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Iron in PDB 3orv: Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex

Enzymatic activity of Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3orv was solved by L.M.R.Jensen, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.49 / 1.91
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.527, 83.524, 107.782, 109.94, 91.54, 105.78
R / Rfree (%) 13.9 / 18.7

Other elements in 3orv:

The structure of Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex (pdb code 3orv). 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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3orv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3orv

Go back to Iron Binding Sites List in 3orv
Iron binding site 1 out of 4 in the Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex


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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:21.9
occ:1.00
FE A:HEC500 0.0 21.9 1.0
NA A:HEC500 2.1 23.6 1.0
ND A:HEC500 2.1 23.2 1.0
NC A:HEC500 2.1 22.1 1.0
NB A:HEC500 2.1 25.4 1.0
NE2 A:HIS35 2.1 21.0 1.0
C1A A:HEC500 3.0 22.7 1.0
C1C A:HEC500 3.1 22.8 1.0
CD2 A:HIS35 3.1 24.9 1.0
C4D A:HEC500 3.1 22.2 1.0
C4B A:HEC500 3.1 23.2 1.0
C1D A:HEC500 3.1 21.1 1.0
C4C A:HEC500 3.1 21.9 1.0
C4A A:HEC500 3.1 25.1 1.0
C1B A:HEC500 3.1 24.1 1.0
CE1 A:HIS35 3.2 20.4 1.0
CHC A:HEC500 3.4 20.0 1.0
CHA A:HEC500 3.4 21.3 1.0
CHD A:HEC500 3.5 21.8 1.0
CHB A:HEC500 3.5 22.3 1.0
O A:HOH436 3.8 32.2 1.0
NE2 A:GLN103 4.2 21.8 1.0
CG A:HIS35 4.3 21.9 1.0
ND1 A:HIS35 4.3 19.7 1.0
CG A:PRO107 4.3 25.0 1.0
C2A A:HEC500 4.3 20.7 1.0
C2C A:HEC500 4.4 20.6 1.0
C2D A:HEC500 4.4 22.4 1.0
C3D A:HEC500 4.4 22.3 1.0
C3C A:HEC500 4.4 23.4 1.0
C3A A:HEC500 4.4 24.3 1.0
C3B A:HEC500 4.4 20.1 1.0
C2B A:HEC500 4.4 25.4 1.0
CB A:PRO107 4.9 25.6 1.0

Iron binding site 2 out of 4 in 3orv

Go back to Iron Binding Sites List in 3orv
Iron binding site 2 out of 4 in the Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex


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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:21.5
occ:1.00
FE A:HEC600 0.0 21.5 1.0
NB A:HEC600 2.0 20.9 1.0
NC A:HEC600 2.1 23.0 1.0
ND A:HEC600 2.1 24.4 1.0
NE2 A:HIS205 2.1 21.7 1.0
NA A:HEC600 2.1 23.3 1.0
NE2 A:HIS294 2.1 24.1 1.0
C4B A:HEC600 3.0 20.9 1.0
C1B A:HEC600 3.0 22.1 1.0
C1C A:HEC600 3.0 23.2 1.0
C4C A:HEC600 3.0 19.1 1.0
CD2 A:HIS205 3.0 19.1 1.0
CE1 A:HIS294 3.1 20.8 1.0
C1D A:HEC600 3.1 21.0 1.0
C4A A:HEC600 3.1 21.1 1.0
C4D A:HEC600 3.1 20.8 1.0
CD2 A:HIS294 3.1 24.1 1.0
C1A A:HEC600 3.1 22.5 1.0
CE1 A:HIS205 3.1 20.8 1.0
CHC A:HEC600 3.4 20.8 1.0
CHB A:HEC600 3.4 21.3 1.0
CHD A:HEC600 3.4 18.4 1.0
CHA A:HEC600 3.5 18.9 1.0
ND1 A:HIS294 4.1 21.0 1.0
CG A:HIS294 4.2 23.7 1.0
CG A:HIS205 4.2 23.3 1.0
ND1 A:HIS205 4.2 24.9 1.0
C3B A:HEC600 4.3 19.1 1.0
C2B A:HEC600 4.3 21.0 1.0
C2C A:HEC600 4.3 20.5 1.0
C3C A:HEC600 4.3 20.3 1.0
C3D A:HEC600 4.4 21.1 1.0
C2D A:HEC600 4.4 20.3 1.0
C3A A:HEC600 4.4 23.9 1.0
C2A A:HEC600 4.4 21.6 1.0

Iron binding site 3 out of 4 in 3orv

Go back to Iron Binding Sites List in 3orv
Iron binding site 3 out of 4 in the Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex


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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:19.5
occ:1.00
FE B:HEC500 0.0 19.5 1.0
NB B:HEC500 2.0 18.5 1.0
NE2 B:HIS35 2.0 17.0 1.0
ND B:HEC500 2.0 21.2 1.0
NC B:HEC500 2.1 19.2 1.0
NA B:HEC500 2.1 19.6 1.0
CE1 B:HIS35 3.0 17.7 1.0
C1B B:HEC500 3.0 18.9 1.0
C1C B:HEC500 3.0 16.3 1.0
C4C B:HEC500 3.0 21.7 1.0
C1D B:HEC500 3.1 20.6 1.0
CD2 B:HIS35 3.1 16.8 1.0
C1A B:HEC500 3.1 19.3 1.0
C4B B:HEC500 3.1 19.5 1.0
C4D B:HEC500 3.1 20.2 1.0
C4A B:HEC500 3.1 20.1 1.0
CHB B:HEC500 3.4 16.0 1.0
CHD B:HEC500 3.4 18.3 1.0
CHC B:HEC500 3.4 17.7 1.0
CHA B:HEC500 3.5 16.7 1.0
O B:HOH406 3.7 29.5 1.0
NE2 B:GLN103 4.1 18.8 1.0
ND1 B:HIS35 4.1 19.9 1.0
CG B:HIS35 4.2 18.4 1.0
CG B:PRO107 4.3 25.5 1.0
C2B B:HEC500 4.3 14.8 1.0
C2C B:HEC500 4.3 18.1 1.0
C3B B:HEC500 4.3 18.2 1.0
C3C B:HEC500 4.3 18.7 1.0
C2D B:HEC500 4.4 22.2 1.0
C2A B:HEC500 4.4 19.2 1.0
C3A B:HEC500 4.4 18.9 1.0
C3D B:HEC500 4.4 19.6 1.0
CB B:PRO107 4.9 24.6 1.0
CD2 B:LEU70 5.0 19.6 1.0

Iron binding site 4 out of 4 in 3orv

Go back to Iron Binding Sites List in 3orv
Iron binding site 4 out of 4 in the Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex


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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:17.9
occ:1.00
FE B:HEC600 0.0 17.9 1.0
NE2 B:HIS205 2.0 18.4 1.0
ND B:HEC600 2.1 19.3 1.0
NC B:HEC600 2.1 18.7 1.0
NB B:HEC600 2.1 18.7 1.0
NA B:HEC600 2.1 17.9 1.0
NE2 B:HIS294 2.1 16.2 1.0
CE1 B:HIS294 3.0 17.4 1.0
CD2 B:HIS205 3.0 15.9 1.0
CE1 B:HIS205 3.0 17.9 1.0
C1A B:HEC600 3.1 16.8 1.0
C1D B:HEC600 3.1 16.7 1.0
C4C B:HEC600 3.1 16.1 1.0
C1C B:HEC600 3.1 14.9 1.0
C4D B:HEC600 3.1 13.7 1.0
C4B B:HEC600 3.1 15.2 1.0
C4A B:HEC600 3.1 16.2 1.0
C1B B:HEC600 3.1 17.4 1.0
CD2 B:HIS294 3.1 17.4 1.0
CHD B:HEC600 3.4 17.0 1.0
CHA B:HEC600 3.5 12.8 1.0
CHB B:HEC600 3.5 16.4 1.0
CHC B:HEC600 3.5 12.7 1.0
ND1 B:HIS294 4.0 17.4 1.0
CG B:HIS294 4.1 17.2 1.0
ND1 B:HIS205 4.1 16.5 1.0
CG B:HIS205 4.2 16.0 1.0
C2D B:HEC600 4.3 19.2 1.0
C3D B:HEC600 4.3 14.5 1.0
C2A B:HEC600 4.4 16.8 1.0
C2C B:HEC600 4.4 17.0 1.0
C3B B:HEC600 4.4 16.6 1.0
C3C B:HEC600 4.4 14.8 1.0
C3A B:HEC600 4.4 16.9 1.0
C2B B:HEC600 4.4 17.4 1.0

Reference:

N.Abu Tarboush, L.M.Jensen, M.Feng, H.Tachikawa, C.M.Wilmot, V.L.Davidson. Functional Importance of Tyrosine 294 and the Catalytic Selectivity For the Bis-Fe(IV) State of Maug Revealed By Replacement of This Axial Heme Ligand with Histidine . Biochemistry V. 49 9783 2010.
ISSN: ISSN 0006-2960
PubMed: 20929212
DOI: 10.1021/BI101254P
Page generated: Sun Aug 4 17:14:37 2024

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