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Iron in PDB 3sjl: Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex

Enzymatic activity of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3sjl 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) 29.39 / 1.63
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.606, 89.001, 104.812, 67.05, 79.51, 79.72
R / Rfree (%) 14.2 / 18

Other elements in 3sjl:

The structure of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex 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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex (pdb code 3sjl). 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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3sjl:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3sjl

Go back to Iron Binding Sites List in 3sjl
Iron binding site 1 out of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:15.6
occ:1.00
FE A:HEC500 0.0 15.6 1.0
NC A:HEC500 2.0 13.7 1.0
NB A:HEC500 2.0 15.1 1.0
ND A:HEC500 2.0 14.7 1.0
NA A:HEC500 2.0 14.6 1.0
OE2 A:GLU113 2.1 16.2 1.0
NE2 A:HIS35 2.1 17.7 1.0
C4B A:HEC500 3.0 16.5 1.0
C4D A:HEC500 3.0 13.5 1.0
C1C A:HEC500 3.0 14.1 1.0
C1D A:HEC500 3.0 16.1 1.0
C4C A:HEC500 3.0 14.9 1.0
C1B A:HEC500 3.0 14.3 1.0
CD2 A:HIS35 3.1 17.7 1.0
C4A A:HEC500 3.1 13.2 1.0
C1A A:HEC500 3.1 14.1 1.0
CE1 A:HIS35 3.1 17.4 1.0
CD A:GLU113 3.2 14.9 1.0
CHD A:HEC500 3.4 14.7 1.0
CHA A:HEC500 3.4 15.0 1.0
CHC A:HEC500 3.5 14.8 1.0
CHB A:HEC500 3.5 14.7 1.0
CG A:GLU113 3.7 15.1 1.0
ND1 A:HIS35 4.2 16.1 1.0
CG A:HIS35 4.2 17.8 1.0
NE2 A:GLN103 4.2 15.5 1.0
OE1 A:GLU113 4.2 15.5 1.0
C2B A:HEC500 4.3 14.6 1.0
OG A:SER107 4.3 13.1 1.0
C3B A:HEC500 4.3 14.8 1.0
C3D A:HEC500 4.3 14.7 1.0
C2D A:HEC500 4.3 15.9 1.0
C3C A:HEC500 4.3 14.4 1.0
C2A A:HEC500 4.3 15.5 1.0
C2C A:HEC500 4.3 13.8 1.0
C3A A:HEC500 4.4 15.2 1.0
CB A:GLU113 4.6 18.0 1.0

Iron binding site 2 out of 4 in 3sjl

Go back to Iron Binding Sites List in 3sjl
Iron binding site 2 out of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:17.1
occ:1.00
FE A:HEC600 0.0 17.1 1.0
NC A:HEC600 1.9 15.6 1.0
OH A:TYR294 2.0 15.1 1.0
NA A:HEC600 2.0 13.3 1.0
NB A:HEC600 2.0 16.8 1.0
ND A:HEC600 2.0 15.5 1.0
NE2 A:HIS205 2.1 14.3 1.0
CZ A:TYR294 3.0 15.6 1.0
C1C A:HEC600 3.0 17.8 1.0
C4C A:HEC600 3.0 14.1 1.0
C1A A:HEC600 3.0 17.1 1.0
C1B A:HEC600 3.0 16.5 1.0
C1D A:HEC600 3.0 14.1 1.0
CE1 A:HIS205 3.0 15.1 1.0
CD2 A:HIS205 3.0 15.2 1.0
C4D A:HEC600 3.0 13.7 1.0
C4A A:HEC600 3.1 17.2 1.0
C4B A:HEC600 3.1 15.7 1.0
CHB A:HEC600 3.4 16.5 1.0
CHD A:HEC600 3.4 14.3 1.0
CHC A:HEC600 3.4 15.3 1.0
CHA A:HEC600 3.5 13.4 1.0
CE1 A:TYR294 3.7 15.2 1.0
CE2 A:TYR294 3.7 16.9 1.0
ND1 A:HIS205 4.1 15.8 1.0
CG A:HIS205 4.2 15.9 1.0
C2C A:HEC600 4.2 16.8 1.0
C2A A:HEC600 4.3 15.4 1.0
C3C A:HEC600 4.3 17.0 1.0
C2B A:HEC600 4.3 17.8 1.0
C3A A:HEC600 4.3 17.1 1.0
C3D A:HEC600 4.3 14.0 1.0
C2D A:HEC600 4.3 13.8 1.0
C3B A:HEC600 4.4 16.8 1.0
CD1 A:TYR294 4.9 16.6 1.0
CD1 A:ILE226 5.0 17.5 1.0
CD2 A:TYR294 5.0 17.3 1.0

Iron binding site 3 out of 4 in 3sjl

Go back to Iron Binding Sites List in 3sjl
Iron binding site 3 out of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:16.6
occ:1.00
FE B:HEC500 0.0 16.6 1.0
ND B:HEC500 2.0 15.5 1.0
NE2 B:HIS35 2.0 14.3 1.0
NA B:HEC500 2.0 15.3 1.0
NB B:HEC500 2.0 14.8 1.0
NC B:HEC500 2.1 16.1 1.0
OE2 B:GLU113 2.1 17.3 1.0
C4D B:HEC500 3.0 13.6 1.0
C4B B:HEC500 3.0 15.5 1.0
CD2 B:HIS35 3.0 16.8 1.0
C1B B:HEC500 3.0 16.4 1.0
CE1 B:HIS35 3.0 14.8 1.0
C4C B:HEC500 3.1 16.4 1.0
C4A B:HEC500 3.1 14.1 1.0
C1A B:HEC500 3.1 16.4 1.0
C1D B:HEC500 3.1 16.3 1.0
C1C B:HEC500 3.1 16.8 1.0
CD B:GLU113 3.2 17.6 1.0
CHA B:HEC500 3.4 12.9 1.0
CHD B:HEC500 3.5 16.5 1.0
CHB B:HEC500 3.5 13.3 1.0
CHC B:HEC500 3.5 16.6 1.0
CG B:GLU113 3.7 18.0 1.0
ND1 B:HIS35 4.2 15.3 1.0
CG B:HIS35 4.2 14.2 1.0
OG B:SER107 4.2 18.0 1.0
NE2 B:GLN103 4.2 16.6 1.0
OE1 B:GLU113 4.2 16.9 1.0
C3B B:HEC500 4.3 16.5 1.0
C3D B:HEC500 4.3 15.8 1.0
C2B B:HEC500 4.3 16.3 1.0
C2D B:HEC500 4.3 14.9 1.0
C3A B:HEC500 4.3 14.9 1.0
C2C B:HEC500 4.3 20.3 1.0
C2A B:HEC500 4.3 14.8 1.0
C3C B:HEC500 4.4 19.2 1.0
CB B:GLU113 4.6 15.4 1.0

Iron binding site 4 out of 4 in 3sjl

Go back to Iron Binding Sites List in 3sjl
Iron binding site 4 out of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:14.1
occ:1.00
FE B:HEC600 0.0 14.1 1.0
OH B:TYR294 1.9 12.5 1.0
NA B:HEC600 2.0 13.1 1.0
ND B:HEC600 2.0 12.7 1.0
NC B:HEC600 2.0 11.1 1.0
NB B:HEC600 2.0 14.1 1.0
NE2 B:HIS205 2.1 14.0 1.0
CZ B:TYR294 2.9 13.9 1.0
C4C B:HEC600 3.0 11.5 1.0
C4A B:HEC600 3.0 13.5 1.0
C1A B:HEC600 3.0 12.3 1.0
C1D B:HEC600 3.0 12.3 1.0
CD2 B:HIS205 3.0 13.0 1.0
C4D B:HEC600 3.0 13.1 1.0
C4B B:HEC600 3.0 14.3 1.0
C1B B:HEC600 3.0 14.3 1.0
C1C B:HEC600 3.0 12.3 1.0
CE1 B:HIS205 3.1 14.2 1.0
CHD B:HEC600 3.4 13.7 1.0
CHA B:HEC600 3.4 9.7 1.0
CHB B:HEC600 3.4 12.8 1.0
CHC B:HEC600 3.5 12.5 1.0
CE1 B:TYR294 3.6 14.8 1.0
CE2 B:TYR294 3.8 12.2 1.0
CG B:HIS205 4.2 13.0 1.0
ND1 B:HIS205 4.2 13.7 1.0
C3A B:HEC600 4.3 14.3 1.0
C3D B:HEC600 4.3 12.3 1.0
C3C B:HEC600 4.3 11.8 1.0
C2D B:HEC600 4.3 14.2 1.0
C2A B:HEC600 4.3 16.4 1.0
C2C B:HEC600 4.3 13.1 1.0
C3B B:HEC600 4.3 13.7 1.0
C2B B:HEC600 4.3 14.8 1.0
CD1 B:TYR294 4.9 12.8 1.0
CD1 B:ILE226 4.9 15.0 1.0
CD2 B:TYR294 5.0 12.4 1.0

Reference:

M.Feng, L.M.Jensen, E.T.Yukl, X.Wei, A.Liu, C.M.Wilmot, V.L.Davidson. Proline 107 Is A Major Determinant in Maintaining the Structure of the Distal Pocket and Reactivity of the High-Spin Heme of Maug. Biochemistry V. 51 1598 2012.
ISSN: ISSN 0006-2960
PubMed: 22299652
DOI: 10.1021/BI201882E
Page generated: Sun Aug 4 19:58:31 2024

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