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Manganese in PDB 1pj4: Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate.

Enzymatic activity of Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate.

All present enzymatic activity of Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate.:
1.1.1.39;

Protein crystallography data

The structure of Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate., PDB code: 1pj4 was solved by X.Tao, Z.Yang, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 226.050, 117.345, 111.310, 90.00, 109.00, 90.00
R / Rfree (%) 21.1 / 25.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate. (pdb code 1pj4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate., PDB code: 1pj4:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1pj4

Go back to Manganese Binding Sites List in 1pj4
Manganese binding site 1 out of 4 in the Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn4604

b:23.9
occ:1.00
 OD1 A:ASP256 2.2 19.2 1.0
OD1 A:ASP279 2.3 17.3 1.0
OE1 A:GLU255 2.3 24.5 1.0
O3 A:MLT701 2.3 27.3 1.0
O1 A:MLT701 2.4 25.6 1.0
O A:HOH4625 2.6 26.2 1.0
NH2 A:ARG165 3.1 40.7 1.0
C1 A:MLT701 3.2 28.5 1.0
CG A:ASP279 3.2 20.8 1.0
C2 A:MLT701 3.2 28.5 1.0
CG A:ASP256 3.3 22.0 1.0
CD A:GLU255 3.3 25.2 1.0
OD2 A:ASP279 3.5 22.7 1.0
OD2 A:ASP256 3.7 19.0 1.0
CG A:GLU255 3.8 22.5 1.0
O5 A:MLT701 3.9 34.0 1.0
O A:HOH4705 4.0 22.6 1.0
NZ A:LYS183 4.2 24.2 1.0
N A:ASP256 4.2 18.6 1.0
CZ A:ARG165 4.3 36.8 1.0
O2 A:MLT701 4.3 28.8 1.0
OE2 A:GLU255 4.4 28.6 1.0
CE A:LYS183 4.4 25.7 1.0
CB A:ASP256 4.5 19.2 1.0
C3 A:MLT701 4.5 28.9 1.0
CB A:ASP279 4.6 21.9 1.0
C4 A:MLT701 4.6 32.0 1.0
CA A:ASP256 4.7 20.5 1.0
ND2 A:ASN467 4.7 23.6 1.0
OD2 A:ASP278 4.8 33.2 1.0
NH1 A:ARG165 4.9 36.8 1.0

Manganese binding site 2 out of 4 in 1pj4

Go back to Manganese Binding Sites List in 1pj4
Manganese binding site 2 out of 4 in the Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1604

b:28.4
occ:1.00
 OD1 B:ASP1279 2.2 17.9 1.0
OD1 B:ASP1256 2.3 19.0 1.0
OE1 B:GLU1255 2.4 28.0 1.0
O3 B:MLT1701 2.4 29.9 1.0
O1 B:MLT1701 2.4 27.3 1.0
O B:HOH12 2.5 18.2 1.0
CG B:ASP1279 3.1 22.8 1.0
C1 B:MLT1701 3.2 31.0 1.0
OD2 B:ASP1279 3.2 21.1 1.0
C2 B:MLT1701 3.3 30.5 1.0
CG B:ASP1256 3.4 22.8 1.0
CD B:GLU1255 3.4 27.8 1.0
O5 B:MLT1701 3.7 34.3 1.0
CG B:GLU1255 3.8 24.9 1.0
OD2 B:ASP1256 3.9 20.6 1.0
NZ B:LYS1183 4.2 20.8 1.0
O B:HOH54 4.3 18.0 1.0
N B:ASP1256 4.3 21.6 1.0
NH2 B:ARG1165 4.3 32.4 1.0
O2 B:MLT1701 4.3 29.6 1.0
CE B:LYS1183 4.3 22.6 1.0
CB B:ASP1279 4.5 23.5 1.0
OE2 B:GLU1255 4.5 27.3 1.0
C3 B:MLT1701 4.5 31.2 1.0
C4 B:MLT1701 4.5 34.1 1.0
CB B:ASP1256 4.6 21.5 1.0
OD2 B:ASP1278 4.7 29.9 1.0
CA B:ASP1256 4.7 21.5 1.0
ND2 B:ASN1467 4.7 27.0 1.0
CA B:ASP1279 5.0 24.1 1.0

Manganese binding site 3 out of 4 in 1pj4

Go back to Manganese Binding Sites List in 1pj4
Manganese binding site 3 out of 4 in the Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2604

b:29.4
occ:1.00
 OD1 C:ASP2256 2.1 17.7 1.0
OD1 C:ASP2279 2.2 22.6 1.0
O3 C:MLT2701 2.3 26.2 1.0
OE1 C:GLU2255 2.4 28.1 1.0
O1 C:MLT2701 2.4 30.4 1.0
O C:HOH112 2.5 31.3 1.0
CG C:ASP2256 3.1 23.7 1.0
C1 C:MLT2701 3.2 31.1 1.0
CG C:ASP2279 3.2 25.7 1.0
C2 C:MLT2701 3.2 30.5 1.0
CD C:GLU2255 3.4 27.6 1.0
OD2 C:ASP2279 3.4 26.4 1.0
OD2 C:ASP2256 3.4 22.6 1.0
CG C:GLU2255 3.8 25.1 1.0
O5 C:MLT2701 3.8 31.1 1.0
NH1 C:ARG2165 4.0 36.9 1.0
NZ C:LYS2183 4.2 24.5 1.0
NH2 C:ARG2165 4.2 33.7 1.0
N C:ASP2256 4.3 20.7 1.0
O2 C:MLT2701 4.3 31.1 1.0
CB C:ASP2256 4.4 21.4 1.0
OE2 C:GLU2255 4.4 30.7 1.0
C3 C:MLT2701 4.5 30.3 1.0
CB C:ASP2279 4.5 25.9 1.0
CZ C:ARG2165 4.5 34.6 1.0
CE C:LYS2183 4.6 27.1 1.0
C4 C:MLT2701 4.6 32.4 1.0
CA C:ASP2256 4.7 21.6 1.0
ND2 C:ASN2467 4.8 27.6 1.0
CG2 C:ILE2179 5.0 13.7 1.0

Manganese binding site 4 out of 4 in 1pj4

Go back to Manganese Binding Sites List in 1pj4
Manganese binding site 4 out of 4 in the Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Atp, Mn++, and Allosteric Activator Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn3604

b:28.1
occ:1.00
 OD1 D:ASP3279 2.2 21.6 1.0
OE1 D:GLU3255 2.2 24.2 1.0
OD1 D:ASP3256 2.4 26.6 1.0
O D:HOH10 2.4 25.0 1.0
O1 D:MLT3701 2.4 27.5 1.0
O3 D:MLT3701 2.4 29.5 1.0
CG D:ASP3279 3.1 25.2 1.0
C1 D:MLT3701 3.2 29.8 1.0
CD D:GLU3255 3.3 24.1 1.0
C2 D:MLT3701 3.3 28.8 1.0
CG D:ASP3256 3.3 25.4 1.0
OD2 D:ASP3279 3.4 24.6 1.0
NH2 D:ARG3165 3.7 37.3 1.0
OD2 D:ASP3256 3.7 24.1 1.0
CG D:GLU3255 3.8 21.7 1.0
O5 D:MLT3701 3.9 33.6 1.0
O D:HOH256 4.1 35.1 1.0
NZ D:LYS3183 4.2 20.2 1.0
N D:ASP3256 4.2 21.4 1.0
CE D:LYS3183 4.3 20.0 1.0
OE2 D:GLU3255 4.3 29.2 1.0
O2 D:MLT3701 4.4 29.5 1.0
CB D:ASP3279 4.5 24.8 1.0
CB D:ASP3256 4.5 22.3 1.0
C3 D:MLT3701 4.6 29.6 1.0
CA D:ASP3256 4.6 22.4 1.0
C4 D:MLT3701 4.7 31.9 1.0
OD2 D:ASP3278 4.7 31.3 1.0
ND2 D:ASN3467 4.8 18.1 1.0
CZ D:ARG3165 4.9 36.0 1.0
CA D:ASP3279 5.0 25.1 1.0

Reference:

X.Tao, Z.Yang, L.Tong. Crystal Structures of Substrate Complexes of Malic Enzyme and Insights Into the Catalytic Mechanism. Structure V. 11 1141 2003.
ISSN: ISSN 0969-2126
PubMed: 12962632
DOI: 10.1016/S0969-2126(03)00168-0
Page generated: Sat Oct 5 12:07:35 2024

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