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Iron in PDB 6lbp: Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana

Enzymatic activity of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana

All present enzymatic activity of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana:
2.4.2.14;

Protein crystallography data

The structure of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana, PDB code: 6lbp was solved by Z.Yi, X.Cao, F.Han, Y.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.66 / 3.07
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 179.736, 179.736, 109.199, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 22.3

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana (pdb code 6lbp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana, PDB code: 6lbp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6lbp

Go back to Iron Binding Sites List in 6lbp
Iron binding site 1 out of 8 in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:0.2
occ:1.00
 FE1 A:SF4600 0.0 0.2 1.0
SG A:CYS523 2.3 72.5 1.0
S3 A:SF4600 2.3 63.4 1.0
S2 A:SF4600 2.3 78.8 1.0
S4 A:SF4600 2.3 76.8 1.0
FE4 A:SF4600 2.7 69.0 1.0
FE3 A:SF4600 2.7 90.2 1.0
FE2 A:SF4600 2.7 68.0 1.0
CB A:CYS523 2.9 64.1 1.0
N A:CYS523 3.4 65.7 1.0
CA A:CYS523 3.7 64.3 1.0
S1 A:SF4600 3.9 72.2 1.0
CB A:CYS469 4.4 91.9 1.0
C A:ALA522 4.5 58.9 1.0
N A:ALA522 4.5 53.7 1.0
SG A:CYS469 4.6 94.2 1.0
SG A:CYS323 4.6 65.0 1.0
SG A:CYS520 4.7 52.3 1.0
CA A:CYS469 4.7 90.4 1.0
C A:TYR521 4.9 52.3 1.0
CA A:ALA522 4.9 55.6 1.0
C A:CYS523 5.0 64.1 1.0

Iron binding site 2 out of 8 in 6lbp

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Iron binding site 2 out of 8 in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:68.0
occ:1.00
 FE2 A:SF4600 0.0 68.0 1.0
SG A:CYS520 2.2 52.3 1.0
S1 A:SF4600 2.3 72.2 1.0
S3 A:SF4600 2.3 63.4 1.0
S4 A:SF4600 2.3 76.8 1.0
FE4 A:SF4600 2.7 69.0 1.0
FE3 A:SF4600 2.7 90.2 1.0
FE1 A:SF4600 2.7 0.2 1.0
CB A:CYS520 3.6 49.2 1.0
S2 A:SF4600 3.9 78.8 1.0
N A:ALA522 3.9 53.7 1.0
CD2 A:TYR471 4.0 74.2 1.0
CB A:ALA522 4.1 64.2 1.0
C A:CYS520 4.3 52.8 1.0
SG A:CYS323 4.4 65.0 1.0
O A:CYS520 4.4 54.2 1.0
N A:CYS523 4.5 65.7 1.0
CA A:ALA522 4.5 55.6 1.0
CA A:CYS520 4.6 49.7 1.0
CE2 A:TYR471 4.6 70.9 1.0
N A:TYR521 4.6 56.2 1.0
SG A:CYS523 4.7 72.5 1.0
C A:TYR521 4.7 52.3 1.0
SG A:CYS469 4.7 94.2 1.0
CA A:TYR521 4.9 51.4 1.0
C A:ALA522 4.9 58.9 1.0

Iron binding site 3 out of 8 in 6lbp

Go back to Iron Binding Sites List in 6lbp
Iron binding site 3 out of 8 in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:90.2
occ:1.00
 FE3 A:SF4600 0.0 90.2 1.0
SG A:CYS469 2.1 94.2 1.0
S1 A:SF4600 2.3 72.2 1.0
S2 A:SF4600 2.3 78.8 1.0
S4 A:SF4600 2.3 76.8 1.0
FE4 A:SF4600 2.7 69.0 1.0
FE2 A:SF4600 2.7 68.0 1.0
FE1 A:SF4600 2.7 0.2 1.0
CB A:CYS469 2.8 91.9 1.0
CA A:CYS469 3.3 90.4 1.0
S3 A:SF4600 3.9 63.4 1.0
C A:CYS469 4.1 93.8 1.0
N A:TYR470 4.2 90.6 1.0
CD2 A:TYR471 4.3 74.2 1.0
SG A:CYS323 4.3 65.0 1.0
CB A:TYR471 4.4 74.2 1.0
N A:TYR471 4.4 72.0 1.0
N A:CYS469 4.5 90.3 1.0
SG A:CYS520 4.8 52.3 1.0
CG A:TYR471 4.8 69.8 1.0
CA A:TYR471 4.8 72.5 1.0
CG2 A:VAL473 4.8 79.7 1.0
SG A:CYS523 4.9 72.5 1.0

Iron binding site 4 out of 8 in 6lbp

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Iron binding site 4 out of 8 in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:69.0
occ:1.00
 FE4 A:SF4600 0.0 69.0 1.0
SG A:CYS323 2.0 65.0 1.0
S3 A:SF4600 2.3 63.4 1.0
S2 A:SF4600 2.3 78.8 1.0
S1 A:SF4600 2.3 72.2 1.0
FE3 A:SF4600 2.7 90.2 1.0
FE2 A:SF4600 2.7 68.0 1.0
FE1 A:SF4600 2.7 0.2 1.0
CB A:CYS323 3.4 49.7 1.0
S4 A:SF4600 3.9 76.8 1.0
CA A:CYS323 3.9 50.5 1.0
CB A:PHE325 4.0 48.4 1.0
N A:PHE325 4.3 53.5 1.0
SG A:CYS469 4.3 94.2 1.0
N A:ILE324 4.4 47.4 1.0
SG A:CYS520 4.5 52.3 1.0
C A:CYS323 4.5 50.0 1.0
SG A:CYS523 4.5 72.5 1.0
CA A:PHE325 4.8 47.6 1.0
NH2 A:ARG264 4.9 77.4 1.0
O A:CYS520 5.0 54.2 1.0

Iron binding site 5 out of 8 in 6lbp

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Iron binding site 5 out of 8 in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:0.2
occ:1.00
 FE1 B:SF4600 0.0 0.2 1.0
S3 B:SF4600 2.3 64.9 1.0
S2 B:SF4600 2.3 79.5 1.0
S4 B:SF4600 2.3 76.8 1.0
SG B:CYS523 2.3 71.4 1.0
FE4 B:SF4600 2.7 70.4 1.0
FE2 B:SF4600 2.7 68.2 1.0
FE3 B:SF4600 2.7 90.2 1.0
CB B:CYS523 2.8 64.7 1.0
N B:CYS523 3.4 61.2 1.0
CA B:CYS523 3.7 62.0 1.0
S1 B:SF4600 3.9 72.5 1.0
CB B:CYS469 4.3 94.5 1.0
C B:ALA522 4.5 57.4 1.0
SG B:CYS469 4.6 94.6 1.0
CA B:CYS469 4.6 89.3 1.0
N B:ALA522 4.6 51.3 1.0
SG B:CYS323 4.6 67.3 1.0
SG B:CYS520 4.8 56.1 1.0
C B:CYS523 4.9 64.0 1.0
CA B:ALA522 5.0 52.6 1.0

Iron binding site 6 out of 8 in 6lbp

Go back to Iron Binding Sites List in 6lbp
Iron binding site 6 out of 8 in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:68.2
occ:1.00
 FE2 B:SF4600 0.0 68.2 1.0
SG B:CYS520 2.2 56.1 1.0
S3 B:SF4600 2.3 64.9 1.0
S4 B:SF4600 2.3 76.8 1.0
S1 B:SF4600 2.3 72.5 1.0
FE3 B:SF4600 2.7 90.2 1.0
FE4 B:SF4600 2.7 70.4 1.0
FE1 B:SF4600 2.7 0.2 1.0
CB B:CYS520 3.7 48.6 1.0
N B:ALA522 3.8 51.3 1.0
S2 B:SF4600 3.9 79.5 1.0
CB B:ALA522 4.0 61.5 1.0
CD2 B:TYR471 4.1 75.2 1.0
C B:CYS520 4.3 54.5 1.0
N B:CYS523 4.3 61.2 1.0
CA B:ALA522 4.4 52.6 1.0
O B:CYS520 4.4 56.2 1.0
SG B:CYS323 4.4 67.3 1.0
N B:TYR521 4.6 54.0 1.0
CE2 B:TYR471 4.6 69.6 1.0
C B:TYR521 4.6 53.3 1.0
CA B:CYS520 4.6 49.9 1.0
SG B:CYS523 4.6 71.4 1.0
SG B:CYS469 4.8 94.6 1.0
C B:ALA522 4.8 57.4 1.0
CA B:TYR521 4.9 48.7 1.0

Iron binding site 7 out of 8 in 6lbp

Go back to Iron Binding Sites List in 6lbp
Iron binding site 7 out of 8 in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:90.2
occ:1.00
 FE3 B:SF4600 0.0 90.2 1.0
SG B:CYS469 2.2 94.6 1.0
S1 B:SF4600 2.3 72.5 1.0
S4 B:SF4600 2.3 76.8 1.0
S2 B:SF4600 2.3 79.5 1.0
FE2 B:SF4600 2.7 68.2 1.0
FE4 B:SF4600 2.7 70.4 1.0
FE1 B:SF4600 2.7 0.2 1.0
CB B:CYS469 2.8 94.5 1.0
CA B:CYS469 3.3 89.3 1.0
S3 B:SF4600 3.8 64.9 1.0
N B:TYR470 4.1 90.0 1.0
C B:CYS469 4.1 92.0 1.0
CD2 B:TYR471 4.2 75.2 1.0
CB B:TYR471 4.3 72.3 1.0
N B:TYR471 4.3 73.2 1.0
SG B:CYS323 4.4 67.3 1.0
N B:CYS469 4.5 90.2 1.0
SG B:CYS520 4.6 56.1 1.0
CG B:TYR471 4.7 70.2 1.0
CA B:TYR471 4.8 71.4 1.0
CG2 B:VAL473 4.9 77.7 1.0

Iron binding site 8 out of 8 in 6lbp

Go back to Iron Binding Sites List in 6lbp
Iron binding site 8 out of 8 in the Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:70.4
occ:1.00
 FE4 B:SF4600 0.0 70.4 1.0
SG B:CYS323 2.0 67.3 1.0
S2 B:SF4600 2.3 79.5 1.0
S3 B:SF4600 2.3 64.9 1.0
S1 B:SF4600 2.3 72.5 1.0
FE3 B:SF4600 2.7 90.2 1.0
FE1 B:SF4600 2.7 0.2 1.0
FE2 B:SF4600 2.7 68.2 1.0
CB B:CYS323 3.5 52.6 1.0
S4 B:SF4600 3.9 76.8 1.0
CB B:PHE325 4.0 50.9 1.0
CA B:CYS323 4.0 50.9 1.0
SG B:CYS469 4.3 94.6 1.0
N B:PHE325 4.3 53.2 1.0
SG B:CYS520 4.4 56.1 1.0
SG B:CYS523 4.5 71.4 1.0
N B:ILE324 4.5 47.9 1.0
C B:CYS323 4.6 50.2 1.0
CA B:PHE325 4.8 48.6 1.0
NH2 B:ARG264 4.9 76.2 1.0
CB B:CYS469 5.0 94.5 1.0

Reference:

X.Cao, B.Du, F.Han, Y.Zhou, J.Ren, W.Wang, Z.Chen, Y.Zhang. Crystal Structure of the Chloroplastic Glutamine Phosphoribosylpyrophosphate Amidotransferase GPRAT2 Fromarabidopsis Thaliana. Front Plant Sci V. 11 157 2020.
ISSN: ESSN 1664-462X
PubMed: 32174940
DOI: 10.3389/FPLS.2020.00157
Page generated: Sun Dec 13 16:39:25 2020

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