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Manganese in PDB 1pj3: Crystal Structure of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme in A Pentary Complex with Natural Substrate Pyruvate, Cofactor Nad+, 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 Pyruvate, Cofactor Nad+, 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 Pyruvate, Cofactor Nad+, 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 Pyruvate, Cofactor Nad+, Mn++, and Allosteric Activator Fumarate., PDB code: 1pj3 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 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 225.828, 117.050, 111.847, 90.00, 109.57, 90.00
R / Rfree (%) 19.2 / 23.6

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 Pyruvate, Cofactor Nad+, Mn++, and Allosteric Activator Fumarate. (pdb code 1pj3). 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 Pyruvate, Cofactor Nad+, Mn++, and Allosteric Activator Fumarate., PDB code: 1pj3:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1pj3

Go back to Manganese Binding Sites List in 1pj3
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 Pyruvate, Cofactor Nad+, 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 Pyruvate, Cofactor Nad+, Mn++, and Allosteric Activator Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:20.6
occ:1.00
 OD1 A:ASP279 2.2 17.1 1.0
OD1 A:ASP256 2.2 18.4 1.0
OE2 A:GLU255 2.3 22.1 1.0
O3 A:PYR603 2.3 18.1 1.0
O1 A:PYR603 2.4 14.4 1.0
O A:HOH4903 2.5 12.4 1.0
C2 A:PYR603 3.0 19.1 1.0
C1 A:PYR603 3.0 17.9 1.0
CG A:ASP279 3.2 19.7 1.0
CG A:ASP256 3.3 19.2 1.0
CD A:GLU255 3.3 19.8 1.0
OD2 A:ASP279 3.6 18.1 1.0
NH2 A:ARG165 3.7 22.8 1.0
OD2 A:ASP256 3.7 16.3 1.0
CG A:GLU255 3.8 18.9 1.0
NZ A:LYS183 4.2 23.4 1.0
N A:ASP256 4.2 16.9 1.0
O2 A:PYR603 4.2 15.8 1.0
C5N A:NAD601 4.3 18.8 1.0
CE A:LYS183 4.4 23.1 1.0
OE1 A:GLU255 4.4 24.1 1.0
NH1 A:ARG165 4.4 23.1 1.0
O A:HOH4995 4.4 38.6 1.0
C3 A:PYR603 4.5 26.2 1.0
CZ A:ARG165 4.5 24.3 1.0
CB A:ASP279 4.5 18.3 1.0
CB A:ASP256 4.5 15.8 1.0
CA A:ASP256 4.6 16.5 1.0
C6N A:NAD601 4.7 16.3 1.0
CA A:ASP279 4.9 20.0 1.0
ND2 A:ASN467 5.0 20.4 1.0

Manganese binding site 2 out of 4 in 1pj3

Go back to Manganese Binding Sites List in 1pj3
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 Pyruvate, Cofactor Nad+, 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 Pyruvate, Cofactor Nad+, Mn++, and Allosteric Activator Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1604

b:26.4
occ:1.00
 OD1 B:ASP1256 2.2 19.3 1.0
O3 B:PYR1603 2.2 27.4 1.0
OD1 B:ASP1279 2.2 27.5 1.0
OE1 B:GLU1255 2.3 26.2 1.0
O1 B:PYR1603 2.3 16.2 1.0
O B:HOH4902 2.4 17.3 1.0
C2 B:PYR1603 3.0 23.5 1.0
C1 B:PYR1603 3.0 23.5 1.0
CG B:ASP1279 3.2 29.4 1.0
CG B:ASP1256 3.3 23.8 1.0
CD B:GLU1255 3.4 25.1 1.0
NH2 B:ARG1165 3.4 25.8 1.0
OD2 B:ASP1279 3.6 29.2 1.0
OD2 B:ASP1256 3.7 23.1 1.0
CG B:GLU1255 3.8 23.3 1.0
NZ B:LYS1183 4.1 19.4 1.0
N B:ASP1256 4.2 21.6 1.0
O2 B:PYR1603 4.2 22.0 1.0
CE B:LYS1183 4.2 24.5 1.0
CZ B:ARG1165 4.4 23.6 1.0
C5N B:NAD1601 4.4 27.0 1.0
C3 B:PYR1603 4.4 29.6 1.0
OE2 B:GLU1255 4.5 24.9 1.0
NH1 B:ARG1165 4.5 24.9 1.0
CB B:ASP1256 4.5 21.5 1.0
CB B:ASP1279 4.5 26.8 1.0
CA B:ASP1256 4.6 21.8 1.0
C6N B:NAD1601 4.8 26.1 1.0
CD2 B:LEU1167 4.9 20.7 1.0
OD2 B:ASP1278 4.9 29.6 1.0
CA B:ASP1279 4.9 25.6 1.0
ND2 B:ASN1467 5.0 28.8 1.0

Manganese binding site 3 out of 4 in 1pj3

Go back to Manganese Binding Sites List in 1pj3
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 Pyruvate, Cofactor Nad+, 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 Pyruvate, Cofactor Nad+, Mn++, and Allosteric Activator Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2604

b:20.9
occ:1.00
 OD1 C:ASP2256 2.2 15.8 1.0
OD1 C:ASP2279 2.3 18.2 1.0
O3 C:PYR2603 2.3 24.7 1.0
OE2 C:GLU2255 2.3 23.1 1.0
O1 C:PYR2603 2.4 16.4 1.0
O C:HOH4904 2.4 13.2 1.0
C2 C:PYR2603 3.0 23.2 1.0
C1 C:PYR2603 3.0 23.8 1.0
CG C:ASP2256 3.2 19.8 1.0
CG C:ASP2279 3.3 20.7 1.0
CD C:GLU2255 3.4 22.0 1.0
NH2 C:ARG2165 3.6 23.8 1.0
OD2 C:ASP2279 3.6 18.2 1.0
OD2 C:ASP2256 3.6 18.9 1.0
CG C:GLU2255 3.9 20.4 1.0
NZ C:LYS2183 4.1 24.7 1.0
CE C:LYS2183 4.2 29.6 1.0
N C:ASP2256 4.2 17.3 1.0
O2 C:PYR2603 4.2 21.3 1.0
C5N C:NAD2601 4.4 22.8 1.0
CZ C:ARG2165 4.4 22.9 1.0
NH1 C:ARG2165 4.4 18.4 1.0
OE1 C:GLU2255 4.5 25.7 1.0
CB C:ASP2256 4.5 15.8 1.0
C3 C:PYR2603 4.5 30.7 1.0
CB C:ASP2279 4.6 19.2 1.0
CA C:ASP2256 4.6 16.2 1.0
C6N C:NAD2601 4.8 20.4 1.0
ND2 C:ASN2467 4.9 19.0 1.0
OD2 C:ASP2278 4.9 21.6 1.0
CA C:ASP2279 4.9 20.2 1.0

Manganese binding site 4 out of 4 in 1pj3

Go back to Manganese Binding Sites List in 1pj3
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 Pyruvate, Cofactor Nad+, 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 Pyruvate, Cofactor Nad+, Mn++, and Allosteric Activator Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn3604

b:24.1
occ:1.00
 OD1 D:ASP3256 2.2 18.8 1.0
O3 D:PYR3603 2.2 19.6 1.0
OE2 D:GLU3255 2.2 26.4 1.0
OD1 D:ASP3279 2.3 21.9 1.0
O D:HOH4001 2.4 20.9 1.0
O1 D:PYR3603 2.4 20.6 1.0
C2 D:PYR3603 3.0 23.3 1.0
C1 D:PYR3603 3.1 24.0 1.0
CG D:ASP3256 3.2 18.9 1.0
CG D:ASP3279 3.3 26.2 1.0
CD D:GLU3255 3.3 25.5 1.0
NH2 D:ARG3165 3.3 30.9 1.0
OD2 D:ASP3279 3.6 25.8 1.0
OD2 D:ASP3256 3.6 15.8 1.0
CG D:GLU3255 3.8 23.4 1.0
NZ D:LYS3183 4.1 18.8 1.0
N D:ASP3256 4.2 18.6 1.0
CZ D:ARG3165 4.2 30.4 1.0
O2 D:PYR3603 4.3 23.2 1.0
CE D:LYS3183 4.3 22.4 1.0
NH1 D:ARG3165 4.3 28.4 1.0
OE1 D:GLU3255 4.4 29.1 1.0
C5N D:NAD3601 4.4 25.2 1.0
CB D:ASP3256 4.4 17.4 1.0
C3 D:PYR3603 4.5 27.8 1.0
CA D:ASP3256 4.6 18.2 1.0
CB D:ASP3279 4.6 24.0 1.0
C6N D:NAD3601 4.8 26.3 1.0
C D:GLU3255 5.0 19.3 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 12:06:37 2024

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