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Iron in PDB 3rlm: Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

Enzymatic activity of Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

All present enzymatic activity of Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide:
1.4.99.3;

Protein crystallography data

The structure of Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide, PDB code: 3rlm was solved by E.T.Yukl, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.49 / 2.13
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.530, 83.520, 107.780, 109.94, 91.54, 105.78
R / Rfree (%) 18.1 / 23.7

Other elements in 3rlm:

The structure of Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide (pdb code 3rlm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide, PDB code: 3rlm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3rlm

Go back to Iron Binding Sites List in 3rlm
Iron binding site 1 out of 4 in the Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide


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 W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:36.6
occ:1.00
 FE A:HEC500 0.0 36.6 1.0
O A:HOH380 2.0 12.1 0.5
NC A:HEC500 2.1 39.0 1.0
NA A:HEC500 2.1 38.4 1.0
NE2 A:HIS35 2.1 33.5 1.0
ND A:HEC500 2.1 38.3 1.0
NB A:HEC500 2.1 36.9 1.0
CD2 A:HIS35 3.0 32.7 1.0
C4D A:HEC500 3.1 38.0 1.0
C1D A:HEC500 3.1 38.6 1.0
C4C A:HEC500 3.1 38.5 1.0
C1B A:HEC500 3.1 36.4 1.0
C4A A:HEC500 3.1 36.9 1.0
C1A A:HEC500 3.1 38.0 1.0
CE1 A:HIS35 3.1 32.7 1.0
C1C A:HEC500 3.1 37.8 1.0
C4B A:HEC500 3.1 36.4 1.0
CHD A:HEC500 3.4 38.2 1.0
CHB A:HEC500 3.4 35.0 1.0
CHA A:HEC500 3.4 38.5 1.0
CHC A:HEC500 3.5 37.1 1.0
O A:HOH380 3.8 25.3 0.5
NE2 A:GLN103 3.9 41.4 1.0
ND1 A:HIS35 4.2 33.5 1.0
CG A:HIS35 4.2 33.4 1.0
C3D A:HEC500 4.3 38.5 1.0
C2D A:HEC500 4.4 38.1 1.0
C3C A:HEC500 4.4 38.3 1.0
C2C A:HEC500 4.4 37.1 1.0
C2B A:HEC500 4.4 36.0 1.0
C3A A:HEC500 4.4 36.5 1.0
C2A A:HEC500 4.4 36.4 1.0
C3B A:HEC500 4.4 34.1 1.0
CG A:PRO107 4.5 42.8 1.0
CB A:PRO107 4.7 43.7 1.0
CD A:GLN103 4.9 40.2 1.0

Iron binding site 2 out of 4 in 3rlm

Go back to Iron Binding Sites List in 3rlm
Iron binding site 2 out of 4 in the Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide


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 W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:34.7
occ:1.00
 FE A:HEC600 0.0 34.7 1.0
OH A:TYR294 2.0 37.7 1.0
NE2 A:HIS205 2.1 33.7 1.0
NB A:HEC600 2.1 32.6 1.0
NC A:HEC600 2.1 33.1 1.0
NA A:HEC600 2.1 34.4 1.0
ND A:HEC600 2.1 33.2 1.0
CZ A:TYR294 2.9 38.1 1.0
CE1 A:HIS205 3.0 32.3 1.0
C1B A:HEC600 3.0 35.1 1.0
C4A A:HEC600 3.1 34.9 1.0
C4C A:HEC600 3.1 33.1 1.0
C1D A:HEC600 3.1 33.6 1.0
C4D A:HEC600 3.1 33.4 1.0
C4B A:HEC600 3.1 32.8 1.0
CD2 A:HIS205 3.1 30.1 1.0
C1C A:HEC600 3.1 31.7 1.0
C1A A:HEC600 3.1 34.0 1.0
CHB A:HEC600 3.4 34.3 1.0
CHD A:HEC600 3.4 32.1 1.0
CHA A:HEC600 3.5 33.0 1.0
CHC A:HEC600 3.5 33.0 1.0
CE1 A:TYR294 3.6 35.7 1.0
CE2 A:TYR294 3.7 35.1 1.0
ND1 A:HIS205 4.1 33.0 1.0
CG A:HIS205 4.2 33.4 1.0
C2B A:HEC600 4.4 34.7 1.0
C3D A:HEC600 4.4 32.9 1.0
C2D A:HEC600 4.4 32.3 1.0
C3B A:HEC600 4.4 33.7 1.0
C3C A:HEC600 4.4 31.2 1.0
C3A A:HEC600 4.4 34.5 1.0
C2C A:HEC600 4.4 32.6 1.0
C2A A:HEC600 4.4 36.0 1.0
CD1 A:TYR294 4.8 35.7 1.0
CD2 A:TYR294 4.9 35.6 1.0

Iron binding site 3 out of 4 in 3rlm

Go back to Iron Binding Sites List in 3rlm
Iron binding site 3 out of 4 in the Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide


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 W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:27.3
occ:1.00
 FE B:HEC500 0.0 27.3 1.0
NC B:HEC500 2.1 28.6 1.0
NA B:HEC500 2.1 27.1 1.0
NB B:HEC500 2.1 25.6 1.0
NE2 B:HIS35 2.1 19.7 1.0
O B:HOH397 2.1 2.0 0.5
ND B:HEC500 2.1 26.1 1.0
CD2 B:HIS35 3.0 24.8 1.0
C1C B:HEC500 3.1 28.8 1.0
C1B B:HEC500 3.1 25.7 1.0
C4A B:HEC500 3.1 26.2 1.0
C1D B:HEC500 3.1 27.4 1.0
C4B B:HEC500 3.1 25.4 1.0
C4C B:HEC500 3.1 28.7 1.0
C1A B:HEC500 3.1 25.9 1.0
C4D B:HEC500 3.1 25.1 1.0
CE1 B:HIS35 3.1 25.1 1.0
CHD B:HEC500 3.4 27.1 1.0
CHB B:HEC500 3.4 22.8 1.0
CHC B:HEC500 3.4 27.0 1.0
CHA B:HEC500 3.5 26.1 1.0
O B:HOH397 3.6 18.7 0.5
NE2 B:GLN103 3.8 30.1 1.0
CG B:HIS35 4.2 25.9 1.0
ND1 B:HIS35 4.2 25.8 1.0
C2C B:HEC500 4.4 29.5 1.0
C2D B:HEC500 4.4 26.7 1.0
C3A B:HEC500 4.4 25.1 1.0
C2B B:HEC500 4.4 25.4 1.0
C3B B:HEC500 4.4 25.5 1.0
C3C B:HEC500 4.4 27.8 1.0
C2A B:HEC500 4.4 25.8 1.0
C3D B:HEC500 4.4 26.6 1.0
CG B:PRO107 4.4 33.2 1.0
CB B:PRO107 4.6 34.6 1.0
CD B:GLN103 4.8 33.0 1.0
CD2 B:LEU70 5.0 29.6 1.0

Iron binding site 4 out of 4 in 3rlm

Go back to Iron Binding Sites List in 3rlm
Iron binding site 4 out of 4 in the Structure of the W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide


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 W199F Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:24.6
occ:1.00
 FE B:HEC600 0.0 24.6 1.0
OH B:TYR294 1.9 22.0 1.0
NE2 B:HIS205 2.0 19.7 1.0
NB B:HEC600 2.1 24.5 1.0
ND B:HEC600 2.1 22.1 1.0
NC B:HEC600 2.1 25.3 1.0
NA B:HEC600 2.1 24.4 1.0
CZ B:TYR294 2.9 21.0 1.0
CD2 B:HIS205 2.9 19.0 1.0
C1D B:HEC600 3.0 22.7 1.0
C1B B:HEC600 3.0 24.0 1.0
C4C B:HEC600 3.1 25.0 1.0
C4A B:HEC600 3.1 23.8 1.0
C4B B:HEC600 3.1 23.5 1.0
C4D B:HEC600 3.1 19.3 1.0
C1A B:HEC600 3.1 21.3 1.0
C1C B:HEC600 3.1 25.4 1.0
CE1 B:HIS205 3.1 21.2 1.0
CHD B:HEC600 3.4 24.3 1.0
CHB B:HEC600 3.4 24.0 1.0
CHA B:HEC600 3.4 19.0 1.0
CHC B:HEC600 3.5 24.6 1.0
CE1 B:TYR294 3.6 22.4 1.0
CE2 B:TYR294 3.7 22.6 1.0
CG B:HIS205 4.1 23.3 1.0
ND1 B:HIS205 4.2 22.7 1.0
C2D B:HEC600 4.3 20.2 1.0
C3B B:HEC600 4.3 23.2 1.0
C2B B:HEC600 4.3 24.2 1.0
C3D B:HEC600 4.3 21.4 1.0
C3C B:HEC600 4.4 25.4 1.0
C3A B:HEC600 4.4 22.8 1.0
C2A B:HEC600 4.4 21.4 1.0
C2C B:HEC600 4.4 26.2 1.0
CD1 B:TYR294 4.8 21.5 1.0
CD2 B:TYR294 4.9 22.2 1.0

Reference:

N.A.Tarboush, L.M.Jensen, E.T.Yukl, J.Geng, A.Liu, C.M.Wilmot, V.L.Davidson. Mutagenesis of TRYPTOPHAN199 Suggests That Hopping Is Required For Maug-Dependent Tryptophan Tryptophylquinone Biosynthesis. Proc.Natl.Acad.Sci.Usa V. 108 16956 2011.
ISSN: ISSN 0027-8424
PubMed: 21969534
DOI: 10.1073/PNAS.1109423108
Page generated: Sun Aug 4 19:20:02 2024

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