Iron in PDB 1ofd: Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution
Enzymatic activity of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution
All present enzymatic activity of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution:
1.4.7.1;
Protein crystallography data
The structure of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution, PDB code: 1ofd
was solved by
R.H.H.Van Den Heuvel,
A.Mattevi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.017,
149.665,
195.926,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.2 /
23.1
|
Iron Binding Sites:
The binding sites of Iron atom in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution
(pdb code 1ofd). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution, PDB code: 1ofd:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1ofd
Go back to
Iron Binding Sites List in 1ofd
Iron binding site 1 out
of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3509
b:11.2
occ:1.00
|
FE1
|
A:F3S3509
|
0.0
|
11.2
|
1.0
|
S2
|
A:F3S3509
|
2.2
|
11.5
|
1.0
|
S3
|
A:F3S3509
|
2.2
|
12.6
|
1.0
|
S1
|
A:F3S3509
|
2.3
|
11.2
|
1.0
|
SG
|
A:CYS1137
|
2.4
|
2.6
|
1.0
|
FE3
|
A:F3S3509
|
2.6
|
10.5
|
1.0
|
FE4
|
A:F3S3509
|
2.7
|
11.1
|
1.0
|
CB
|
A:CYS1137
|
3.4
|
2.5
|
1.0
|
N
|
A:MET1139
|
3.7
|
3.5
|
1.0
|
S4
|
A:F3S3509
|
3.9
|
11.0
|
1.0
|
CA
|
A:CYS1137
|
4.0
|
3.4
|
1.0
|
N
|
A:ILE1138
|
4.0
|
3.3
|
1.0
|
CA
|
A:MET1139
|
4.1
|
3.9
|
1.0
|
N
|
A:ALA1140
|
4.2
|
3.3
|
1.0
|
C
|
A:CYS1137
|
4.3
|
3.5
|
1.0
|
C
|
A:MET1139
|
4.6
|
4.2
|
1.0
|
CE
|
A:MET1132
|
4.7
|
3.0
|
1.0
|
C
|
A:ILE1138
|
4.7
|
3.2
|
1.0
|
SG
|
A:CYS1143
|
4.7
|
5.5
|
1.0
|
SG
|
A:CYS1148
|
4.8
|
2.5
|
1.0
|
N
|
A:ARG1141
|
4.9
|
2.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 1ofd
Go back to
Iron Binding Sites List in 1ofd
Iron binding site 2 out
of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3509
b:10.5
occ:1.00
|
FE3
|
A:F3S3509
|
0.0
|
10.5
|
1.0
|
S1
|
A:F3S3509
|
2.2
|
11.2
|
1.0
|
S4
|
A:F3S3509
|
2.2
|
11.0
|
1.0
|
S3
|
A:F3S3509
|
2.2
|
12.6
|
1.0
|
SG
|
A:CYS1148
|
2.4
|
2.5
|
1.0
|
FE1
|
A:F3S3509
|
2.6
|
11.2
|
1.0
|
FE4
|
A:F3S3509
|
2.7
|
11.1
|
1.0
|
CB
|
A:CYS1148
|
3.4
|
2.7
|
1.0
|
S2
|
A:F3S3509
|
3.8
|
11.5
|
1.0
|
CA
|
A:CYS1148
|
4.0
|
2.6
|
1.0
|
CD
|
A:PRO1149
|
4.2
|
3.0
|
1.0
|
CG1
|
A:VAL1150
|
4.4
|
4.1
|
1.0
|
CB
|
A:ALA1153
|
4.4
|
2.2
|
1.0
|
N
|
A:ALA1153
|
4.5
|
3.2
|
1.0
|
CB
|
A:ALA1140
|
4.7
|
2.6
|
1.0
|
CB
|
A:VAL1152
|
4.7
|
2.9
|
1.0
|
C
|
A:CYS1148
|
4.7
|
2.6
|
1.0
|
N
|
A:PRO1149
|
4.7
|
3.0
|
1.0
|
SG
|
A:CYS1137
|
4.8
|
2.6
|
1.0
|
SG
|
A:CYS1143
|
4.9
|
5.5
|
1.0
|
N
|
A:ALA1140
|
5.0
|
3.3
|
1.0
|
|
Iron binding site 3 out
of 6 in 1ofd
Go back to
Iron Binding Sites List in 1ofd
Iron binding site 3 out
of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3509
b:11.1
occ:1.00
|
FE4
|
A:F3S3509
|
0.0
|
11.1
|
1.0
|
S2
|
A:F3S3509
|
2.2
|
11.5
|
1.0
|
S3
|
A:F3S3509
|
2.2
|
12.6
|
1.0
|
S4
|
A:F3S3509
|
2.3
|
11.0
|
1.0
|
SG
|
A:CYS1143
|
2.3
|
5.5
|
1.0
|
FE1
|
A:F3S3509
|
2.7
|
11.2
|
1.0
|
FE3
|
A:F3S3509
|
2.7
|
10.5
|
1.0
|
CB
|
A:CYS1143
|
3.5
|
3.8
|
1.0
|
N
|
A:CYS1143
|
3.8
|
2.8
|
1.0
|
CA
|
A:CYS1143
|
3.9
|
4.1
|
1.0
|
S1
|
A:F3S3509
|
4.0
|
11.2
|
1.0
|
CB
|
A:ALA1153
|
4.0
|
2.2
|
1.0
|
N
|
A:ARG1141
|
4.3
|
2.6
|
1.0
|
N
|
A:VAL1142
|
4.3
|
2.6
|
1.0
|
CA
|
A:ARG1141
|
4.6
|
3.0
|
1.0
|
C
|
A:VAL1142
|
4.6
|
3.0
|
1.0
|
CE
|
A:MET1132
|
4.8
|
3.0
|
1.0
|
SG
|
A:CYS1137
|
4.8
|
2.6
|
1.0
|
SG
|
A:CYS1148
|
4.8
|
2.5
|
1.0
|
C
|
A:ARG1141
|
4.9
|
3.0
|
1.0
|
|
Iron binding site 4 out
of 6 in 1ofd
Go back to
Iron Binding Sites List in 1ofd
Iron binding site 4 out
of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe3509
b:12.0
occ:1.00
|
FE1
|
B:F3S3509
|
0.0
|
12.0
|
1.0
|
S2
|
B:F3S3509
|
2.2
|
11.0
|
1.0
|
S3
|
B:F3S3509
|
2.2
|
11.3
|
1.0
|
S1
|
B:F3S3509
|
2.2
|
13.0
|
1.0
|
SG
|
B:CYS1137
|
2.3
|
2.2
|
1.0
|
FE3
|
B:F3S3509
|
2.6
|
11.6
|
1.0
|
FE4
|
B:F3S3509
|
2.7
|
11.3
|
1.0
|
CB
|
B:CYS1137
|
3.4
|
2.7
|
1.0
|
N
|
B:MET1139
|
3.7
|
2.3
|
1.0
|
S4
|
B:F3S3509
|
3.9
|
11.8
|
1.0
|
CA
|
B:CYS1137
|
3.9
|
2.5
|
1.0
|
N
|
B:ILE1138
|
4.1
|
2.0
|
1.0
|
CA
|
B:MET1139
|
4.1
|
3.0
|
1.0
|
N
|
B:ALA1140
|
4.2
|
2.7
|
1.0
|
C
|
B:CYS1137
|
4.3
|
2.5
|
1.0
|
CE
|
B:MET1132
|
4.6
|
3.8
|
1.0
|
C
|
B:MET1139
|
4.7
|
2.8
|
1.0
|
C
|
B:ILE1138
|
4.7
|
2.5
|
1.0
|
SG
|
B:CYS1143
|
4.8
|
3.2
|
1.0
|
SG
|
B:CYS1148
|
4.8
|
1.8
|
1.0
|
N
|
B:ARG1141
|
4.9
|
2.2
|
1.0
|
|
Iron binding site 5 out
of 6 in 1ofd
Go back to
Iron Binding Sites List in 1ofd
Iron binding site 5 out
of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe3509
b:11.6
occ:1.00
|
FE3
|
B:F3S3509
|
0.0
|
11.6
|
1.0
|
S4
|
B:F3S3509
|
2.2
|
11.8
|
1.0
|
S1
|
B:F3S3509
|
2.2
|
13.0
|
1.0
|
S3
|
B:F3S3509
|
2.2
|
11.3
|
1.0
|
SG
|
B:CYS1148
|
2.4
|
1.8
|
1.0
|
FE1
|
B:F3S3509
|
2.6
|
12.0
|
1.0
|
FE4
|
B:F3S3509
|
2.7
|
11.3
|
1.0
|
CB
|
B:CYS1148
|
3.3
|
2.1
|
1.0
|
S2
|
B:F3S3509
|
3.8
|
11.0
|
1.0
|
CA
|
B:CYS1148
|
4.0
|
1.3
|
1.0
|
CD
|
B:PRO1149
|
4.3
|
1.7
|
1.0
|
CB
|
B:ALA1153
|
4.3
|
2.8
|
1.0
|
N
|
B:ALA1153
|
4.5
|
3.3
|
1.0
|
CG1
|
B:VAL1150
|
4.5
|
3.4
|
1.0
|
CB
|
B:VAL1152
|
4.7
|
3.6
|
1.0
|
C
|
B:CYS1148
|
4.7
|
1.6
|
1.0
|
CB
|
B:ALA1140
|
4.8
|
2.8
|
1.0
|
SG
|
B:CYS1137
|
4.8
|
2.2
|
1.0
|
N
|
B:PRO1149
|
4.8
|
1.2
|
1.0
|
SG
|
B:CYS1143
|
4.9
|
3.2
|
1.0
|
CA
|
B:ALA1153
|
5.0
|
3.2
|
1.0
|
|
Iron binding site 6 out
of 6 in 1ofd
Go back to
Iron Binding Sites List in 1ofd
Iron binding site 6 out
of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate at 2.0 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe3509
b:11.3
occ:1.00
|
FE4
|
B:F3S3509
|
0.0
|
11.3
|
1.0
|
S3
|
B:F3S3509
|
2.2
|
11.3
|
1.0
|
S2
|
B:F3S3509
|
2.2
|
11.0
|
1.0
|
S4
|
B:F3S3509
|
2.2
|
11.8
|
1.0
|
SG
|
B:CYS1143
|
2.3
|
3.2
|
1.0
|
FE3
|
B:F3S3509
|
2.7
|
11.6
|
1.0
|
FE1
|
B:F3S3509
|
2.7
|
12.0
|
1.0
|
CB
|
B:CYS1143
|
3.5
|
2.4
|
1.0
|
N
|
B:CYS1143
|
3.8
|
2.0
|
1.0
|
CA
|
B:CYS1143
|
3.8
|
2.9
|
1.0
|
S1
|
B:F3S3509
|
3.9
|
13.0
|
1.0
|
CB
|
B:ALA1153
|
4.0
|
2.8
|
1.0
|
N
|
B:VAL1142
|
4.3
|
2.2
|
1.0
|
N
|
B:ARG1141
|
4.3
|
2.2
|
1.0
|
CA
|
B:ARG1141
|
4.5
|
2.2
|
1.0
|
C
|
B:VAL1142
|
4.6
|
2.3
|
1.0
|
CE
|
B:MET1132
|
4.7
|
3.8
|
1.0
|
SG
|
B:CYS1137
|
4.7
|
2.2
|
1.0
|
SG
|
B:CYS1148
|
4.8
|
1.8
|
1.0
|
C
|
B:ARG1141
|
4.9
|
2.2
|
1.0
|
CB
|
B:CYS1148
|
5.0
|
2.1
|
1.0
|
|
Reference:
R.H.H.Van Den Heuvel,
D.I.Svergun,
M.V.Petoukhov,
A.Coda,
B.Curti,
S.Ravasio,
M.A.Vanoni,
A.Mattevi.
The Active Conformation of Glutamate Synthase and Its Binding to Ferredoxin J.Mol.Biol. V. 330 113 2003.
ISSN: ISSN 0022-2836
PubMed: 12818206
DOI: 10.1016/S0022-2836(03)00522-9
Page generated: Sat Aug 3 12:20:27 2024
|