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
|