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Iron in PDB 1ofe: Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 Angstrom Resolution

Enzymatic activity of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 Angstrom Resolution

All present enzymatic activity of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 Angstrom Resolution:
1.4.7.1;

Protein crystallography data

The structure of Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 Angstrom Resolution, PDB code: 1ofe 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 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.669, 134.377, 198.774, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.7

Iron Binding Sites:

The binding sites of Iron atom in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 Angstrom Resolution (pdb code 1ofe). 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 and L-Don at 2.45 Angstrom Resolution, PDB code: 1ofe:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1ofe

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Iron binding site 1 out of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 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 and L-Don at 2.45 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2509

b:23.7
occ:1.00
 FE1 A:F3S2509 0.0 23.7 1.0
S1 A:F3S2509 2.2 24.8 1.0
S3 A:F3S2509 2.2 20.5 1.0
S2 A:F3S2509 2.2 24.0 1.0
SG A:CYS1137 2.3 10.5 1.0
FE4 A:F3S2509 2.6 19.6 1.0
FE3 A:F3S2509 2.6 22.4 1.0
O A:ILE1138 2.7 18.3 1.0
CB A:CYS1137 3.5 14.7 1.0
S4 A:F3S2509 3.7 24.4 1.0
C A:ILE1138 3.8 17.8 1.0
CA A:CYS1137 4.0 14.5 1.0
N A:ILE1138 4.1 16.9 1.0
C A:CYS1137 4.4 15.7 1.0
SG A:CYS1143 4.5 16.9 1.0
CE A:MET1132 4.5 15.8 1.0
SG A:CYS1148 4.6 12.4 1.0
CA A:MET1139 4.6 17.3 1.0
N A:ALA1140 4.6 15.4 1.0
CA A:ILE1138 4.6 17.2 1.0
N A:MET1139 4.7 17.4 1.0
N A:ARG1141 4.9 12.9 1.0

Iron binding site 2 out of 6 in 1ofe

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Iron binding site 2 out of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 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 and L-Don at 2.45 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2509

b:22.4
occ:1.00
 FE3 A:F3S2509 0.0 22.4 1.0
S1 A:F3S2509 2.2 24.8 1.0
SG A:CYS1143 2.2 16.9 1.0
S4 A:F3S2509 2.2 24.4 1.0
S3 A:F3S2509 2.2 20.5 1.0
FE1 A:F3S2509 2.6 23.7 1.0
FE4 A:F3S2509 2.6 19.6 1.0
CB A:CYS1143 3.4 13.1 1.0
S2 A:F3S2509 3.8 24.0 1.0
CA A:CYS1143 3.8 13.6 1.0
N A:CYS1143 3.9 13.2 1.0
CB A:ALA1153 4.1 11.9 1.0
SG A:CYS1148 4.5 12.4 1.0
N A:ARG1141 4.5 12.9 1.0
N A:VAL1142 4.5 14.1 1.0
CE A:MET1132 4.6 15.8 1.0
SG A:CYS1137 4.7 10.5 1.0
CA A:ARG1141 4.7 14.1 1.0
C A:VAL1142 4.7 13.6 1.0
O A:ILE1138 5.0 18.3 1.0

Iron binding site 3 out of 6 in 1ofe

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Iron binding site 3 out of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 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 and L-Don at 2.45 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2509

b:19.6
occ:1.00
 FE4 A:F3S2509 0.0 19.6 1.0
SG A:CYS1148 2.2 12.4 1.0
S3 A:F3S2509 2.2 20.5 1.0
S2 A:F3S2509 2.2 24.0 1.0
S4 A:F3S2509 2.2 24.4 1.0
FE1 A:F3S2509 2.6 23.7 1.0
FE3 A:F3S2509 2.6 22.4 1.0
CB A:CYS1148 3.4 11.6 1.0
S1 A:F3S2509 3.6 24.8 1.0
CA A:CYS1148 4.0 11.9 1.0
CD A:PRO1149 4.3 11.2 1.0
N A:ALA1153 4.5 13.7 1.0
CB A:ALA1153 4.6 11.9 1.0
SG A:CYS1137 4.7 10.5 1.0
SG A:CYS1143 4.7 16.9 1.0
CB A:VAL1152 4.7 14.1 1.0
C A:CYS1148 4.7 11.7 1.0
O A:ILE1138 4.8 18.3 1.0
CB A:ALA1140 4.8 11.7 1.0
N A:PRO1149 4.8 11.1 1.0

Iron binding site 4 out of 6 in 1ofe

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Iron binding site 4 out of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 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 and L-Don at 2.45 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe2509

b:29.4
occ:1.00
 FE1 B:F3S2509 0.0 29.4 1.0
S2 B:F3S2509 2.1 30.2 1.0
SG B:CYS1148 2.1 15.9 1.0
S3 B:F3S2509 2.2 31.4 1.0
S1 B:F3S2509 2.3 29.2 1.0
FE4 B:F3S2509 2.4 30.3 1.0
FE3 B:F3S2509 2.7 27.4 1.0
CB B:CYS1148 3.5 14.5 1.0
S4 B:F3S2509 3.7 28.0 1.0
CA B:CYS1148 4.0 14.2 1.0
CD B:PRO1149 4.1 13.4 1.0
O B:ILE1138 4.5 18.1 1.0
CB B:ALA1153 4.5 16.7 1.0
SG B:CYS1137 4.5 14.3 1.0
N B:ALA1153 4.5 16.4 1.0
CB B:VAL1152 4.6 15.2 1.0
CG1 B:VAL1150 4.7 13.2 1.0
C B:CYS1148 4.7 13.7 1.0
N B:PRO1149 4.8 13.4 1.0
CA B:CYS1137 4.9 14.5 1.0
CB B:CYS1137 5.0 14.4 1.0
SG B:CYS1143 5.0 14.7 1.0

Iron binding site 5 out of 6 in 1ofe

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Iron binding site 5 out of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 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 and L-Don at 2.45 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe2509

b:27.4
occ:1.00
 FE3 B:F3S2509 0.0 27.4 1.0
S4 B:F3S2509 2.1 28.0 1.0
S1 B:F3S2509 2.2 29.2 1.0
S3 B:F3S2509 2.2 31.4 1.0
SG B:CYS1143 2.3 14.7 1.0
FE4 B:F3S2509 2.4 30.3 1.0
FE1 B:F3S2509 2.7 29.4 1.0
CB B:CYS1143 3.5 14.8 1.0
S2 B:F3S2509 3.8 30.2 1.0
CA B:CYS1143 3.9 14.9 1.0
N B:CYS1143 3.9 15.1 1.0
CB B:ALA1153 4.0 16.7 1.0
SG B:CYS1137 4.4 14.3 1.0
SG B:CYS1148 4.5 15.9 1.0
N B:VAL1142 4.6 15.0 1.0
N B:ARG1141 4.6 17.0 1.0
CE B:MET1132 4.6 16.4 1.0
O B:ILE1138 4.7 18.1 1.0
CA B:ARG1141 4.8 16.5 1.0
C B:VAL1142 4.9 14.8 1.0

Iron binding site 6 out of 6 in 1ofe

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Iron binding site 6 out of 6 in the Glutamate Synthase From Synechocystis Sp in Complex with 2-Oxoglutarate and L-Don at 2.45 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 and L-Don at 2.45 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe2509

b:30.3
occ:1.00
 FE4 B:F3S2509 0.0 30.3 1.0
S1 B:F3S2509 2.1 29.2 1.0
S4 B:F3S2509 2.2 28.0 1.0
S2 B:F3S2509 2.2 30.2 1.0
SG B:CYS1137 2.3 14.3 1.0
FE3 B:F3S2509 2.4 27.4 1.0
FE1 B:F3S2509 2.4 29.4 1.0
O B:ILE1138 2.7 18.1 1.0
S3 B:F3S2509 3.4 31.4 1.0
CB B:CYS1137 3.5 14.4 1.0
C B:ILE1138 3.8 17.8 1.0
CA B:CYS1137 4.0 14.5 1.0
N B:ILE1138 4.1 15.8 1.0
C B:CYS1137 4.4 15.1 1.0
SG B:CYS1148 4.4 15.9 1.0
CA B:MET1139 4.5 17.8 1.0
SG B:CYS1143 4.6 14.7 1.0
N B:MET1139 4.6 17.9 1.0
CE B:MET1132 4.6 16.4 1.0
N B:ALA1140 4.7 18.0 1.0
CA B:ILE1138 4.7 16.8 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 12:20:34 2024

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