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Iron in PDB 1ao0: Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp

Enzymatic activity of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp

All present enzymatic activity of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp:
2.4.2.14;

Protein crystallography data

The structure of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp, PDB code: 1ao0 was solved by D.R.Tomchick, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 160.300, 70.400, 182.700, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.4

Other elements in 1ao0:

The structure of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp (pdb code 1ao0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp, PDB code: 1ao0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 1ao0

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Iron binding site 1 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe466

b:15.7
occ:1.00
 FE1 A:SF4466 0.0 15.7 1.0
S3 A:SF4466 2.3 15.6 1.0
S4 A:SF4466 2.3 13.4 1.0
SG A:CYS437 2.3 15.3 1.0
S2 A:SF4466 2.3 14.6 1.0
FE4 A:SF4466 2.6 15.7 1.0
FE2 A:SF4466 2.7 12.7 1.0
FE3 A:SF4466 2.7 15.2 1.0
CB A:CYS437 3.4 13.1 1.0
S1 A:SF4466 3.9 15.1 1.0
C A:CYS437 4.2 12.9 1.0
O A:CYS437 4.2 19.3 1.0
N A:ALA439 4.3 11.8 1.0
CA A:CYS236 4.3 20.9 1.0
CD2 A:TYR384 4.4 40.0 1.0
CB A:ALA439 4.4 10.0 1.0
CA A:CYS437 4.4 16.5 1.0
SG A:CYS236 4.6 13.2 1.0
N A:LEU438 4.6 10.0 1.0
SG A:CYS440 4.6 17.5 1.0
CB A:CYS236 4.7 10.1 1.0
N A:SER237 4.7 24.4 1.0
CE2 A:TYR384 4.7 37.0 1.0
SG A:CYS382 4.7 10.2 1.0
CD2 A:LEU177 4.8 19.1 1.0
CA A:ALA439 4.9 19.1 1.0
N A:CYS440 4.9 25.8 1.0

Iron binding site 2 out of 16 in 1ao0

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Iron binding site 2 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe466

b:12.7
occ:1.00
 FE2 A:SF4466 0.0 12.7 1.0
SG A:CYS236 2.2 13.2 1.0
S1 A:SF4466 2.3 15.1 1.0
S4 A:SF4466 2.3 13.4 1.0
S3 A:SF4466 2.3 15.6 1.0
FE4 A:SF4466 2.6 15.7 1.0
FE1 A:SF4466 2.7 15.7 1.0
FE3 A:SF4466 2.7 15.2 1.0
CB A:CYS236 3.1 10.1 1.0
CA A:CYS236 3.5 20.9 1.0
N A:SER237 3.8 24.4 1.0
S2 A:SF4466 3.9 14.6 1.0
C A:CYS236 4.0 25.5 1.0
N A:MET238 4.0 16.9 1.0
CB A:MET238 4.2 11.5 1.0
CG A:MET238 4.2 15.7 1.0
SG A:CYS382 4.5 10.2 1.0
NH2 A:ARG178 4.6 51.3 1.0
CA A:MET238 4.7 10.1 1.0
CG2 A:THR388 4.7 27.2 1.0
SG A:CYS437 4.8 15.3 1.0
N A:CYS236 4.8 21.3 1.0
CB A:THR388 4.8 34.6 1.0
CA A:SER237 4.9 19.8 1.0
SG A:CYS440 4.9 17.5 1.0
O A:CYS236 4.9 30.8 1.0
C A:SER237 5.0 20.6 1.0

Iron binding site 3 out of 16 in 1ao0

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Iron binding site 3 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe466

b:15.2
occ:1.00
 FE3 A:SF4466 0.0 15.2 1.0
SG A:CYS440 2.3 17.5 1.0
S4 A:SF4466 2.3 13.4 1.0
S1 A:SF4466 2.3 15.1 1.0
S2 A:SF4466 2.3 14.6 1.0
FE4 A:SF4466 2.7 15.7 1.0
FE1 A:SF4466 2.7 15.7 1.0
FE2 A:SF4466 2.7 12.7 1.0
CB A:CYS440 3.4 16.9 1.0
N A:CYS440 3.9 25.8 1.0
S3 A:SF4466 4.0 15.6 1.0
CG A:MET238 4.3 15.7 1.0
CA A:CYS440 4.3 24.5 1.0
SG A:CYS382 4.6 10.2 1.0
SG A:CYS437 4.7 15.3 1.0
N A:ALA439 4.7 11.8 1.0
SG A:CYS236 4.8 13.2 1.0
CB A:CYS382 4.8 13.0 1.0

Iron binding site 4 out of 16 in 1ao0

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Iron binding site 4 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe466

b:15.7
occ:1.00
 FE4 A:SF4466 0.0 15.7 1.0
SG A:CYS382 2.3 10.2 1.0
S2 A:SF4466 2.3 14.6 1.0
S3 A:SF4466 2.3 15.6 1.0
S1 A:SF4466 2.3 15.1 1.0
FE2 A:SF4466 2.6 12.7 1.0
FE1 A:SF4466 2.6 15.7 1.0
FE3 A:SF4466 2.7 15.2 1.0
CB A:CYS382 3.3 13.0 1.0
S4 A:SF4466 3.8 13.4 1.0
CA A:CYS382 4.1 20.0 1.0
CD2 A:TYR384 4.1 40.0 1.0
OG1 A:THR388 4.4 34.3 1.0
CB A:THR388 4.5 34.6 1.0
SG A:CYS236 4.5 13.2 1.0
SG A:CYS440 4.7 17.5 1.0
CB A:TYR384 4.7 35.8 1.0
SG A:CYS437 4.8 15.3 1.0
N A:PHE383 4.9 21.2 1.0
CG A:TYR384 4.9 41.2 1.0
CE2 A:TYR384 5.0 37.0 1.0
C A:CYS382 5.0 20.2 1.0

Iron binding site 5 out of 16 in 1ao0

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Iron binding site 5 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe466

b:25.2
occ:1.00
 FE1 B:SF4466 0.0 25.2 1.0
SG B:CYS437 2.3 22.8 1.0
S3 B:SF4466 2.3 18.8 1.0
S4 B:SF4466 2.3 12.7 1.0
S2 B:SF4466 2.4 21.4 1.0
FE2 B:SF4466 2.7 21.0 1.0
FE3 B:SF4466 2.7 24.9 1.0
FE4 B:SF4466 2.7 29.3 1.0
CB B:CYS437 3.3 18.3 1.0
S1 B:SF4466 4.0 20.8 1.0
C B:CYS437 4.2 21.7 1.0
N B:ALA439 4.2 19.5 1.0
O B:CYS437 4.2 26.4 1.0
CB B:ALA439 4.3 14.6 1.0
CD2 B:TYR384 4.4 38.8 1.0
CA B:CYS437 4.4 18.1 1.0
CA B:CYS236 4.4 21.6 1.0
N B:LEU438 4.6 18.8 1.0
SG B:CYS236 4.6 15.4 1.0
SG B:CYS440 4.7 23.1 1.0
CE2 B:TYR384 4.7 42.4 1.0
CB B:CYS236 4.7 22.7 1.0
N B:SER237 4.7 26.2 1.0
CD2 B:LEU177 4.8 30.1 1.0
CA B:ALA439 4.8 19.6 1.0
SG B:CYS382 4.8 22.2 1.0
N B:CYS440 4.9 31.7 1.0

Iron binding site 6 out of 16 in 1ao0

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Iron binding site 6 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe466

b:21.0
occ:1.00
 FE2 B:SF4466 0.0 21.0 1.0
SG B:CYS236 2.2 15.4 1.0
S3 B:SF4466 2.3 18.8 1.0
S1 B:SF4466 2.3 20.8 1.0
S4 B:SF4466 2.3 12.7 1.0
FE4 B:SF4466 2.6 29.3 1.0
FE1 B:SF4466 2.7 25.2 1.0
FE3 B:SF4466 2.8 24.9 1.0
CB B:CYS236 3.1 22.7 1.0
CA B:CYS236 3.5 21.6 1.0
N B:SER237 3.7 26.2 1.0
S2 B:SF4466 3.9 21.4 1.0
C B:CYS236 3.9 24.6 1.0
N B:MET238 4.0 14.6 1.0
CB B:MET238 4.2 14.5 1.0
CG B:MET238 4.3 12.8 1.0
SG B:CYS382 4.6 22.2 1.0
NH2 B:ARG178 4.7 53.2 1.0
CA B:MET238 4.8 13.8 1.0
CG2 B:THR388 4.8 31.0 1.0
N B:CYS236 4.8 23.9 1.0
CA B:SER237 4.8 22.1 1.0
SG B:CYS437 4.9 22.8 1.0
O B:CYS236 4.9 27.7 1.0
SG B:CYS440 4.9 23.1 1.0
CB B:THR388 4.9 36.8 1.0
C B:SER237 5.0 23.9 1.0

Iron binding site 7 out of 16 in 1ao0

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Iron binding site 7 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe466

b:24.9
occ:1.00
 FE3 B:SF4466 0.0 24.9 1.0
SG B:CYS440 2.3 23.1 1.0
S1 B:SF4466 2.3 20.8 1.0
S2 B:SF4466 2.3 21.4 1.0
S4 B:SF4466 2.4 12.7 1.0
FE4 B:SF4466 2.7 29.3 1.0
FE1 B:SF4466 2.7 25.2 1.0
FE2 B:SF4466 2.8 21.0 1.0
CB B:CYS440 3.3 16.6 1.0
N B:CYS440 3.9 31.7 1.0
S3 B:SF4466 4.0 18.8 1.0
CA B:CYS440 4.2 29.8 1.0
CG B:MET238 4.3 12.8 1.0
SG B:CYS382 4.7 22.2 1.0
N B:ALA439 4.7 19.5 1.0
SG B:CYS437 4.7 22.8 1.0
CB B:CYS382 4.8 24.9 1.0
SG B:CYS236 4.8 15.4 1.0

Iron binding site 8 out of 16 in 1ao0

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Iron binding site 8 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe466

b:29.3
occ:1.00
 FE4 B:SF4466 0.0 29.3 1.0
SG B:CYS382 2.3 22.2 1.0
S2 B:SF4466 2.3 21.4 1.0
S1 B:SF4466 2.3 20.8 1.0
S3 B:SF4466 2.4 18.8 1.0
FE2 B:SF4466 2.6 21.0 1.0
FE3 B:SF4466 2.7 24.9 1.0
FE1 B:SF4466 2.7 25.2 1.0
CB B:CYS382 3.2 24.9 1.0
S4 B:SF4466 3.9 12.7 1.0
CA B:CYS382 4.0 24.3 1.0
CD2 B:TYR384 4.1 38.8 1.0
CB B:THR388 4.4 36.8 1.0
OG1 B:THR388 4.4 31.8 1.0
SG B:CYS236 4.5 15.4 1.0
CB B:TYR384 4.7 27.4 1.0
SG B:CYS440 4.7 23.1 1.0
N B:PHE383 4.8 29.0 1.0
C B:CYS382 4.9 28.8 1.0
SG B:CYS437 4.9 22.8 1.0
CG B:TYR384 4.9 37.5 1.0
N B:TYR384 4.9 28.5 1.0
CE2 B:TYR384 5.0 42.4 1.0

Iron binding site 9 out of 16 in 1ao0

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Iron binding site 9 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe466

b:24.8
occ:1.00
 FE1 C:SF4466 0.0 24.8 1.0
S3 C:SF4466 2.3 21.9 1.0
S4 C:SF4466 2.3 22.9 1.0
S2 C:SF4466 2.3 23.9 1.0
SG C:CYS437 2.4 23.6 1.0
FE4 C:SF4466 2.6 21.6 1.0
FE2 C:SF4466 2.6 28.9 1.0
FE3 C:SF4466 2.7 22.2 1.0
CB C:CYS437 3.4 13.5 1.0
S1 C:SF4466 3.9 20.2 1.0
CD2 C:TYR384 4.2 39.7 1.0
C C:CYS437 4.3 19.3 1.0
N C:ALA439 4.4 11.2 1.0
CB C:ALA439 4.4 14.7 1.0
O C:CYS437 4.4 17.9 1.0
CA C:CYS236 4.4 18.8 1.0
CA C:CYS437 4.5 20.0 1.0
SG C:CYS236 4.6 14.4 1.0
CE2 C:TYR384 4.6 35.9 1.0
SG C:CYS382 4.7 25.2 1.0
SG C:CYS440 4.7 21.5 1.0
CB C:CYS236 4.7 20.9 1.0
N C:LEU438 4.8 15.3 1.0
CD2 C:LEU177 4.8 29.7 1.0
N C:SER237 4.8 20.1 1.0
N C:CYS440 4.9 26.4 1.0
CA C:ALA439 4.9 17.4 1.0

Iron binding site 10 out of 16 in 1ao0

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Iron binding site 10 out of 16 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe466

b:28.9
occ:1.00
 FE2 C:SF4466 0.0 28.9 1.0
SG C:CYS236 2.2 14.4 1.0
S1 C:SF4466 2.3 20.2 1.0
S3 C:SF4466 2.3 21.9 1.0
S4 C:SF4466 2.3 22.9 1.0
FE4 C:SF4466 2.5 21.6 1.0
FE1 C:SF4466 2.6 24.8 1.0
FE3 C:SF4466 2.8 22.2 1.0
CB C:CYS236 3.1 20.9 1.0
CA C:CYS236 3.5 18.8 1.0
N C:SER237 3.9 20.1 1.0
S2 C:SF4466 3.9 23.9 1.0
C C:CYS236 4.0 24.3 1.0
N C:MET238 4.2 11.3 1.0
CB C:MET238 4.3 10.2 1.0
CG C:MET238 4.3 10.1 1.0
SG C:CYS382 4.5 25.2 1.0
NH2 C:ARG178 4.6 57.7 1.0
CG2 C:THR388 4.7 31.5 1.0
N C:CYS236 4.8 21.6 1.0
CB C:THR388 4.8 41.1 1.0
SG C:CYS437 4.8 23.6 1.0
CA C:MET238 4.8 10.0 1.0
O C:CYS236 4.9 21.7 1.0
CA C:SER237 4.9 14.4 1.0
SG C:CYS440 4.9 21.5 1.0

Reference:

S.Chen, D.R.Tomchick, D.Wolle, P.Hu, J.L.Smith, R.L.Switzer, H.Zalkin. Mechanism of the Synergistic End-Product Regulation of Bacillus Subtilis Glutamine Phosphoribosylpyrophosphate Amidotransferase By Nucleotides. Biochemistry V. 36 10718 1997.
ISSN: ISSN 0006-2960
PubMed: 9271502
DOI: 10.1021/BI9711893
Page generated: Sat Aug 3 02:12:47 2024

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