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Manganese in PDB 1do8: Crystal Structure of A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme

Enzymatic activity of Crystal Structure of A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme

All present enzymatic activity of Crystal Structure of A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme:
1.1.1.39;

Protein crystallography data

The structure of Crystal Structure of A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme, PDB code: 1do8 was solved by Z.Yang, D.L.Floyd, G.Loeber, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 229.000, 118.700, 113.000, 90.00, 109.60, 90.00
R / Rfree (%) 20.4 / 26.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme (pdb code 1do8). 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 A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme, PDB code: 1do8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1do8

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Manganese binding site 1 out of 4 in the Crystal Structure of A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme


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 A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:18.3
occ:1.00
 OD1 A:ASP256 2.2 18.6 1.0
OD1 A:ASP279 2.2 9.8 1.0
O4 A:OXL603 2.3 16.7 1.0
O A:HOH606 2.4 13.8 1.0
OE1 A:GLU255 2.4 17.3 1.0
O1 A:OXL603 2.4 16.1 1.0
C2 A:OXL603 3.0 19.1 1.0
C1 A:OXL603 3.1 20.5 1.0
CG A:ASP279 3.2 15.1 1.0
CG A:ASP256 3.3 18.7 1.0
OD2 A:ASP279 3.4 14.0 1.0
CD A:GLU255 3.5 17.5 1.0
NH2 A:ARG165 3.7 24.0 1.0
OD2 A:ASP256 3.7 16.9 1.0
CG A:GLU255 3.9 13.4 1.0
O2 A:OXL603 4.2 19.3 1.0
N A:ASP256 4.2 16.2 1.0
O3 A:OXL603 4.3 16.8 1.0
NZ A:LYS183 4.4 19.9 1.0
CZ A:ARG165 4.5 22.9 1.0
NH1 A:ARG165 4.5 17.6 1.0
O A:HOH4750 4.5 50.9 1.0
CB A:ASP256 4.5 16.2 1.0
CB A:ASP279 4.5 15.3 1.0
C5N A:NAD601 4.6 15.8 1.0
CE A:LYS183 4.6 18.1 1.0
OE2 A:GLU255 4.6 21.8 1.0
ND2 A:ASN467 4.6 15.1 1.0
CA A:ASP256 4.7 16.8 1.0
CD2 A:LEU167 4.8 19.4 1.0

Manganese binding site 2 out of 4 in 1do8

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Manganese binding site 2 out of 4 in the Crystal Structure of A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme


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 A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1604

b:19.5
occ:1.00
 OD1 B:ASP1256 2.2 13.4 1.0
OE1 B:GLU1255 2.3 15.0 1.0
OD1 B:ASP1279 2.3 21.7 1.0
O1 B:OXL1603 2.4 21.2 1.0
O B:HOH1606 2.4 15.7 1.0
O4 B:OXL1603 2.6 20.8 1.0
C1 B:OXL1603 3.1 20.7 1.0
C2 B:OXL1603 3.2 20.3 1.0
CD B:GLU1255 3.2 16.9 1.0
CG B:ASP1279 3.2 20.8 1.0
CG B:ASP1256 3.4 17.4 1.0
CG B:GLU1255 3.5 15.8 1.0
OD2 B:ASP1279 3.5 21.6 1.0
NH2 B:ARG1165 3.6 18.7 1.0
OD2 B:ASP1256 4.0 17.7 1.0
N B:ASP1256 4.2 16.3 1.0
NZ B:LYS1183 4.2 8.3 1.0
O3 B:OXL1603 4.2 15.3 1.0
O2 B:OXL1603 4.3 25.4 1.0
CE B:LYS1183 4.4 6.9 1.0
OE2 B:GLU1255 4.4 19.7 1.0
CZ B:ARG1165 4.5 13.7 1.0
CB B:ASP1256 4.5 18.2 1.0
NH1 B:ARG1165 4.6 12.6 1.0
CB B:ASP1279 4.6 18.5 1.0
CA B:ASP1256 4.6 17.9 1.0
C5N B:NAD1601 4.8 16.4 1.0
ND2 B:ASN1467 4.8 14.6 1.0
CB B:GLU1255 4.8 15.2 1.0
O B:HOH4687 4.8 43.9 1.0
OD2 B:ASP1278 4.9 14.5 1.0
C B:GLU1255 5.0 16.2 1.0

Manganese binding site 3 out of 4 in 1do8

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Manganese binding site 3 out of 4 in the Crystal Structure of A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme


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 A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2604

b:17.6
occ:1.00
 OD1 C:ASP2279 2.2 18.4 1.0
O1 C:OXL2603 2.2 20.1 1.0
OD1 C:ASP2256 2.2 21.3 1.0
OE1 C:GLU2255 2.3 11.4 1.0
O4 C:OXL2603 2.4 21.5 1.0
O C:HOH2606 2.6 16.1 1.0
C1 C:OXL2603 2.9 22.5 1.0
C2 C:OXL2603 3.0 20.7 1.0
CG C:ASP2279 3.2 20.1 1.0
CG C:ASP2256 3.2 22.6 1.0
CD C:GLU2255 3.4 19.6 1.0
OD2 C:ASP2279 3.6 16.0 1.0
OD2 C:ASP2256 3.6 15.8 1.0
NH2 C:ARG2165 3.7 13.6 1.0
CG C:GLU2255 3.8 15.3 1.0
NZ C:LYS2183 3.9 6.6 1.0
O3 C:OXL2603 4.1 15.8 1.0
O2 C:OXL2603 4.2 24.5 1.0
N C:ASP2256 4.3 19.0 1.0
OE2 C:GLU2255 4.5 14.3 1.0
CB C:ASP2256 4.5 19.8 1.0
CB C:ASP2279 4.5 16.5 1.0
C5N C:NAD2601 4.5 14.6 1.0
CZ C:ARG2165 4.6 14.8 1.0
NH1 C:ARG2165 4.6 10.7 1.0
ND2 C:ASN2467 4.7 11.1 1.0
CA C:ASP2256 4.7 19.1 1.0
CA C:ASP2279 5.0 15.3 1.0
OD2 C:ASP2278 5.0 14.3 1.0

Manganese binding site 4 out of 4 in 1do8

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Manganese binding site 4 out of 4 in the Crystal Structure of A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme


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 A Closed Form of Human Mitochondrial Nad(P)+- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn3604

b:18.6
occ:1.00
 OD1 D:ASP3279 2.2 7.6 1.0
OD1 D:ASP3256 2.3 18.5 1.0
OE1 D:GLU3255 2.3 16.9 1.0
O1 D:OXL3603 2.3 18.0 1.0
O4 D:OXL3603 2.4 17.5 1.0
O D:HOH3606 2.4 16.4 1.0
C1 D:OXL3603 3.0 20.1 1.0
C2 D:OXL3603 3.0 18.8 1.0
CG D:ASP3256 3.2 15.3 1.0
CG D:ASP3279 3.3 16.6 1.0
CD D:GLU3255 3.3 20.2 1.0
NH2 D:ARG3165 3.6 22.2 1.0
OD2 D:ASP3256 3.6 15.1 1.0
OD2 D:ASP3279 3.7 16.9 1.0
CG D:GLU3255 3.7 17.8 1.0
N D:ASP3256 4.2 17.3 1.0
O3 D:OXL3603 4.2 13.3 1.0
O2 D:OXL3603 4.2 22.7 1.0
NZ D:LYS3183 4.3 14.6 1.0
OE2 D:GLU3255 4.4 25.1 1.0
CZ D:ARG3165 4.4 20.1 1.0
NH1 D:ARG3165 4.4 13.9 1.0
CB D:ASP3256 4.4 13.8 1.0
C5N D:NAD3601 4.5 15.7 1.0
CB D:ASP3279 4.6 16.4 1.0
CA D:ASP3256 4.6 16.1 1.0
CE D:LYS3183 4.7 20.2 1.0
ND2 D:ASN3467 4.7 18.0 1.0
O D:HOH4349 4.8 20.2 1.0
CD2 D:LEU3167 5.0 8.9 1.0
CB D:GLU3255 5.0 17.9 1.0

Reference:

Z.Yang, D.L.Floyd, G.Loeber, L.Tong. Structure of A Closed Form of Human Malic Enzyme and Implications For Catalytic Mechanism. Nat.Struct.Biol. V. 7 251 2000.
ISSN: ISSN 1072-8368
PubMed: 10700286
DOI: 10.1038/73378
Page generated: Tue Dec 15 03:47:12 2020

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