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Manganese in PDB 1pj2: Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Malate, Cofactor Nadh, 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, Cofactor Nadh, 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, Cofactor Nadh, 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, Cofactor Nadh, Mn++, and Allosteric Activator Fumarate, PDB code: 1pj2 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) 20.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 227.283, 117.345, 113.024, 90.00, 109.79, 90.00
R / Rfree (%) 20.5 / 25.6

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, Cofactor Nadh, Mn++, and Allosteric Activator Fumarate (pdb code 1pj2). 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, Cofactor Nadh, Mn++, and Allosteric Activator Fumarate, PDB code: 1pj2:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1pj2

Go back to Manganese Binding Sites List in 1pj2
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, Cofactor Nadh, 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, Cofactor Nadh, Mn++, and Allosteric Activator Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:25.9
occ:1.00
 OD1 A:ASP256 2.2 23.4 1.0
O2 A:LMR701 2.2 15.7 1.0
OD1 A:ASP279 2.3 29.5 1.0
OE1 A:GLU255 2.3 25.1 1.0
O1A A:LMR701 2.4 20.9 1.0
O A:HOH4544 2.5 22.1 1.0
C2 A:LMR701 3.1 20.1 1.0
C1 A:LMR701 3.1 21.1 1.0
CG A:ASP256 3.2 25.4 1.0
CG A:ASP279 3.2 33.0 1.0
NH2 A:ARG165 3.4 27.5 1.0
CD A:GLU255 3.4 24.4 1.0
OD2 A:ASP279 3.5 34.5 1.0
OD2 A:ASP256 3.5 22.9 1.0
O4B A:LMR701 4.0 22.0 1.0
CG A:GLU255 4.1 22.2 1.0
NZ A:LYS183 4.2 23.4 1.0
N A:ASP256 4.2 21.4 1.0
O1B A:LMR701 4.3 22.8 1.0
CZ A:ARG165 4.4 24.6 1.0
CE A:LYS183 4.4 24.1 1.0
OE2 A:GLU255 4.4 27.9 1.0
CB A:ASP256 4.5 24.1 1.0
NH1 A:ARG165 4.5 20.2 1.0
C3 A:LMR701 4.5 18.4 1.0
ND2 A:ASN467 4.6 33.4 1.0
CB A:ASP279 4.6 30.7 1.0
CA A:ASP256 4.6 21.8 1.0
C4 A:LMR701 4.7 21.7 1.0
C5N A:NAI601 4.9 28.6 1.0

Manganese binding site 2 out of 4 in 1pj2

Go back to Manganese Binding Sites List in 1pj2
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, Cofactor Nadh, 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, Cofactor Nadh, Mn++, and Allosteric Activator Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1604

b:31.3
occ:1.00
 OD2 B:ASP1256 2.1 14.6 1.0
O2 B:LMR1701 2.2 30.0 1.0
OD1 B:ASP1279 2.3 36.4 1.0
OE1 B:GLU1255 2.3 34.5 1.0
O1A B:LMR1701 2.3 25.1 1.0
O B:HOH4003 2.5 20.4 1.0
C1 B:LMR1701 3.0 25.9 1.0
C2 B:LMR1701 3.1 28.4 1.0
CG B:ASP1279 3.1 37.9 1.0
CG B:ASP1256 3.2 22.4 1.0
OD2 B:ASP1279 3.3 37.8 1.0
CD B:GLU1255 3.4 31.8 1.0
NH2 B:ARG1165 3.7 32.8 1.0
CG B:GLU1255 3.7 29.1 1.0
OD1 B:ASP1256 3.8 20.9 1.0
O4B B:LMR1701 3.8 32.6 1.0
NZ B:LYS1183 4.1 28.0 1.0
N B:ASP1256 4.1 26.3 1.0
O1B B:LMR1701 4.2 26.1 1.0
CE B:LYS1183 4.3 29.9 1.0
C3 B:LMR1701 4.4 30.9 1.0
CB B:ASP1279 4.4 35.7 1.0
CB B:ASP1256 4.5 22.4 1.0
OE2 B:GLU1255 4.5 31.9 1.0
CA B:ASP1256 4.5 24.8 1.0
ND2 B:ASN1467 4.5 32.5 1.0
C4 B:LMR1701 4.6 33.5 1.0
CZ B:ARG1165 4.6 28.7 1.0
NH1 B:ARG1165 4.7 28.6 1.0
OD2 B:ASP1278 4.7 40.8 1.0
CA B:ASP1279 4.8 35.4 1.0
N B:ASP1279 5.0 35.3 1.0
CB B:GLU1255 5.0 28.0 1.0

Manganese binding site 3 out of 4 in 1pj2

Go back to Manganese Binding Sites List in 1pj2
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, Cofactor Nadh, 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, Cofactor Nadh, Mn++, and Allosteric Activator Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2604

b:27.0
occ:1.00
 O2 C:LMR2701 2.1 19.9 1.0
OD1 C:ASP2256 2.2 24.0 1.0
OD1 C:ASP2279 2.2 25.1 1.0
OE1 C:GLU2255 2.4 28.5 1.0
O C:HOH4002 2.4 20.1 1.0
O1B C:LMR2701 2.5 21.9 1.0
C2 C:LMR2701 3.0 20.6 1.0
C1 C:LMR2701 3.1 24.8 1.0
CG C:ASP2279 3.2 26.4 1.0
CG C:ASP2256 3.2 28.1 1.0
NH2 C:ARG2165 3.3 28.9 1.0
CD C:GLU2255 3.4 28.4 1.0
OD2 C:ASP2279 3.5 26.6 1.0
OD2 C:ASP2256 3.7 26.1 1.0
CG C:GLU2255 3.8 29.9 1.0
O4A C:LMR2701 4.0 19.3 1.0
NZ C:LYS2183 4.0 18.9 1.0
N C:ASP2256 4.3 26.4 1.0
O1A C:LMR2701 4.3 25.4 1.0
CZ C:ARG2165 4.3 24.8 1.0
C3 C:LMR2701 4.3 18.2 1.0
CE C:LYS2183 4.4 21.7 1.0
OE2 C:GLU2255 4.5 32.2 1.0
CB C:ASP2256 4.5 25.1 1.0
CB C:ASP2279 4.5 25.1 1.0
NH1 C:ARG2165 4.5 23.0 1.0
C4 C:LMR2701 4.6 21.9 1.0
ND2 C:ASN2467 4.6 23.8 1.0
CA C:ASP2256 4.6 26.6 1.0
CA C:ASP2279 4.9 27.1 1.0
OD2 C:ASP2278 4.9 35.5 1.0
C5N C:NAI2601 5.0 28.8 1.0
CD2 C:LEU2167 5.0 20.4 1.0

Manganese binding site 4 out of 4 in 1pj2

Go back to Manganese Binding Sites List in 1pj2
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, Cofactor Nadh, 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, Cofactor Nadh, Mn++, and Allosteric Activator Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn3604

b:30.9
occ:1.00
 O2 D:LMR3701 2.2 24.3 1.0
OD1 D:ASP3256 2.3 30.8 1.0
OD1 D:ASP3279 2.3 34.1 1.0
O1B D:LMR3701 2.4 31.9 1.0
O D:HOH4547 2.4 27.7 1.0
OE1 D:GLU3255 2.5 39.1 1.0
CD D:GLU3255 3.1 34.9 1.0
C2 D:LMR3701 3.1 30.2 1.0
C1 D:LMR3701 3.1 31.6 1.0
NH2 D:ARG3165 3.2 37.4 1.0
CG D:ASP3279 3.3 36.4 1.0
CG D:ASP3256 3.3 30.9 1.0
OE2 D:GLU3255 3.6 38.1 1.0
OD2 D:ASP3279 3.6 35.3 1.0
OD2 D:ASP3256 3.6 29.3 1.0
O4A D:LMR3701 3.8 32.5 1.0
CG D:GLU3255 3.9 32.7 1.0
CZ D:ARG3165 4.3 34.3 1.0
NZ D:LYS3183 4.3 23.3 1.0
O1A D:LMR3701 4.3 35.2 1.0
C3 D:LMR3701 4.4 28.6 1.0
N D:ASP3256 4.4 30.2 1.0
NH1 D:ARG3165 4.5 35.1 1.0
C4 D:LMR3701 4.5 30.9 1.0
CE D:LYS3183 4.6 24.4 1.0
CB D:ASP3256 4.6 30.1 1.0
CB D:ASP3279 4.7 35.6 1.0
ND2 D:ASN3467 4.7 27.6 1.0
C5N D:NAI3601 4.9 32.0 1.0
CA D:ASP3256 4.9 30.6 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 12:06:26 2024

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