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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

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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

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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

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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

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