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Iron in PDB 3lmx: Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis

Enzymatic activity of Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis

All present enzymatic activity of Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis:
1.13.11.3;

Protein crystallography data

The structure of Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis, PDB code: 3lmx was solved by V.M.Purpero, J.D.Lipscomb, K.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.85 / 2.20
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 127.982, 140.578, 167.824, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.3

Other elements in 3lmx:

The structure of Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis (pdb code 3lmx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis, PDB code: 3lmx:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3lmx

Go back to Iron Binding Sites List in 3lmx
Iron binding site 1 out of 3 in the Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:38.0
occ:1.00
O4 M:DHB1 1.8 48.8 0.9
OH M:TYR408 2.0 36.7 1.0
NE2 M:HIS462 2.1 21.5 1.0
NE2 M:HIS460 2.2 26.6 1.0
O3 M:DHB1 2.4 46.1 0.9
C4 M:DHB1 2.7 46.7 0.9
C3 M:DHB1 2.9 44.1 0.9
CZ M:TYR408 3.0 33.8 1.0
CE1 M:HIS462 3.0 19.9 1.0
CD2 M:HIS460 3.1 25.1 1.0
CD2 M:HIS462 3.2 21.3 1.0
CE1 M:HIS460 3.3 27.3 1.0
CE2 M:TYR408 3.6 33.2 1.0
CE1 M:TYR408 3.9 35.1 1.0
C5 M:DHB1 3.9 45.8 0.9
NH1 M:ARG457 4.1 22.8 1.0
ND1 M:HIS462 4.2 21.6 1.0
O A:HOH378 4.2 38.0 1.0
O M:HOH184 4.2 25.2 1.0
C2 M:DHB1 4.2 44.9 0.9
CG M:HIS462 4.3 22.5 1.0
CG M:HIS460 4.3 25.6 1.0
ND1 M:HIS460 4.4 26.1 1.0
OE1 M:GLN477 4.7 28.6 1.0
CD2 M:TYR408 4.9 34.7 1.0
CD2 A:TYR16 5.0 50.3 1.0
C6 M:DHB1 5.0 44.8 0.9

Iron binding site 2 out of 3 in 3lmx

Go back to Iron Binding Sites List in 3lmx
Iron binding site 2 out of 3 in the Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:37.2
occ:1.00
O4 N:DHB2 2.0 45.3 0.9
OH N:TYR408 2.0 43.7 1.0
NE2 N:HIS460 2.2 23.3 1.0
NE2 N:HIS462 2.3 26.4 1.0
O3 N:DHB2 2.4 45.4 0.9
C4 N:DHB2 2.8 43.4 0.9
C3 N:DHB2 2.9 43.1 0.9
CZ N:TYR408 3.0 42.1 1.0
CE1 N:HIS462 3.2 26.0 1.0
CD2 N:HIS460 3.2 23.7 1.0
CE1 N:HIS460 3.2 25.3 1.0
CD2 N:HIS462 3.4 24.9 1.0
CE2 N:TYR408 3.7 40.5 1.0
CE1 N:TYR408 3.9 42.1 1.0
NH1 N:ARG457 3.9 23.6 1.0
C5 N:DHB2 4.1 44.6 0.9
O N:HOH34 4.3 25.3 1.0
C2 N:DHB2 4.3 44.2 0.9
O B:HOH219 4.3 32.0 1.0
ND1 N:HIS460 4.3 25.8 1.0
ND1 N:HIS462 4.3 25.9 1.0
CG N:HIS460 4.4 23.8 1.0
CG N:HIS462 4.5 26.3 1.0
OE1 N:GLN477 4.7 28.8 1.0
CD2 N:TYR408 5.0 40.1 1.0

Iron binding site 3 out of 3 in 3lmx

Go back to Iron Binding Sites List in 3lmx
Iron binding site 3 out of 3 in the Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:37.3
occ:1.00
OH O:TYR408 1.9 41.0 1.0
O4 O:DHB3 2.0 51.0 0.9
O3 O:DHB3 2.2 45.1 0.9
NE2 O:HIS460 2.3 24.7 1.0
NE2 O:HIS462 2.4 25.2 1.0
C4 O:DHB3 2.7 46.7 0.9
C3 O:DHB3 2.8 45.3 0.9
CZ O:TYR408 2.9 38.8 1.0
CE1 O:HIS460 3.2 24.1 1.0
CE1 O:HIS462 3.2 24.9 1.0
CD2 O:HIS460 3.4 26.1 1.0
CD2 O:HIS462 3.4 22.5 1.0
CE2 O:TYR408 3.7 37.2 1.0
CE1 O:TYR408 3.7 37.5 1.0
C5 O:DHB3 4.0 48.2 0.9
O C:HOH324 4.1 34.4 1.0
C2 O:DHB3 4.2 46.6 0.9
NH1 O:ARG457 4.2 23.8 1.0
ND1 O:HIS460 4.3 23.6 1.0
ND1 O:HIS462 4.4 25.3 1.0
O O:HOH167 4.4 27.1 1.0
CG O:HIS460 4.5 25.2 1.0
CG O:HIS462 4.5 25.9 1.0
CD2 C:TYR16 4.6 53.4 1.0
OE1 O:GLN477 4.8 26.4 1.0
CD2 O:TYR408 4.9 38.2 1.0
CD1 O:TYR408 5.0 39.6 1.0

Reference:

V.M.Purpero, J.D.Lipscomb, D.H.Ohlendorf, K.Shi, K.B.Dolbeare, C.K.Brown, D.Burk. Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis To Be Published.
Page generated: Sun Dec 13 15:11:34 2020

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