256 4.3 24.1 1.0
CE C:LYS183 4.5 3.1 1.0
CB C:ASP279 4.5 16.8 1.0
CA C:ASP256 4.5 23.0 1.0
CZ C:ARG165 4.6 22.3 1.0
C5N C:NAD2601 4.7 19.8 1.0
NH1 C:ARG165 4.8 21.9 1.0
ND2 C:ASN467 4.9 17.5 1.0
CB C:GLU255 5.0 16.4 1.0

Magnesium binding site 4 out of 4 in 1efl

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Magnesium binding site 4 out of 4 in the Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Malic Enzyme in A Quaternary Complex with Nad, Mg, and Tartronate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3604

b:21.4
occ:1.00
OE1 D:GLU255 2.2 20.1 1.0
OD1 D:ASP279 2.2 21.4 1.0
OD1 D:ASP256 2.3 26.4 1.0
O3 D:TTN3603 2.4 36.7 1.0
O5 D:TTN3603 2.4 51.6 1.0
O1 D:TTN3603 2.5 33.3 1.0
OD2 D:ASP256 2.8 21.3 1.0
CG D:ASP256 2.8 22.8 1.0
C2 D:TTN3603 2.9 42.7 1.0
C3 D:TTN3603 3.0 50.0 1.0
C1 D:TTN3603 3.1 37.5 1.0
CD D:GLU255 3.3 20.9 1.0
CG D:ASP279 3.4 21.5 1.0
NH2 D:ARG165 3.7 16.2 1.0
CG D:GLU255 3.8 12.7 1.0
OD2 D:ASP279 3.8 25.1 1.0
NZ D:LYS183 3.9 25.4 1.0
CB D:ASP256 4.2 22.3 1.0
O4 D:TTN3603 4.2 52.4 1.0
N D:ASP256 4.3 18.2 1.0
O2 D:TTN3603 4.3 30.9 1.0
OE2 D:GLU255 4.4 26.5 1.0
C5N D:NAD3601 4.4 17.8 1.0
CZ D:ARG165 4.6 12.7 1.0
CA D:ASP256 4.6 19.7 1.0
CB D:ASP279 4.6 18.8 1.0
NH1 D:ARG165 4.6 6.7 1.0
OD2 D:ASP278 4.8 36.1 1.0
CE D:LYS183 4.9 20.1 1.0
C6N D:NAD3601 4.9 20.2 1.0
C4N D:NAD3601 5.0 20.3 1.0

Reference:

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
Page generated: Mon Dec 14 05:52:03 2020

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