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Iron in PDB 1djn: Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)

Enzymatic activity of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)

All present enzymatic activity of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1):
1.5.99.7;

Protein crystallography data

The structure of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1), PDB code: 1djn was solved by P.Trickey, J.Basran, L.-Y.Lian, Z.-W.Chen, J.D.Barton, M.J.Sutcliffe, N.S.Scrutton, F.S.Mathews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 148.160, 72.000, 83.810, 90.00, 97.73, 90.00
R / Rfree (%) 13.9 / 18.5

Iron Binding Sites:

The binding sites of Iron atom in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1) (pdb code 1djn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1), PDB code: 1djn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1djn

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Iron binding site 1 out of 8 in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:10.5
occ:1.00
 FE1 A:SF4801 0.0 10.5 1.0
SG A:CYS345 2.3 11.1 1.0
S2 A:SF4801 2.3 13.2 1.0
S3 A:SF4801 2.3 11.5 1.0
S4 A:SF4801 2.3 9.3 1.0
FE4 A:SF4801 2.6 12.3 1.0
FE3 A:SF4801 2.6 13.5 1.0
FE2 A:SF4801 2.7 17.8 1.0
CB A:CYS345 3.4 14.0 1.0
S1 A:SF4801 3.9 9.7 1.0
CA A:CYS345 3.9 11.5 1.0
N A:ILE346 4.1 9.0 1.0
CB A:ARG322 4.1 10.3 1.0
N A:GLY347 4.2 14.9 1.0
C A:CYS345 4.4 11.4 1.0
O A:ARG322 4.4 17.4 1.0
CB A:ALA326 4.5 14.1 1.0
CG A:ARG322 4.6 9.8 1.0
SG A:CYS364 4.6 11.7 1.0
CA A:GLY347 4.7 10.9 1.0
C A:ARG322 4.8 13.1 1.0
CD A:ARG322 4.8 4.2 1.0
N A:CYS348 4.8 11.6 1.0
CA A:ARG322 4.8 10.1 1.0
SG A:CYS351 4.9 13.4 1.0
SG A:CYS348 4.9 11.9 1.0

Iron binding site 2 out of 8 in 1djn

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Iron binding site 2 out of 8 in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:17.8
occ:1.00
 FE2 A:SF4801 0.0 17.8 1.0
S1 A:SF4801 2.3 9.7 1.0
S4 A:SF4801 2.3 9.3 1.0
S3 A:SF4801 2.3 11.5 1.0
SG A:CYS348 2.3 11.9 1.0
FE3 A:SF4801 2.7 13.5 1.0
FE4 A:SF4801 2.7 12.3 1.0
FE1 A:SF4801 2.7 10.5 1.0
N A:CYS348 3.7 11.6 1.0
CB A:CYS348 3.7 9.6 1.0
N A:ASN349 3.8 15.3 1.0
S2 A:SF4801 3.9 13.2 1.0
OG1 A:THR365 4.1 14.8 1.0
CA A:CYS348 4.1 12.7 1.0
CB A:THR365 4.3 15.3 1.0
CG1 A:ILE346 4.3 10.3 1.0
C A:CYS348 4.3 13.8 1.0
N A:VAL350 4.3 10.4 1.0
N A:THR365 4.4 13.4 1.0
SG A:CYS345 4.6 11.1 1.0
N A:GLY347 4.6 14.9 1.0
CA A:ASN349 4.7 13.3 1.0
SG A:CYS351 4.7 13.4 1.0
C A:GLY347 4.7 11.8 1.0
SG A:CYS364 4.8 11.7 1.0
N A:ILE346 4.9 9.0 1.0
CA A:GLY347 4.9 10.9 1.0
N A:CYS351 5.0 7.8 1.0
CA A:THR365 5.0 10.2 1.0

Iron binding site 3 out of 8 in 1djn

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Iron binding site 3 out of 8 in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:13.5
occ:1.00
 FE3 A:SF4801 0.0 13.5 1.0
S4 A:SF4801 2.3 9.3 1.0
S2 A:SF4801 2.3 13.2 1.0
S1 A:SF4801 2.3 9.7 1.0
SG A:CYS351 2.4 13.4 1.0
FE1 A:SF4801 2.6 10.5 1.0
FE4 A:SF4801 2.6 12.3 1.0
FE2 A:SF4801 2.7 17.8 1.0
CB A:CYS351 3.4 4.0 1.0
S3 A:SF4801 3.9 11.5 1.0
N A:CYS351 4.0 7.8 1.0
CG A:ARG322 4.2 9.8 1.0
CA A:CYS351 4.4 10.2 1.0
N A:ASN349 4.4 15.3 1.0
CD A:ARG322 4.5 4.2 1.0
CB A:ARG322 4.5 10.3 1.0
SG A:CYS345 4.5 11.1 1.0
CA A:ASN349 4.6 13.3 1.0
N A:VAL350 4.6 10.4 1.0
SG A:CYS348 4.6 11.9 1.0
SG A:CYS364 4.7 11.7 1.0
C A:ASN349 4.9 14.8 1.0

Iron binding site 4 out of 8 in 1djn

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Iron binding site 4 out of 8 in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:12.3
occ:1.00
 FE4 A:SF4801 0.0 12.3 1.0
S2 A:SF4801 2.3 13.2 1.0
S1 A:SF4801 2.3 9.7 1.0
S3 A:SF4801 2.3 11.5 1.0
SG A:CYS364 2.3 11.7 1.0
FE1 A:SF4801 2.6 10.5 1.0
FE3 A:SF4801 2.6 13.5 1.0
FE2 A:SF4801 2.7 17.8 1.0
CB A:CYS364 3.5 10.1 1.0
N A:THR365 3.8 13.4 1.0
CA A:CYS364 3.8 12.2 1.0
S4 A:SF4801 3.9 9.3 1.0
C A:CYS364 4.2 16.0 1.0
N A:GLN366 4.4 10.9 1.0
CB A:ALA326 4.5 14.1 1.0
SG A:CYS351 4.6 13.4 1.0
CG2 A:ILE325 4.7 13.2 1.0
SG A:CYS348 4.7 11.9 1.0
CA A:THR365 4.7 10.2 1.0
SG A:CYS345 4.7 11.1 1.0
CA A:ALA326 4.7 12.0 1.0
N A:ALA326 4.8 11.7 1.0
CB A:THR365 4.8 15.3 1.0
CB A:GLN366 4.9 8.3 1.0
CB A:CYS351 4.9 4.0 1.0

Iron binding site 5 out of 8 in 1djn

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Iron binding site 5 out of 8 in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1801

b:15.5
occ:1.00
 FE1 B:SF41801 0.0 15.5 1.0
S2 B:SF41801 2.3 11.4 1.0
SG B:CYS345 2.3 16.4 1.0
S4 B:SF41801 2.3 13.8 1.0
S3 B:SF41801 2.3 16.3 1.0
FE3 B:SF41801 2.5 12.0 1.0
FE4 B:SF41801 2.6 14.4 1.0
FE2 B:SF41801 2.7 19.6 1.0
CB B:CYS345 3.4 15.7 1.0
S1 B:SF41801 3.8 15.3 1.0
CA B:CYS345 3.9 14.7 1.0
CB B:ARG322 4.0 13.2 1.0
N B:ILE346 4.1 17.7 1.0
N B:GLY347 4.1 19.8 1.0
C B:CYS345 4.4 12.4 1.0
O B:ARG322 4.4 15.9 1.0
CG B:ARG322 4.5 4.0 1.0
CB B:ALA326 4.6 10.0 1.0
SG B:CYS364 4.6 14.9 1.0
CA B:GLY347 4.7 14.6 1.0
C B:ARG322 4.7 15.8 1.0
SG B:CYS351 4.8 16.3 1.0
CA B:ARG322 4.8 16.6 1.0
CD B:ARG322 4.8 10.7 1.0
N B:CYS348 4.8 16.0 1.0
SG B:CYS348 4.9 16.3 1.0

Iron binding site 6 out of 8 in 1djn

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Iron binding site 6 out of 8 in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1801

b:19.6
occ:1.00
 FE2 B:SF41801 0.0 19.6 1.0
S1 B:SF41801 2.3 15.3 1.0
S4 B:SF41801 2.3 13.8 1.0
SG B:CYS348 2.3 16.3 1.0
S3 B:SF41801 2.3 16.3 1.0
FE3 B:SF41801 2.6 12.0 1.0
FE4 B:SF41801 2.7 14.4 1.0
FE1 B:SF41801 2.7 15.5 1.0
N B:CYS348 3.7 16.0 1.0
CB B:CYS348 3.7 10.7 1.0
N B:ASN349 3.9 12.9 1.0
S2 B:SF41801 3.9 11.4 1.0
OG1 B:THR365 4.1 13.3 1.0
CA B:CYS348 4.1 11.8 1.0
CG1 B:ILE346 4.2 13.8 1.0
CB B:THR365 4.3 17.6 1.0
N B:VAL350 4.4 14.2 1.0
C B:CYS348 4.4 15.3 1.0
N B:THR365 4.4 13.3 1.0
N B:GLY347 4.5 19.8 1.0
SG B:CYS345 4.6 16.4 1.0
SG B:CYS351 4.6 16.3 1.0
C B:GLY347 4.7 15.7 1.0
SG B:CYS364 4.8 14.9 1.0
CA B:ASN349 4.8 14.7 1.0
N B:ILE346 4.8 17.7 1.0
CA B:GLY347 4.9 14.6 1.0
N B:CYS351 5.0 14.0 1.0
CD1 B:ILE346 5.0 17.5 1.0
CA B:THR365 5.0 9.1 1.0

Iron binding site 7 out of 8 in 1djn

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Iron binding site 7 out of 8 in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1801

b:12.0
occ:1.00
 FE3 B:SF41801 0.0 12.0 1.0
S4 B:SF41801 2.3 13.8 1.0
S2 B:SF41801 2.3 11.4 1.0
S1 B:SF41801 2.3 15.3 1.0
SG B:CYS351 2.3 16.3 1.0
FE1 B:SF41801 2.5 15.5 1.0
FE2 B:SF41801 2.6 19.6 1.0
FE4 B:SF41801 2.6 14.4 1.0
CB B:CYS351 3.4 13.9 1.0
S3 B:SF41801 3.9 16.3 1.0
N B:CYS351 4.1 14.0 1.0
CG B:ARG322 4.1 4.0 1.0
CA B:CYS351 4.4 13.9 1.0
CB B:ARG322 4.4 13.2 1.0
CD B:ARG322 4.5 10.7 1.0
N B:ASN349 4.5 12.9 1.0
SG B:CYS345 4.5 16.4 1.0
SG B:CYS348 4.5 16.3 1.0
N B:VAL350 4.6 14.2 1.0
CA B:ASN349 4.6 14.7 1.0
SG B:CYS364 4.7 14.9 1.0
C B:ASN349 4.9 15.5 1.0

Iron binding site 8 out of 8 in 1djn

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Iron binding site 8 out of 8 in the Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structural and Biochemical Characterization of Recombinant Wild Type Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W3A1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1801

b:14.4
occ:1.00
 FE4 B:SF41801 0.0 14.4 1.0
SG B:CYS364 2.3 14.9 1.0
S2 B:SF41801 2.3 11.4 1.0
S1 B:SF41801 2.3 15.3 1.0
S3 B:SF41801 2.3 16.3 1.0
FE1 B:SF41801 2.6 15.5 1.0
FE3 B:SF41801 2.6 12.0 1.0
FE2 B:SF41801 2.7 19.6 1.0
CB B:CYS364 3.5 8.4 1.0
N B:THR365 3.8 13.3 1.0
CA B:CYS364 3.8 10.9 1.0
S4 B:SF41801 3.9 13.8 1.0
C B:CYS364 4.2 11.8 1.0
N B:GLN366 4.3 13.1 1.0
CB B:ALA326 4.5 10.0 1.0
CG2 B:ILE325 4.6 9.7 1.0
SG B:CYS351 4.6 16.3 1.0
SG B:CYS348 4.7 16.3 1.0
CA B:ALA326 4.7 15.0 1.0
CA B:THR365 4.7 9.1 1.0
CB B:GLN366 4.8 9.7 1.0
SG B:CYS345 4.8 16.4 1.0
N B:ALA326 4.8 7.4 1.0
CB B:THR365 4.9 17.6 1.0
CB B:CYS351 4.9 13.9 1.0

Reference:

P.Trickey, J.Basran, L.Y.Lian, Z.Chen, J.D.Barton, M.J.Sutcliffe, N.S.Scrutton, F.S.Mathews. Structural and Biochemical Characterization of Recombinant Wild Type and A C30A Mutant of Trimethylamine Dehydrogenase From Methylophilus Methylotrophus (Sp. W(3)A(1)). Biochemistry V. 39 7678 2000.
ISSN: ISSN 0006-2960
PubMed: 10869173
DOI: 10.1021/BI9927181
Page generated: Sat Aug 3 03:48:38 2024

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