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Iron in PDB 2tmd: Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase

Enzymatic activity of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase

All present enzymatic activity of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase:
1.5.99.7;

Protein crystallography data

The structure of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase, PDB code: 2tmd was solved by F.S.Mathews, L.W.Lim, S.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 147.750, 71.950, 83.820, 90.00, 97.69, 90.00
R / Rfree (%) 15.4 / n/a

Iron Binding Sites:

The binding sites of Iron atom in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase (pdb code 2tmd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase, PDB code: 2tmd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2tmd

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Iron binding site 1 out of 8 in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:12.1
occ:1.00
FE1 A:SF4801 0.0 12.1 1.0
SG A:CYS345 2.3 7.9 1.0
S2 A:SF4801 2.3 12.7 1.0
S4 A:SF4801 2.3 14.2 1.0
S3 A:SF4801 2.3 13.5 1.0
FE4 A:SF4801 2.7 14.9 1.0
FE3 A:SF4801 2.7 13.4 1.0
FE2 A:SF4801 2.8 18.3 1.0
CB A:CYS345 3.4 13.1 1.0
CA A:CYS345 3.8 11.6 1.0
S1 A:SF4801 3.9 13.5 1.0
N A:ILE346 4.0 10.1 1.0
N A:GLY347 4.1 10.8 1.0
CB A:ARG322 4.1 3.6 1.0
C A:CYS345 4.3 10.2 1.0
CD A:ARG322 4.4 7.7 1.0
O A:ARG322 4.4 10.9 1.0
CB A:ALA326 4.5 7.5 1.0
CA A:GLY347 4.7 8.0 1.0
SG A:CYS364 4.7 10.9 1.0
CG A:ARG322 4.7 6.1 1.0
C A:ARG322 4.8 7.1 1.0
N A:CYS348 4.8 6.8 1.0
SG A:CYS351 4.9 8.2 1.0
CA A:ARG322 4.9 7.5 1.0
C A:ILE346 5.0 11.3 1.0

Iron binding site 2 out of 8 in 2tmd

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Iron binding site 2 out of 8 in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:18.3
occ:1.00
FE2 A:SF4801 0.0 18.3 1.0
S1 A:SF4801 2.3 13.5 1.0
S3 A:SF4801 2.3 13.5 1.0
S4 A:SF4801 2.3 14.2 1.0
SG A:CYS348 2.3 11.0 1.0
FE4 A:SF4801 2.8 14.9 1.0
FE3 A:SF4801 2.8 13.4 1.0
FE1 A:SF4801 2.8 12.1 1.0
N A:CYS348 3.7 6.8 1.0
CB A:CYS348 3.7 6.6 1.0
N A:ASN349 3.8 8.3 1.0
OG1 A:THR365 4.0 11.8 1.0
S2 A:SF4801 4.0 12.7 1.0
CA A:CYS348 4.1 8.0 1.0
CB A:THR365 4.2 11.3 1.0
CG1 A:ILE346 4.2 9.4 1.0
C A:CYS348 4.3 9.8 1.0
N A:VAL350 4.3 7.5 1.0
N A:THR365 4.4 11.5 1.0
N A:GLY347 4.6 10.8 1.0
CA A:ASN349 4.7 7.0 1.0
SG A:CYS345 4.7 7.9 1.0
SG A:CYS351 4.8 8.2 1.0
C A:GLY347 4.8 10.1 1.0
SG A:CYS364 4.9 10.9 1.0
N A:ILE346 4.9 10.1 1.0
N A:CYS351 4.9 5.9 1.0
CA A:THR365 5.0 9.8 1.0
CD1 A:ILE346 5.0 9.1 1.0
CB A:VAL350 5.0 4.5 1.0
C A:ASN349 5.0 6.5 1.0

Iron binding site 3 out of 8 in 2tmd

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Iron binding site 3 out of 8 in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:13.4
occ:1.00
FE3 A:SF4801 0.0 13.4 1.0
S4 A:SF4801 2.3 14.2 1.0
S1 A:SF4801 2.3 13.5 1.0
S2 A:SF4801 2.3 12.7 1.0
SG A:CYS351 2.3 8.2 1.0
FE4 A:SF4801 2.6 14.9 1.0
FE1 A:SF4801 2.7 12.1 1.0
FE2 A:SF4801 2.8 18.3 1.0
CB A:CYS351 3.4 2.3 1.0
S3 A:SF4801 3.9 13.5 1.0
N A:CYS351 4.0 5.9 1.0
CD A:ARG322 4.2 7.7 1.0
CA A:CYS351 4.3 8.4 1.0
CG A:ARG322 4.4 6.1 1.0
N A:ASN349 4.5 8.3 1.0
CB A:ARG322 4.5 3.6 1.0
CA A:ASN349 4.6 7.0 1.0
SG A:CYS345 4.6 7.9 1.0
SG A:CYS364 4.7 10.9 1.0
N A:VAL350 4.7 7.5 1.0
SG A:CYS348 4.8 11.0 1.0
C A:ASN349 4.9 6.5 1.0
CG2 A:ILE325 5.0 4.7 1.0

Iron binding site 4 out of 8 in 2tmd

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Iron binding site 4 out of 8 in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:14.9
occ:1.00
FE4 A:SF4801 0.0 14.9 1.0
S2 A:SF4801 2.3 12.7 1.0
S1 A:SF4801 2.3 13.5 1.0
SG A:CYS364 2.3 10.9 1.0
S3 A:SF4801 2.3 13.5 1.0
FE3 A:SF4801 2.6 13.4 1.0
FE1 A:SF4801 2.7 12.1 1.0
FE2 A:SF4801 2.8 18.3 1.0
CB A:CYS364 3.4 10.3 1.0
CA A:CYS364 3.7 12.8 1.0
N A:THR365 3.8 11.5 1.0
S4 A:SF4801 3.9 14.2 1.0
C A:CYS364 4.1 11.4 1.0
N A:GLN366 4.3 8.8 1.0
CB A:ALA326 4.5 7.5 1.0
CG2 A:ILE325 4.6 4.7 1.0
CA A:THR365 4.7 9.8 1.0
SG A:CYS351 4.7 8.2 1.0
CA A:ALA326 4.7 9.9 1.0
CB A:GLN366 4.8 7.1 1.0
N A:ALA326 4.8 10.8 1.0
CB A:THR365 4.8 11.3 1.0
SG A:CYS348 4.9 11.0 1.0
SG A:CYS345 4.9 7.9 1.0
CB A:CYS351 5.0 2.3 1.0

Iron binding site 5 out of 8 in 2tmd

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Iron binding site 5 out of 8 in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:12.3
occ:1.00
FE1 B:SF4801 0.0 12.3 1.0
S2 B:SF4801 2.3 12.5 1.0
SG B:CYS345 2.3 10.8 1.0
S4 B:SF4801 2.3 12.6 1.0
S3 B:SF4801 2.4 12.4 1.0
FE4 B:SF4801 2.6 13.4 1.0
FE3 B:SF4801 2.6 13.0 1.0
FE2 B:SF4801 2.8 17.4 1.0
CB B:CYS345 3.3 13.8 1.0
CA B:CYS345 3.8 14.1 1.0
S1 B:SF4801 3.9 11.7 1.0
N B:ILE346 4.0 12.8 1.0
CB B:ARG322 4.1 8.6 1.0
N B:GLY347 4.1 15.8 1.0
C B:CYS345 4.3 13.8 1.0
O B:ARG322 4.4 10.3 1.0
CB B:ALA326 4.5 4.9 1.0
CD B:ARG322 4.5 12.0 1.0
SG B:CYS364 4.7 11.9 1.0
CA B:GLY347 4.7 10.6 1.0
C B:ARG322 4.7 11.1 1.0
CG B:ARG322 4.8 8.6 1.0
CA B:ARG322 4.8 11.2 1.0
SG B:CYS351 4.9 8.2 1.0
N B:CYS348 4.9 9.2 1.0
SG B:CYS348 5.0 10.2 1.0

Iron binding site 6 out of 8 in 2tmd

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Iron binding site 6 out of 8 in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:17.4
occ:1.00
FE2 B:SF4801 0.0 17.4 1.0
S1 B:SF4801 2.3 11.7 1.0
SG B:CYS348 2.3 10.2 1.0
S3 B:SF4801 2.3 12.4 1.0
S4 B:SF4801 2.3 12.6 1.0
FE3 B:SF4801 2.7 13.0 1.0
FE4 B:SF4801 2.7 13.4 1.0
FE1 B:SF4801 2.8 12.3 1.0
N B:CYS348 3.7 9.2 1.0
CB B:CYS348 3.8 7.0 1.0
N B:ASN349 3.9 8.0 1.0
S2 B:SF4801 4.0 12.5 1.0
OG1 B:THR365 4.1 10.4 1.0
CA B:CYS348 4.2 8.7 1.0
CG1 B:ILE346 4.2 9.4 1.0
CB B:THR365 4.3 12.4 1.0
N B:VAL350 4.3 8.3 1.0
N B:THR365 4.4 7.3 1.0
C B:CYS348 4.4 10.1 1.0
N B:GLY347 4.6 15.8 1.0
SG B:CYS351 4.7 8.2 1.0
SG B:CYS345 4.7 10.8 1.0
CA B:ASN349 4.7 9.5 1.0
C B:GLY347 4.8 11.6 1.0
SG B:CYS364 4.8 11.9 1.0
N B:ILE346 4.9 12.8 1.0
N B:CYS351 4.9 7.5 1.0
CD1 B:ILE346 4.9 8.2 1.0
CA B:THR365 4.9 10.1 1.0
CA B:GLY347 5.0 10.6 1.0

Iron binding site 7 out of 8 in 2tmd

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Iron binding site 7 out of 8 in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:13.0
occ:1.00
FE3 B:SF4801 0.0 13.0 1.0
S4 B:SF4801 2.3 12.6 1.0
SG B:CYS351 2.3 8.2 1.0
S2 B:SF4801 2.3 12.5 1.0
S1 B:SF4801 2.3 11.7 1.0
FE1 B:SF4801 2.6 12.3 1.0
FE4 B:SF4801 2.7 13.4 1.0
FE2 B:SF4801 2.7 17.4 1.0
CB B:CYS351 3.4 6.0 1.0
S3 B:SF4801 3.9 12.4 1.0
N B:CYS351 4.0 7.5 1.0
CD B:ARG322 4.3 12.0 1.0
CA B:CYS351 4.3 9.1 1.0
CB B:ARG322 4.5 8.6 1.0
CG B:ARG322 4.5 8.6 1.0
N B:ASN349 4.5 8.0 1.0
SG B:CYS345 4.6 10.8 1.0
CA B:ASN349 4.6 9.5 1.0
N B:VAL350 4.7 8.3 1.0
SG B:CYS348 4.7 10.2 1.0
SG B:CYS364 4.7 11.9 1.0
C B:ASN349 5.0 9.6 1.0
CG2 B:ILE325 5.0 2.0 1.0

Iron binding site 8 out of 8 in 2tmd

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Iron binding site 8 out of 8 in the Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:13.4
occ:1.00
FE4 B:SF4801 0.0 13.4 1.0
S1 B:SF4801 2.3 11.7 1.0
S2 B:SF4801 2.3 12.5 1.0
S3 B:SF4801 2.3 12.4 1.0
SG B:CYS364 2.3 11.9 1.0
FE1 B:SF4801 2.6 12.3 1.0
FE3 B:SF4801 2.7 13.0 1.0
FE2 B:SF4801 2.7 17.4 1.0
CB B:CYS364 3.5 9.1 1.0
N B:THR365 3.8 7.3 1.0
CA B:CYS364 3.8 9.2 1.0
S4 B:SF4801 3.9 12.6 1.0
C B:CYS364 4.1 10.1 1.0
N B:GLN366 4.2 10.8 1.0
CB B:ALA326 4.4 4.9 1.0
CG2 B:ILE325 4.5 2.0 1.0
SG B:CYS351 4.7 8.2 1.0
CA B:ALA326 4.7 11.2 1.0
CA B:THR365 4.7 10.1 1.0
CB B:GLN366 4.7 2.0 1.0
N B:ALA326 4.8 8.8 1.0
SG B:CYS348 4.8 10.2 1.0
SG B:CYS345 4.8 10.8 1.0
CB B:THR365 4.9 12.4 1.0
CB B:CYS351 4.9 6.0 1.0
C B:THR365 5.0 11.8 1.0

Reference:

M.J.Barber, P.J.Neame, L.W.Lim, S.White, F.S.Matthews. Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase. J.Biol.Chem. V. 267 6611 1992.
ISSN: ISSN 0021-9258
PubMed: 1551870
Page generated: Thu Jul 17 04:02:33 2025

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