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Iron in PDB 3pcd: Protocatechuate 3,4-Dioxygenase Y447H Mutant

Enzymatic activity of Protocatechuate 3,4-Dioxygenase Y447H Mutant

All present enzymatic activity of Protocatechuate 3,4-Dioxygenase Y447H Mutant:
1.13.11.3;

Protein crystallography data

The structure of Protocatechuate 3,4-Dioxygenase Y447H Mutant, PDB code: 3pcd was solved by A.M.Orville, J.D.Lipscomb, D.H.Ohlendorf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.10
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 197.400, 127.200, 134.600, 90.00, 97.70, 90.00
R / Rfree (%) n/a / n/a

Iron Binding Sites:

The binding sites of Iron atom in the Protocatechuate 3,4-Dioxygenase Y447H Mutant (pdb code 3pcd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Protocatechuate 3,4-Dioxygenase Y447H Mutant, PDB code: 3pcd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pcd

Go back to Iron Binding Sites List in 3pcd
Iron binding site 1 out of 6 in the Protocatechuate 3,4-Dioxygenase Y447H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Protocatechuate 3,4-Dioxygenase Y447H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:17.8
occ:1.00
 O2 M:CO3550 1.8 17.4 1.0
OH M:TYR408 1.9 15.0 1.0
NE2 M:HIS462 2.1 11.9 1.0
NE2 M:HIS460 2.3 12.4 1.0
C M:CO3550 2.5 17.2 1.0
O1 M:CO3550 2.5 17.1 1.0
CZ M:TYR408 3.0 16.1 1.0
CE1 M:HIS462 3.0 10.9 1.0
CD2 M:HIS462 3.1 10.6 1.0
CE1 M:HIS460 3.2 12.1 1.0
CD2 M:HIS460 3.3 12.3 1.0
CE1 M:TYR408 3.6 15.6 1.0
O3 M:CO3550 3.8 20.1 1.0
CE2 M:TYR408 3.9 16.5 1.0
ND1 M:HIS462 4.1 10.7 1.0
O M:HOH604 4.2 14.9 1.0
CG M:HIS462 4.2 10.7 1.0
NE2 M:HIS447 4.3 19.4 1.0
O M:HOH626 4.3 10.8 1.0
ND1 M:HIS460 4.4 12.2 1.0
CG M:HIS460 4.4 11.8 1.0
NH1 M:ARG457 4.5 12.2 1.0
O M:HOH727 4.5 16.4 1.0
CD1 M:TYR408 4.9 16.6 1.0
CD2 M:HIS447 4.9 18.5 1.0
OE1 M:GLN477 5.0 11.0 1.0

Iron binding site 2 out of 6 in 3pcd

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Iron binding site 2 out of 6 in the Protocatechuate 3,4-Dioxygenase Y447H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Protocatechuate 3,4-Dioxygenase Y447H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:17.1
occ:1.00
 OH N:TYR408 1.9 15.5 1.0
NE2 N:HIS462 2.2 11.6 1.0
O1 N:CO3550 2.2 15.7 1.0
NE2 N:HIS460 2.3 12.4 1.0
O2 N:CO3550 2.3 18.3 1.0
C N:CO3550 2.6 16.6 1.0
CZ N:TYR408 2.9 16.2 1.0
CD2 N:HIS462 3.1 10.6 1.0
CE1 N:HIS462 3.2 11.1 1.0
CD2 N:HIS460 3.2 13.1 1.0
CE1 N:HIS460 3.3 11.6 1.0
CE1 N:TYR408 3.7 16.4 1.0
CE2 N:TYR408 3.8 16.0 1.0
O3 N:CO3550 3.9 18.7 1.0
O N:HOH607 4.1 14.8 1.0
O N:HOH631 4.2 11.1 1.0
CG N:HIS462 4.3 11.1 1.0
ND1 N:HIS462 4.3 11.6 1.0
NE2 N:HIS447 4.4 19.4 1.0
ND1 N:HIS460 4.4 11.8 1.0
CG N:HIS460 4.4 12.3 1.0
NH1 N:ARG457 4.5 11.2 1.0
O N:HOH733 4.5 16.3 1.0
CD1 N:TYR408 4.9 16.8 1.0

Iron binding site 3 out of 6 in 3pcd

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Iron binding site 3 out of 6 in the Protocatechuate 3,4-Dioxygenase Y447H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Protocatechuate 3,4-Dioxygenase Y447H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:16.7
occ:1.00
 OH O:TYR408 2.0 15.5 1.0
NE2 O:HIS462 2.0 12.6 1.0
O2 O:CO3550 2.0 20.0 1.0
NE2 O:HIS460 2.2 12.8 1.0
O1 O:CO3550 2.3 18.4 1.0
C O:CO3550 2.5 20.2 1.0
CZ O:TYR408 2.9 15.9 1.0
CD2 O:HIS462 2.9 11.2 1.0
CE1 O:HIS462 3.0 11.3 1.0
CE1 O:HIS460 3.1 11.8 1.0
CD2 O:HIS460 3.2 12.9 1.0
CE1 O:TYR408 3.7 16.5 1.0
CE2 O:TYR408 3.7 16.7 1.0
O3 O:CO3550 3.9 21.2 1.0
O O:HOH606 4.1 15.2 0.8
O O:HOH630 4.1 11.2 1.0
CG O:HIS462 4.1 10.9 1.0
ND1 O:HIS462 4.1 10.5 1.0
ND1 O:HIS460 4.2 11.9 1.0
CG O:HIS460 4.3 12.3 1.0
NE2 O:HIS447 4.3 20.0 1.0
NH1 O:ARG457 4.6 12.0 1.0
O O:HOH733 4.6 16.5 0.8
CD1 O:TYR408 4.9 16.9 1.0
CD2 O:TYR408 5.0 17.4 1.0

Iron binding site 4 out of 6 in 3pcd

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Iron binding site 4 out of 6 in the Protocatechuate 3,4-Dioxygenase Y447H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Protocatechuate 3,4-Dioxygenase Y447H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe600

b:16.9
occ:1.00
 OH P:TYR408 1.9 15.2 1.0
O2 P:CO3550 2.1 19.5 1.0
NE2 P:HIS462 2.1 12.0 1.0
NE2 P:HIS460 2.2 12.4 1.0
O1 P:CO3550 2.2 17.4 1.0
C P:CO3550 2.5 17.8 1.0
CE1 P:HIS462 3.0 10.8 1.0
CE1 P:HIS460 3.0 11.7 1.0
CZ P:TYR408 3.0 15.4 1.0
CD2 P:HIS462 3.2 10.5 1.0
CD2 P:HIS460 3.2 12.7 1.0
CE2 P:TYR408 3.7 16.2 1.0
O3 P:CO3550 3.8 18.5 1.0
CE1 P:TYR408 3.9 16.2 1.0
ND1 P:HIS462 4.2 11.3 1.0
NE2 P:HIS447 4.2 20.2 1.0
ND1 P:HIS460 4.2 11.0 1.0
O P:HOH632 4.2 11.4 1.0
O P:HOH611 4.3 15.2 1.0
CG P:HIS462 4.3 10.8 1.0
CG P:HIS460 4.4 12.2 1.0
O P:HOH726 4.5 16.4 1.0
NH1 P:ARG457 4.6 10.9 1.0

Iron binding site 5 out of 6 in 3pcd

Go back to Iron Binding Sites List in 3pcd
Iron binding site 5 out of 6 in the Protocatechuate 3,4-Dioxygenase Y447H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Protocatechuate 3,4-Dioxygenase Y447H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe600

b:17.0
occ:1.00
 O2 Q:CO3550 1.9 19.6 1.0
OH Q:TYR408 1.9 16.3 1.0
NE2 Q:HIS462 2.1 12.4 1.0
NE2 Q:HIS460 2.2 12.7 1.0
O1 Q:CO3550 2.6 19.4 1.0
C Q:CO3550 2.6 19.6 1.0
CZ Q:TYR408 2.9 15.6 1.0
CD2 Q:HIS460 3.0 13.0 1.0
CE1 Q:HIS462 3.1 11.3 1.0
CD2 Q:HIS462 3.1 11.6 1.0
CE1 Q:HIS460 3.3 12.4 1.0
CE1 Q:TYR408 3.6 16.0 1.0
CE2 Q:TYR408 3.7 16.1 1.0
O3 Q:CO3550 3.9 20.7 1.0
NE2 Q:HIS447 4.1 20.0 1.0
ND1 Q:HIS462 4.2 11.1 1.0
O E:HOH206 4.2 15.2 1.0
O Q:HOH991 4.2 11.5 1.0
CG Q:HIS460 4.3 12.5 1.0
CG Q:HIS462 4.3 11.6 1.0
ND1 Q:HIS460 4.4 12.4 1.0
NH1 Q:ARG457 4.5 11.9 1.0
O Q:HOH1147 4.6 16.5 1.0
CD1 Q:TYR408 4.8 16.4 1.0
CD2 Q:HIS447 4.9 19.4 1.0
CD2 Q:TYR408 5.0 17.1 1.0
CD2 E:TYR16 5.0 22.3 1.0

Iron binding site 6 out of 6 in 3pcd

Go back to Iron Binding Sites List in 3pcd
Iron binding site 6 out of 6 in the Protocatechuate 3,4-Dioxygenase Y447H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Protocatechuate 3,4-Dioxygenase Y447H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe600

b:18.6
occ:1.00
 OH R:TYR408 1.9 16.2 1.0
O1 R:CO3550 2.0 16.8 1.0
O2 R:CO3550 2.1 18.4 1.0
NE2 R:HIS462 2.2 12.6 1.0
NE2 R:HIS460 2.3 13.0 1.0
C R:CO3550 2.3 18.1 1.0
CZ R:TYR408 2.9 15.6 1.0
CE1 R:HIS462 3.1 11.3 1.0
CD2 R:HIS460 3.2 12.6 1.0
CD2 R:HIS462 3.2 11.0 1.0
CE1 R:HIS460 3.2 11.8 1.0
CE2 R:TYR408 3.5 16.3 1.0
O3 R:CO3550 3.6 20.7 1.0
CE1 R:TYR408 3.9 16.4 1.0
O F:HOH1191 4.0 15.5 1.0
NE2 R:HIS447 4.0 19.8 1.0
O R:HOH1228 4.2 11.1 1.0
ND1 R:HIS462 4.3 11.0 1.0
O R:HOH1384 4.3 16.6 1.0
ND1 R:HIS460 4.4 12.0 1.0
CG R:HIS462 4.4 10.9 1.0
CG R:HIS460 4.4 12.7 1.0
NH1 R:ARG457 4.6 11.5 1.0
CD2 R:TYR408 4.8 17.1 1.0
CD2 R:HIS447 4.9 19.1 1.0
CD2 F:TYR16 5.0 22.4 1.0
CE1 R:HIS447 5.0 19.7 1.0

Reference:

R.W.Frazee, A.M.Orville, K.B.Dolbeare, H.Yu, D.H.Ohlendorf, J.D.Lipscomb. The Axial Tyrosinate FE3+ Ligand in Protocatechuate 3,4-Dioxygenase Influences Substrate Binding and Product Release: Evidence For New Reaction Cycle Intermediates. Biochemistry V. 37 2131 1998.
ISSN: ISSN 0006-2960
PubMed: 9485360
DOI: 10.1021/BI972047B
Page generated: Sun Dec 13 15:17:12 2020

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