Iron in PDB 1nit: Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound
Enzymatic activity of Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound
All present enzymatic activity of Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound:
4.2.1.3;
Protein crystallography data
The structure of Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound, PDB code: 1nit
was solved by
H.Lauble,
M.C.Kennedy,
H.Beinert,
C.D.Stout,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.05
|
Space group
|
B 1 1 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
185.500,
72.000,
73.000,
90.00,
90.00,
77.70
|
R / Rfree (%)
|
17.2 /
n/a
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound
(pdb code 1nit). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound, PDB code: 1nit:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1nit
Go back to
Iron Binding Sites List in 1nit
Iron binding site 1 out
of 4 in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe999
b:23.0
occ:1.00
|
FE1
|
A:SF4999
|
0.0
|
23.0
|
1.0
|
S3
|
A:SF4999
|
2.3
|
25.6
|
1.0
|
S2
|
A:SF4999
|
2.3
|
19.5
|
1.0
|
S4
|
A:SF4999
|
2.3
|
15.8
|
1.0
|
SG
|
A:CYS358
|
2.3
|
22.4
|
1.0
|
FE4
|
A:SF4999
|
2.7
|
29.2
|
1.0
|
FE2
|
A:SF4999
|
2.7
|
22.1
|
1.0
|
FE3
|
A:SF4999
|
2.8
|
15.9
|
1.0
|
CB
|
A:CYS358
|
3.6
|
20.2
|
1.0
|
S1
|
A:SF4999
|
3.9
|
17.2
|
1.0
|
CG2
|
A:ILE145
|
4.0
|
4.9
|
1.0
|
N
|
A:CYS358
|
4.0
|
27.9
|
1.0
|
CD2
|
A:HIS147
|
4.3
|
7.3
|
1.0
|
CA
|
A:CYS358
|
4.5
|
25.2
|
1.0
|
O
|
A:HOH1000
|
4.5
|
19.3
|
0.2
|
SG
|
A:CYS424
|
4.8
|
19.4
|
1.0
|
SG
|
A:CYS421
|
4.8
|
7.3
|
1.0
|
ND2
|
A:ASN446
|
4.8
|
15.4
|
1.0
|
CB
|
A:SER357
|
4.9
|
27.2
|
1.0
|
NE2
|
A:HIS147
|
4.9
|
7.5
|
1.0
|
CB
|
A:HIS167
|
5.0
|
8.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 1nit
Go back to
Iron Binding Sites List in 1nit
Iron binding site 2 out
of 4 in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe999
b:22.1
occ:1.00
|
FE2
|
A:SF4999
|
0.0
|
22.1
|
1.0
|
S1
|
A:SF4999
|
2.3
|
17.2
|
1.0
|
SG
|
A:CYS424
|
2.3
|
19.4
|
1.0
|
S4
|
A:SF4999
|
2.3
|
15.8
|
1.0
|
S3
|
A:SF4999
|
2.3
|
25.6
|
1.0
|
FE1
|
A:SF4999
|
2.7
|
23.0
|
1.0
|
FE3
|
A:SF4999
|
2.7
|
15.9
|
1.0
|
FE4
|
A:SF4999
|
2.9
|
29.2
|
1.0
|
CB
|
A:CYS424
|
3.1
|
16.6
|
1.0
|
O
|
A:HOH1288
|
3.9
|
41.4
|
1.0
|
S2
|
A:SF4999
|
4.0
|
19.5
|
1.0
|
O
|
A:HOH1000
|
4.1
|
19.3
|
0.2
|
CB
|
A:SER357
|
4.4
|
27.2
|
1.0
|
CA
|
A:CYS424
|
4.4
|
16.2
|
1.0
|
C
|
A:CYS424
|
4.5
|
16.4
|
1.0
|
CB
|
A:CYS421
|
4.6
|
6.5
|
1.0
|
SG
|
A:CYS421
|
4.7
|
7.3
|
1.0
|
NH2
|
A:ARG452
|
4.7
|
22.1
|
1.0
|
SG
|
A:CYS358
|
4.7
|
22.4
|
1.0
|
O
|
A:CYS424
|
4.7
|
19.2
|
1.0
|
OG
|
A:SER357
|
4.8
|
33.0
|
1.0
|
H1
|
A:HOH1000
|
4.8
|
0.0
|
0.2
|
ND2
|
A:ASN446
|
4.8
|
15.4
|
1.0
|
OD1
|
A:ASN446
|
4.9
|
22.8
|
1.0
|
CA
|
A:CYS421
|
4.9
|
10.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 1nit
Go back to
Iron Binding Sites List in 1nit
Iron binding site 3 out
of 4 in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe999
b:15.9
occ:1.00
|
FE3
|
A:SF4999
|
0.0
|
15.9
|
1.0
|
SG
|
A:CYS421
|
2.2
|
7.3
|
1.0
|
S2
|
A:SF4999
|
2.4
|
19.5
|
1.0
|
S4
|
A:SF4999
|
2.4
|
15.8
|
1.0
|
S1
|
A:SF4999
|
2.4
|
17.2
|
1.0
|
FE2
|
A:SF4999
|
2.7
|
22.1
|
1.0
|
FE1
|
A:SF4999
|
2.8
|
23.0
|
1.0
|
FE4
|
A:SF4999
|
2.8
|
29.2
|
1.0
|
CB
|
A:CYS421
|
3.1
|
6.5
|
1.0
|
CA
|
A:CYS421
|
3.8
|
10.3
|
1.0
|
CE1
|
A:HIS101
|
3.8
|
6.7
|
1.0
|
S3
|
A:SF4999
|
3.9
|
25.6
|
1.0
|
O
|
A:HOH1000
|
3.9
|
19.3
|
0.2
|
CG2
|
A:ILE145
|
4.1
|
4.9
|
1.0
|
NE2
|
A:HIS101
|
4.1
|
4.5
|
1.0
|
N
|
A:CYS421
|
4.5
|
6.3
|
1.0
|
ND1
|
A:HIS101
|
4.6
|
10.0
|
1.0
|
SG
|
A:CYS424
|
4.8
|
19.4
|
1.0
|
CB
|
A:CYS424
|
4.8
|
16.6
|
1.0
|
H1
|
A:HOH1000
|
4.9
|
0.0
|
0.2
|
CG1
|
A:ILE425
|
4.9
|
18.9
|
1.0
|
SG
|
A:CYS358
|
4.9
|
22.4
|
1.0
|
C
|
A:CYS421
|
5.0
|
9.6
|
1.0
|
CD2
|
A:HIS101
|
5.0
|
8.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 1nit
Go back to
Iron Binding Sites List in 1nit
Iron binding site 4 out
of 4 in the Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Aconitase with Trans-Aconitate and Nitrocitrate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe999
b:29.2
occ:1.00
|
FE4
|
A:SF4999
|
0.0
|
29.2
|
1.0
|
O
|
A:HOH1000
|
1.9
|
19.3
|
0.2
|
S3
|
A:SF4999
|
2.3
|
25.6
|
1.0
|
S2
|
A:SF4999
|
2.3
|
19.5
|
1.0
|
S1
|
A:SF4999
|
2.4
|
17.2
|
1.0
|
H1
|
A:HOH1000
|
2.6
|
0.0
|
0.2
|
FE1
|
A:SF4999
|
2.7
|
23.0
|
1.0
|
FE3
|
A:SF4999
|
2.8
|
15.9
|
1.0
|
FE2
|
A:SF4999
|
2.9
|
22.1
|
1.0
|
OD1
|
A:ASP165
|
3.9
|
10.7
|
1.0
|
S4
|
A:SF4999
|
4.0
|
15.8
|
1.0
|
ND1
|
A:HIS167
|
4.1
|
7.8
|
1.0
|
OD2
|
A:ASP165
|
4.1
|
10.1
|
1.0
|
NE2
|
A:HIS101
|
4.4
|
4.5
|
1.0
|
CG
|
A:ASP165
|
4.5
|
10.1
|
1.0
|
CE1
|
A:HIS101
|
4.5
|
6.7
|
1.0
|
SG
|
A:CYS358
|
4.7
|
22.4
|
1.0
|
SG
|
A:CYS421
|
4.7
|
7.3
|
1.0
|
CG
|
A:HIS167
|
4.8
|
8.2
|
1.0
|
NH2
|
A:ARG452
|
4.8
|
22.1
|
1.0
|
O
|
A:HOH1288
|
4.8
|
41.4
|
1.0
|
CB
|
A:HIS167
|
4.8
|
8.1
|
1.0
|
SG
|
A:CYS424
|
4.9
|
19.4
|
1.0
|
|
Reference:
H.Lauble,
M.C.Kennedy,
H.Beinert,
C.D.Stout.
Crystal Structures of Aconitase with Trans-Aconitate and Nitrocitrate Bound. J.Mol.Biol. V. 237 437 1994.
ISSN: ISSN 0022-2836
PubMed: 8151704
DOI: 10.1006/JMBI.1994.1246
Page generated: Sat Aug 3 11:39:07 2024
|