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Iron in PDB 4l3h: Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

Enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

All present enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide, PDB code: 4l3h 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 / 1.79
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 (%) 15.4 / 19.8

Other elements in 4l3h:

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide (pdb code 4l3h). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide, PDB code: 4l3h:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4l3h

Go back to Iron Binding Sites List in 4l3h
Iron binding site 1 out of 4 in the Crystal Structure of the E113Q-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 Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:36.2
occ:1.00
 FE A:HEC402 0.0 36.2 1.0
NB A:HEC402 2.0 33.6 1.0
NC A:HEC402 2.0 35.7 1.0
NE2 A:HIS35 2.0 34.4 1.0
ND A:HEC402 2.1 35.8 1.0
NA A:HEC402 2.1 34.1 1.0
C4C A:HEC402 3.0 38.5 1.0
C4D A:HEC402 3.0 36.8 1.0
CD2 A:HIS35 3.0 34.5 1.0
CE1 A:HIS35 3.0 35.3 1.0
C4B A:HEC402 3.0 35.7 1.0
C1D A:HEC402 3.0 36.7 1.0
C1B A:HEC402 3.1 33.0 1.0
C4A A:HEC402 3.1 32.5 1.0
C1C A:HEC402 3.1 37.0 1.0
C1A A:HEC402 3.1 34.2 1.0
O A:HOH719 3.2 45.7 1.0
CHD A:HEC402 3.3 36.3 1.0
CHA A:HEC402 3.4 35.7 1.0
CHC A:HEC402 3.4 34.1 1.0
CHB A:HEC402 3.4 33.3 1.0
NE2 A:GLN103 4.1 34.5 1.0
ND1 A:HIS35 4.1 34.9 1.0
CG A:HIS35 4.2 35.1 1.0
C3C A:HEC402 4.3 37.9 1.0
C2B A:HEC402 4.3 33.1 1.0
C3B A:HEC402 4.3 33.8 1.0
C2C A:HEC402 4.3 36.8 1.0
CG A:PRO107 4.3 39.7 1.0
C3D A:HEC402 4.3 37.2 1.0
C2D A:HEC402 4.3 36.5 1.0
C2A A:HEC402 4.4 31.8 1.0
C3A A:HEC402 4.4 32.5 1.0
NE2 A:GLN113 4.8 40.2 1.0
CB A:PRO107 4.8 39.5 1.0

Iron binding site 2 out of 4 in 4l3h

Go back to Iron Binding Sites List in 4l3h
Iron binding site 2 out of 4 in the Crystal Structure of the E113Q-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 Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:34.8
occ:1.00
 FE A:HEC403 0.0 34.8 1.0
OH A:TYR294 1.9 35.8 1.0
NB A:HEC403 2.0 34.4 1.0
ND A:HEC403 2.0 34.3 1.0
NC A:HEC403 2.0 33.4 1.0
NA A:HEC403 2.1 32.8 1.0
NE2 A:HIS205 2.1 31.2 1.0
CZ A:TYR294 2.9 35.5 1.0
C4D A:HEC403 3.0 33.6 1.0
C4B A:HEC403 3.0 33.4 1.0
C1B A:HEC403 3.0 35.4 1.0
C1D A:HEC403 3.0 33.4 1.0
C4C A:HEC403 3.0 33.4 1.0
C1C A:HEC403 3.0 32.4 1.0
C1A A:HEC403 3.0 34.0 1.0
CD2 A:HIS205 3.0 32.1 1.0
C4A A:HEC403 3.0 35.7 1.0
CE1 A:HIS205 3.1 32.4 1.0
CHA A:HEC403 3.4 34.9 1.0
CHB A:HEC403 3.4 35.8 1.0
CHC A:HEC403 3.4 32.8 1.0
CHD A:HEC403 3.4 31.7 1.0
CE2 A:TYR294 3.6 36.0 1.0
CE1 A:TYR294 3.7 36.1 1.0
ND1 A:HIS205 4.2 32.1 1.0
CG A:HIS205 4.2 32.8 1.0
C3D A:HEC403 4.2 34.7 1.0
C2D A:HEC403 4.3 33.4 1.0
C3B A:HEC403 4.3 34.7 1.0
C2B A:HEC403 4.3 35.1 1.0
C2C A:HEC403 4.3 32.3 1.0
C3C A:HEC403 4.3 31.8 1.0
C3A A:HEC403 4.3 33.9 1.0
C2A A:HEC403 4.3 33.7 1.0
CD2 A:TYR294 4.8 36.3 1.0
CD1 A:TYR294 4.9 37.4 1.0
CD1 A:ILE226 4.9 38.4 1.0

Iron binding site 3 out of 4 in 4l3h

Go back to Iron Binding Sites List in 4l3h
Iron binding site 3 out of 4 in the Crystal Structure of the E113Q-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 Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:26.8
occ:1.00
 FE B:HEC402 0.0 26.8 1.0
O B:HOH861 1.8 21.2 0.5
NC B:HEC402 2.0 26.5 1.0
ND B:HEC402 2.0 25.0 1.0
NB B:HEC402 2.0 24.4 1.0
NA B:HEC402 2.1 28.1 1.0
NE2 B:HIS35 2.1 26.1 1.0
C4C B:HEC402 3.0 25.8 1.0
C4D B:HEC402 3.0 24.4 1.0
C1B B:HEC402 3.0 26.6 1.0
C1D B:HEC402 3.0 26.4 1.0
C4B B:HEC402 3.0 27.1 1.0
C4A B:HEC402 3.0 25.3 1.0
C1C B:HEC402 3.0 25.2 1.0
CE1 B:HIS35 3.1 25.4 1.0
C1A B:HEC402 3.1 23.7 1.0
CD2 B:HIS35 3.1 28.9 1.0
O B:HOH861 3.3 20.2 0.5
CHB B:HEC402 3.3 24.9 1.0
CHD B:HEC402 3.4 26.1 1.0
CHC B:HEC402 3.4 25.8 1.0
CHA B:HEC402 3.4 23.1 1.0
NE2 B:GLN103 4.1 28.7 1.0
ND1 B:HIS35 4.2 26.2 1.0
CG B:HIS35 4.3 26.6 1.0
C3C B:HEC402 4.3 27.1 1.0
C2D B:HEC402 4.3 25.9 1.0
C3D B:HEC402 4.3 24.9 1.0
C3A B:HEC402 4.3 25.6 1.0
C2B B:HEC402 4.3 27.4 1.0
C2C B:HEC402 4.3 27.1 1.0
C3B B:HEC402 4.3 26.4 1.0
C2A B:HEC402 4.4 25.3 1.0
CG B:PRO107 4.4 34.0 1.0
CB B:PRO107 4.8 31.8 1.0
CG2 B:THR67 4.9 28.7 1.0
NE2 B:GLN113 4.9 35.1 1.0

Iron binding site 4 out of 4 in 4l3h

Go back to Iron Binding Sites List in 4l3h
Iron binding site 4 out of 4 in the Crystal Structure of the E113Q-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 Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:22.4
occ:1.00
 FE B:HEC403 0.0 22.4 1.0
ND B:HEC403 2.0 22.6 1.0
OH B:TYR294 2.0 22.0 1.0
NB B:HEC403 2.0 23.3 1.0
NA B:HEC403 2.0 20.5 1.0
NC B:HEC403 2.0 19.9 1.0
NE2 B:HIS205 2.1 21.7 1.0
CZ B:TYR294 2.9 22.2 1.0
C1C B:HEC403 3.0 19.3 1.0
C1D B:HEC403 3.0 22.1 1.0
C1A B:HEC403 3.0 20.9 1.0
C4A B:HEC403 3.0 21.4 1.0
C1B B:HEC403 3.0 21.8 1.0
CD2 B:HIS205 3.0 19.6 1.0
C4D B:HEC403 3.0 22.4 1.0
C4C B:HEC403 3.0 23.3 1.0
C4B B:HEC403 3.1 20.4 1.0
CE1 B:HIS205 3.1 20.8 1.0
CHB B:HEC403 3.3 21.8 1.0
CHC B:HEC403 3.4 19.8 1.0
CHA B:HEC403 3.4 20.0 1.0
CHD B:HEC403 3.4 20.9 1.0
CE2 B:TYR294 3.6 22.4 1.0
CE1 B:TYR294 3.7 22.1 1.0
CG B:HIS205 4.2 20.4 1.0
C2D B:HEC403 4.2 21.0 1.0
ND1 B:HIS205 4.2 21.1 1.0
C3D B:HEC403 4.3 22.5 1.0
C2A B:HEC403 4.3 21.4 1.0
C3A B:HEC403 4.3 20.7 1.0
C2B B:HEC403 4.3 24.1 1.0
C2C B:HEC403 4.3 23.3 1.0
C3B B:HEC403 4.3 23.5 1.0
C3C B:HEC403 4.3 21.0 1.0
CD2 B:TYR294 4.8 24.4 1.0
CD1 B:TYR294 4.9 21.4 1.0

Reference:

N.Abu Tarboush, E.T.Yukl, S.Shin, M.Feng, C.M.Wilmot, V.L.Davidson. Carboxyl Group of GLU113 Is Required For Stabilization of the Diferrous and Bis-Fe(IV) States of Maug. Biochemistry V. 52 6358 2013.
ISSN: ISSN 0006-2960
PubMed: 23952537
DOI: 10.1021/BI400905S
Page generated: Mon Aug 5 06:05:29 2024

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