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Manganese in PDB 1gz3: Molecular Mechanism For the Regulation of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme By Atp and Fumarate

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

All present enzymatic activity of Molecular Mechanism For the Regulation of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme By Atp and Fumarate:
1.1.1.38;

Protein crystallography data

The structure of Molecular Mechanism For the Regulation of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme By Atp and Fumarate, PDB code: 1gz3 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) 20.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.815, 192.653, 110.161, 90.00, 89.77, 90.00
R / Rfree (%) 19.4 / 23.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Molecular Mechanism For the Regulation of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme By Atp and Fumarate (pdb code 1gz3). 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 For the Regulation of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme By Atp and Fumarate, PDB code: 1gz3:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1gz3

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Manganese binding site 1 out of 4 in the Molecular Mechanism For 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 For 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:21.3
occ:1.00
 OD1 A:ASP279 2.2 21.4 1.0
OD1 A:ASP256 2.3 19.5 1.0
OE1 A:GLU255 2.3 19.6 1.0
O2 A:OXL603 2.4 25.4 1.0
O3 A:OXL603 2.4 25.3 1.0
O A:HOH2265 2.5 19.0 1.0
C1 A:OXL603 3.1 27.6 1.0
C2 A:OXL603 3.1 26.9 1.0
NH2 A:ARG165 3.1 35.8 1.0
CG A:ASP279 3.3 23.6 1.0
CG A:ASP256 3.4 18.7 1.0
CD A:GLU255 3.4 17.2 1.0
OD2 A:ASP279 3.6 23.9 1.0
O A:HOH2129 3.8 21.8 1.0
OD2 A:ASP256 3.9 16.0 1.0
CG A:GLU255 3.9 15.4 1.0
NZ A:LYS183 4.2 11.1 1.0
N A:ASP256 4.3 16.9 1.0
CZ A:ARG165 4.3 33.9 1.0
O1 A:OXL603 4.3 29.3 1.0
CE A:LYS183 4.3 13.2 1.0
O4 A:OXL603 4.4 27.3 1.0
OE2 A:GLU255 4.5 19.4 1.0
CB A:ASP279 4.6 20.4 1.0
CB A:ASP256 4.6 17.1 1.0
CA A:ASP256 4.7 17.6 1.0
ND2 A:ASN467 4.7 15.0 1.0
NH1 A:ARG165 4.8 36.2 1.0
CD2 A:LEU167 4.8 17.8 1.0
OD2 A:ASP278 4.8 20.8 1.0

Manganese binding site 2 out of 4 in 1gz3

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Manganese binding site 2 out of 4 in the Molecular Mechanism For 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 For 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:20.6
occ:1.00
 OD1 B:ASP256 2.2 18.3 1.0
OD1 B:ASP279 2.2 17.4 1.0
O2 B:OXL603 2.3 19.7 1.0
OE1 B:GLU255 2.3 22.8 1.0
O3 B:OXL603 2.4 19.7 1.0
O B:HOH2287 2.4 13.2 1.0
NH2 B:ARG165 3.0 35.2 1.0
C2 B:OXL603 3.1 24.2 1.0
CG B:ASP279 3.1 20.3 1.0
C1 B:OXL603 3.1 23.9 1.0
OD2 B:ASP279 3.2 15.8 1.0
CG B:ASP256 3.3 18.4 1.0
CD B:GLU255 3.4 19.1 1.0
OD2 B:ASP256 3.8 18.9 1.0
CG B:GLU255 3.8 18.7 1.0
O B:HOH2134 4.0 20.1 1.0
NZ B:LYS183 4.1 11.3 1.0
N B:ASP256 4.2 17.4 1.0
O1 B:OXL603 4.3 25.6 1.0
CZ B:ARG165 4.3 32.6 1.0
O4 B:OXL603 4.3 24.4 1.0
CE B:LYS183 4.4 7.0 1.0
CB B:ASP279 4.5 18.9 1.0
OE2 B:GLU255 4.5 20.0 1.0
CB B:ASP256 4.5 18.2 1.0
CA B:ASP256 4.6 19.1 1.0
ND2 B:ASN467 4.7 15.9 1.0
CA B:ASP279 5.0 18.7 1.0

Manganese binding site 3 out of 4 in 1gz3

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Manganese binding site 3 out of 4 in the Molecular Mechanism For 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 For 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:22.8
occ:1.00
 OD1 C:ASP256 2.2 15.8 1.0
OD1 C:ASP279 2.2 19.5 1.0
OE1 C:GLU255 2.2 21.1 1.0
O3 C:OXL603 2.3 21.0 1.0
O2 C:OXL603 2.4 18.5 1.0
O C:HOH2299 2.5 15.0 1.0
C1 C:OXL603 3.0 22.5 1.0
CG C:ASP279 3.1 21.8 1.0
C2 C:OXL603 3.1 21.2 1.0
NH2 C:ARG165 3.1 31.9 1.0
CG C:ASP256 3.2 16.4 1.0
OD2 C:ASP279 3.3 21.9 1.0
CD C:GLU255 3.3 18.1 1.0
OD2 C:ASP256 3.7 16.0 1.0
CG C:GLU255 3.8 18.0 1.0
NZ C:LYS183 4.0 21.3 1.0
O C:HOH2151 4.1 22.9 1.0
N C:ASP256 4.2 17.2 1.0
O1 C:OXL603 4.2 26.7 1.0
CZ C:ARG165 4.3 29.9 1.0
O4 C:OXL603 4.4 22.5 1.0
OE2 C:GLU255 4.4 18.6 1.0
CB C:ASP256 4.5 16.8 1.0
CB C:ASP279 4.5 20.9 1.0
CA C:ASP256 4.6 17.6 1.0
CE C:LYS183 4.7 23.2 1.0
ND2 C:ASN467 4.7 18.6 1.0
CD2 C:LEU167 4.8 13.4 1.0
NH1 C:ARG165 4.9 29.3 1.0
OD2 C:ASP278 5.0 21.8 1.0
CA C:ASP279 5.0 20.1 1.0

Manganese binding site 4 out of 4 in 1gz3

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Manganese binding site 4 out of 4 in the Molecular Mechanism For 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 For 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:20.6
occ:1.00
 OD1 D:ASP256 2.2 17.0 1.0
OD1 D:ASP279 2.3 22.9 1.0
OE1 D:GLU255 2.3 20.6 1.0
O2 D:OXL603 2.3 20.9 1.0
O3 D:OXL603 2.4 21.3 1.0
O D:HOH2299 2.5 15.1 1.0
C2 D:OXL603 3.0 23.5 1.0
C1 D:OXL603 3.1 22.7 1.0
CG D:ASP279 3.2 20.9 1.0
CG D:ASP256 3.3 16.2 1.0
CD D:GLU255 3.3 16.6 1.0
OD2 D:ASP279 3.4 16.6 1.0
NH2 D:ARG165 3.4 29.9 1.0
CG D:GLU255 3.7 15.4 1.0
OD2 D:ASP256 3.8 15.1 1.0
NZ D:LYS183 4.2 11.3 1.0
N D:ASP256 4.2 16.8 1.0
O1 D:OXL603 4.3 24.6 1.0
O D:HOH2142 4.3 20.2 1.0
O4 D:OXL603 4.3 22.7 1.0
CE D:LYS183 4.4 15.2 1.0
OE2 D:GLU255 4.4 18.1 1.0
CB D:ASP256 4.5 17.5 1.0
CB D:ASP279 4.5 20.2 1.0
CA D:ASP256 4.6 16.5 1.0
ND2 D:ASN467 4.7 18.4 1.0
CZ D:ARG165 4.7 29.1 1.0
OD2 D:ASP278 4.9 21.7 1.0
CA D:ASP279 5.0 18.9 1.0
CD2 D:LEU167 5.0 18.3 1.0
CB D:GLU255 5.0 15.6 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 10:49:10 2024

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