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Manganese in PDB 1gz4: Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate

Enzymatic activity of Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate

All present enzymatic activity of Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate:
1.1.1.40;

Protein crystallography data

The structure of Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate, PDB code: 1gz4 was solved by Z.Yang, C.W.Lanks, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 2.2
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.944, 117.454, 111.610, 90.00, 109.33, 90.00
R / Rfree (%) 20.9 / 24.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate (pdb code 1gz4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate, PDB code: 1gz4:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1gz4

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Manganese binding site 1 out of 4 in the Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:34.6
occ:1.00
 O3 A:TTN603 2.2 42.5 1.0
OD1 A:ASP256 2.3 34.0 1.0
OD1 A:ASP279 2.3 26.9 1.0
OE1 A:GLU255 2.3 32.1 1.0
O1 A:TTN603 2.4 45.2 1.0
O A:HOH2148 2.7 24.3 1.0
C1 A:TTN603 3.1 49.3 1.0
C2 A:TTN603 3.1 47.8 1.0
CG A:ASP279 3.2 31.0 1.0
CG A:ASP256 3.3 33.3 1.0
OD2 A:ASP279 3.3 35.7 1.0
CD A:GLU255 3.4 32.6 1.0
OD2 A:ASP256 3.7 36.7 1.0
CG A:GLU255 3.9 29.9 1.0
NH2 A:ARG165 3.9 44.3 1.0
N A:ASP256 4.2 27.8 1.0
O2 A:TTN603 4.3 52.8 1.0
NZ A:LYS183 4.3 36.5 1.0
C3 A:TTN603 4.4 51.8 1.0
OE2 A:GLU255 4.5 34.7 1.0
CE A:LYS183 4.5 36.7 1.0
CB A:ASP256 4.5 30.7 1.0
CB A:ASP279 4.6 29.8 1.0
O5 A:TTN603 4.6 53.1 1.0
O A:HOH2146 4.6 42.9 1.0
CA A:ASP256 4.6 29.2 1.0
ND2 A:ASN467 4.8 33.1 1.0
CD2 A:LEU167 4.9 31.6 1.0

Manganese binding site 2 out of 4 in 1gz4

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Manganese binding site 2 out of 4 in the Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn604

b:34.6
occ:1.00
 O3 B:TTN603 2.2 49.8 1.0
OD1 B:ASP256 2.2 32.1 1.0
OD1 B:ASP279 2.3 31.0 1.0
OE1 B:GLU255 2.4 36.8 1.0
O1 B:TTN603 2.4 44.3 1.0
O B:HOH2138 2.6 22.5 1.0
C2 B:TTN603 3.1 51.3 1.0
C1 B:TTN603 3.1 49.5 1.0
CG B:ASP279 3.2 32.5 1.0
OD2 B:ASP279 3.3 31.3 1.0
CG B:ASP256 3.3 32.7 1.0
CD B:GLU255 3.5 32.9 1.0
NH2 B:ARG165 3.7 42.9 1.0
OD2 B:ASP256 3.8 31.8 1.0
CG B:GLU255 4.0 27.2 1.0
NZ B:LYS183 4.2 32.7 1.0
N B:ASP256 4.3 24.0 1.0
O2 B:TTN603 4.3 50.5 1.0
CE B:LYS183 4.4 33.7 1.0
C3 B:TTN603 4.4 54.5 1.0
O B:HOH2071 4.5 35.6 1.0
O5 B:TTN603 4.5 56.7 1.0
CB B:ASP256 4.6 28.7 1.0
CB B:ASP279 4.6 31.4 1.0
OE2 B:GLU255 4.6 33.9 1.0
CA B:ASP256 4.7 26.0 1.0
ND2 B:ASN467 4.7 36.5 1.0
CZ B:ARG165 4.9 42.5 1.0
CD2 B:LEU167 4.9 25.2 1.0

Manganese binding site 3 out of 4 in 1gz4

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Manganese binding site 3 out of 4 in the Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn604

b:39.6
occ:1.00
 OD1 C:ASP256 2.2 24.3 1.0
O1 C:TTN603 2.2 43.3 1.0
OE1 C:GLU255 2.3 39.4 1.0
OD1 C:ASP279 2.3 33.6 1.0
O3 C:TTN603 2.4 46.4 1.0
C1 C:TTN603 3.0 47.6 1.0
NH2 C:ARG165 3.1 49.3 1.0
C2 C:TTN603 3.2 49.8 1.0
CG C:ASP256 3.2 30.1 1.0
CG C:ASP279 3.3 33.7 1.0
CD C:GLU255 3.4 35.8 1.0
OD2 C:ASP279 3.5 34.7 1.0
OD2 C:ASP256 3.7 29.3 1.0
CG C:GLU255 3.7 32.2 1.0
NZ C:LYS183 4.0 37.9 1.0
O2 C:TTN603 4.2 46.3 1.0
N C:ASP256 4.3 25.3 1.0
C3 C:TTN603 4.3 52.9 1.0
O5 C:TTN603 4.3 56.1 1.0
CZ C:ARG165 4.3 46.5 1.0
OE2 C:GLU255 4.5 38.9 1.0
CB C:ASP256 4.5 27.5 1.0
CE C:LYS183 4.6 34.6 1.0
CB C:ASP279 4.6 31.8 1.0
CA C:ASP256 4.7 27.4 1.0
ND2 C:ASN467 4.8 34.9 1.0
NH1 C:ARG165 4.9 46.5 1.0
CD2 C:LEU167 4.9 30.6 1.0
OD2 C:ASP278 5.0 38.2 1.0

Manganese binding site 4 out of 4 in 1gz4

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Manganese binding site 4 out of 4 in the Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Molecular Mechanism of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn604

b:35.6
occ:1.00
 OD1 D:ASP279 2.2 26.5 1.0
OE1 D:GLU255 2.3 29.1 1.0
O3 D:TTN603 2.3 41.9 1.0
OD1 D:ASP256 2.3 28.5 1.0
O1 D:TTN603 2.4 41.4 1.0
O D:HOH2147 2.5 34.1 1.0
CG D:ASP279 3.1 28.9 1.0
C1 D:TTN603 3.1 45.2 1.0
C2 D:TTN603 3.2 46.1 1.0
NH2 D:ARG165 3.2 35.4 1.0
OD2 D:ASP279 3.3 29.5 1.0
CG D:ASP256 3.3 27.1 1.0
CD D:GLU255 3.4 29.2 1.0
OD2 D:ASP256 3.7 27.8 1.0
CG D:GLU255 3.8 25.8 1.0
N D:ASP256 4.3 24.6 1.0
O2 D:TTN603 4.3 42.9 1.0
NZ D:LYS183 4.4 29.1 1.0
CZ D:ARG165 4.4 35.2 1.0
CE D:LYS183 4.4 27.0 1.0
OE2 D:GLU255 4.5 29.5 1.0
O D:HOH2087 4.5 45.1 1.0
C3 D:TTN603 4.5 50.3 1.0
CB D:ASP279 4.5 27.7 1.0
CB D:ASP256 4.6 26.1 1.0
O D:HOH2146 4.7 36.9 1.0
ND2 D:ASN467 4.7 27.6 1.0
CA D:ASP256 4.7 25.7 1.0
O5 D:TTN603 4.7 53.5 1.0
OD2 D:ASP278 4.8 33.1 1.0
CD2 D:LEU167 5.0 27.2 1.0

Reference:

Z.Yang, C.W.Lanks, L.Tong. Molecular Mechanism For the Regulation of Human Mitochondrial Nad(P)(+)-Dependent Malic Enzyme By Atp and Fumarate Structure V. 10 951 2002.
ISSN: ISSN 0969-2126
PubMed: 12121650
DOI: 10.1016/S0969-2126(02)00788-8
Page generated: Sat Oct 5 10:49:27 2024

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