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Iron in PDB 3lkt: Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis

Enzymatic activity of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis

All present enzymatic activity of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis:
1.13.11.3;

Protein crystallography data

The structure of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis, PDB code: 3lkt was solved by J.D.Lipscomb, V.M.Purpero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.57 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 190.310, 168.040, 128.160, 90.00, 132.30, 90.00
R / Rfree (%) 14.8 / 17.3

Other elements in 3lkt:

The structure of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis (pdb code 3lkt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis, PDB code: 3lkt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3lkt

Go back to Iron Binding Sites List in 3lkt
Iron binding site 1 out of 6 in the Tyrosine 447 of Protocatechuate 3,4-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 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:15.9
occ:1.00
OH M:TYR408 1.9 20.9 1.0
NE2 M:HIS462 2.1 13.1 1.0
NE2 M:HIS460 2.1 15.1 1.0
O1 M:BME29 2.3 23.5 0.9
S2 M:BME29 2.5 28.5 0.9
C1 M:BME29 2.6 21.6 0.9
CZ M:TYR408 2.9 19.2 1.0
C2 M:BME29 3.0 25.3 0.9
CE1 M:HIS460 3.0 14.6 1.0
CE1 M:HIS462 3.1 16.0 1.0
CD2 M:HIS462 3.1 13.8 1.0
CD2 M:HIS460 3.2 14.8 1.0
CE2 M:TYR408 3.6 17.7 1.0
CE1 M:TYR408 3.8 17.3 1.0
O M:HOH165 4.1 15.4 1.0
ND1 M:HIS460 4.2 14.1 1.0
ND1 M:HIS462 4.2 14.4 1.0
CG M:HIS462 4.3 15.1 1.0
NH1 M:ARG457 4.3 14.8 1.0
O M:HOH874 4.3 19.8 1.0
CG M:HIS460 4.3 14.5 1.0
O M:HOH225 4.4 18.5 1.0
CD2 M:TYR408 4.9 17.5 1.0
OE1 M:GLN477 4.9 14.5 1.0

Iron binding site 2 out of 6 in 3lkt

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Iron binding site 2 out of 6 in the Tyrosine 447 of Protocatechuate 3,4-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 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:16.6
occ:1.00
OH N:TYR408 1.9 21.0 1.0
NE2 N:HIS462 2.1 15.0 1.0
NE2 N:HIS460 2.1 13.8 1.0
O1 N:BME32 2.3 17.4 0.5
O1 N:BME32 2.4 43.5 0.5
C2 N:BME32 2.4 42.7 0.5
S2 N:BME32 2.4 44.5 0.5
S2 N:BME32 2.4 23.2 0.5
C1 N:BME32 2.7 17.3 0.5
C1 N:BME32 2.7 43.3 0.5
CZ N:TYR408 2.9 19.3 1.0
C2 N:BME32 3.0 18.7 0.5
CE1 N:HIS460 3.0 14.0 1.0
CE1 N:HIS462 3.1 14.3 1.0
CD2 N:HIS462 3.1 14.2 1.0
CD2 N:HIS460 3.2 14.5 1.0
CE2 N:TYR408 3.7 17.4 1.0
CE1 N:TYR408 3.8 18.1 1.0
O N:HOH285 4.1 15.4 1.0
ND1 N:HIS462 4.2 14.9 1.0
ND1 N:HIS460 4.2 14.8 1.0
CG N:HIS462 4.2 14.9 1.0
NH1 N:ARG457 4.3 16.4 1.0
O N:HOH2285 4.3 18.5 1.0
CG N:HIS460 4.3 13.8 1.0
O N:HOH552 4.3 19.1 1.0
OE1 N:GLN477 4.9 15.7 1.0
CD2 N:TYR408 4.9 16.5 1.0

Iron binding site 3 out of 6 in 3lkt

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Iron binding site 3 out of 6 in the Tyrosine 447 of Protocatechuate 3,4-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 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:16.0
occ:1.00
OH O:TYR408 1.9 20.5 1.0
NE2 O:HIS462 2.1 13.5 1.0
NE2 O:HIS460 2.1 15.0 1.0
O1 O:BME30 2.3 24.8 0.9
S2 O:BME30 2.4 28.7 0.9
C1 O:BME30 2.5 23.1 0.9
CZ O:TYR408 2.9 18.6 1.0
C2 O:BME30 3.0 26.3 0.9
CE1 O:HIS460 3.0 15.6 1.0
CE1 O:HIS462 3.1 13.1 1.0
CD2 O:HIS462 3.1 13.7 1.0
CD2 O:HIS460 3.2 14.4 1.0
CE2 O:TYR408 3.7 17.9 1.0
CE1 O:TYR408 3.7 17.6 1.0
O O:HOH119 4.2 15.9 1.0
ND1 O:HIS460 4.2 13.6 1.0
ND1 O:HIS462 4.2 13.4 1.0
O O:HOH704 4.2 18.7 1.0
CG O:HIS462 4.2 13.4 1.0
NH1 O:ARG457 4.3 15.5 1.0
CG O:HIS460 4.3 13.4 1.0
O O:HOH605 4.3 17.1 1.0
OE1 O:GLN477 4.8 15.2 1.0
CD2 O:TYR408 4.9 17.1 1.0
CD1 O:TYR408 5.0 16.9 1.0

Iron binding site 4 out of 6 in 3lkt

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Iron binding site 4 out of 6 in the Tyrosine 447 of Protocatechuate 3,4-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 4 of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe600

b:16.0
occ:1.00
OH P:TYR408 1.9 19.4 1.0
NE2 P:HIS460 2.1 16.1 1.0
NE2 P:HIS462 2.1 13.8 1.0
O1 P:BME31 2.3 24.1 0.9
S2 P:BME31 2.5 28.6 0.9
C1 P:BME31 2.6 23.2 0.9
CZ P:TYR408 2.9 16.4 1.0
C2 P:BME31 3.0 26.3 0.9
CE1 P:HIS460 3.0 14.7 1.0
CE1 P:HIS462 3.1 15.8 1.0
CD2 P:HIS462 3.1 14.5 1.0
CD2 P:HIS460 3.2 14.7 1.0
CE2 P:TYR408 3.6 16.2 1.0
CE1 P:TYR408 3.8 17.5 1.0
O P:HOH147 4.1 14.9 1.0
ND1 P:HIS460 4.1 14.1 1.0
ND1 P:HIS462 4.2 14.5 1.0
CG P:HIS460 4.3 14.6 1.0
CG P:HIS462 4.3 14.0 1.0
NH1 P:ARG457 4.3 16.6 1.0
O P:HOH2287 4.3 20.1 1.0
O P:HOH540 4.3 17.6 1.0
CD2 P:TYR408 4.9 16.7 1.0
OE1 P:GLN477 4.9 15.4 1.0

Iron binding site 5 out of 6 in 3lkt

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Iron binding site 5 out of 6 in the Tyrosine 447 of Protocatechuate 3,4-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 5 of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe600

b:16.5
occ:1.00
OH Q:TYR408 1.9 20.4 1.0
NE2 Q:HIS462 2.1 15.6 1.0
NE2 Q:HIS460 2.1 13.5 1.0
C2 Q:BME34 2.3 57.0 0.5
O1 Q:BME34 2.3 57.7 0.5
O1 Q:BME34 2.4 14.0 0.5
C1 Q:BME34 2.5 11.4 0.5
S2 Q:BME34 2.5 57.0 0.5
S2 Q:BME34 2.5 16.8 0.5
C1 Q:BME34 2.7 57.1 0.5
CZ Q:TYR408 3.0 18.9 1.0
C2 Q:BME34 3.0 13.7 0.5
CE1 Q:HIS460 3.0 13.7 1.0
CE1 Q:HIS462 3.1 13.9 1.0
CD2 Q:HIS462 3.1 14.7 1.0
CD2 Q:HIS460 3.2 16.0 1.0
CE2 Q:TYR408 3.7 18.2 1.0
CE1 Q:TYR408 3.8 18.4 1.0
O Q:HOH184 4.1 14.6 1.0
ND1 Q:HIS460 4.2 15.0 1.0
ND1 Q:HIS462 4.2 15.6 1.0
CG Q:HIS462 4.2 14.3 1.0
CG Q:HIS460 4.3 14.1 1.0
O Q:HOH623 4.3 18.1 1.0
NH1 Q:ARG457 4.3 15.3 1.0
O Q:HOH251 4.4 18.1 1.0
OE1 Q:GLN477 4.9 15.5 1.0
CD2 Q:TYR408 4.9 16.8 1.0

Iron binding site 6 out of 6 in 3lkt

Go back to Iron Binding Sites List in 3lkt
Iron binding site 6 out of 6 in the Tyrosine 447 of Protocatechuate 3,4-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 6 of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe600

b:15.6
occ:1.00
OH R:TYR408 2.0 19.7 1.0
NE2 R:HIS460 2.1 15.2 1.0
NE2 R:HIS462 2.1 13.5 1.0
O1 R:BME28 2.1 15.0 0.9
S2 R:BME28 2.4 18.4 0.9
C1 R:BME28 2.8 14.8 0.9
CZ R:TYR408 2.9 18.1 1.0
CE1 R:HIS460 3.0 15.8 1.0
CE1 R:HIS462 3.1 13.8 1.0
CD2 R:HIS462 3.1 13.2 1.0
C2 R:BME28 3.1 15.2 0.9
CD2 R:HIS460 3.2 15.5 1.0
CE2 R:TYR408 3.7 17.0 1.0
CE1 R:TYR408 3.8 17.5 1.0
O R:HOH174 4.2 16.8 1.0
ND1 R:HIS460 4.2 14.3 1.0
ND1 R:HIS462 4.2 14.0 1.0
NH1 R:ARG457 4.2 15.5 1.0
CG R:HIS462 4.2 13.1 1.0
CG R:HIS460 4.3 13.7 1.0
O R:HOH757 4.3 19.1 1.0
O R:HOH35 4.3 16.9 1.0
OE1 R:GLN477 4.9 15.0 1.0
CD2 R:TYR408 5.0 17.5 1.0
CD1 R:TYR408 5.0 18.4 1.0

Reference:

V.M.Purpero, M.P.Valley, D.H.Ohlendorf, J.D.Lipscomb, D.Burk, K.B.Dolbeare, K.C.Brown. Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis To Be Published.
Page generated: Tue Aug 5 03:35:46 2025

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