Atomistry » Manganese » PDB 1ciw-1en5 » 1do8
Atomistry »
  Manganese »
    PDB 1ciw-1en5 »
      1do8 »

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

Go back to Manganese Binding Sites List in 1do8
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

Go back to Manganese Binding Sites List in 1do8
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

Go back to Manganese Binding Sites List in 1do8
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

Go back to Manganese Binding Sites List in 1do8
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: Sat Oct 5 10:07:12 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy