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Iron in PDB 2pcd: Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution

Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution

All present enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution:
1.13.11.3;

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution, PDB code: 2pcd was solved by D.H.Ohlendorf, A.M.Orville, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 2.15
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 197.170, 127.030, 134.180, 90.00, 97.64, 90.00
R / Rfree (%) n/a / n/a

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution (pdb code 2pcd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution, PDB code: 2pcd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2pcd

Go back to Iron Binding Sites List in 2pcd
Iron binding site 1 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:33.4
occ:1.00
 OH M:TYR408 1.8 22.6 1.0
OH M:TYR447 1.9 23.5 1.0
O M:HOH733 1.9 21.6 0.7
NE2 M:HIS460 2.3 19.1 1.0
NE2 M:HIS462 2.3 19.1 1.0
CZ M:TYR408 2.9 23.1 1.0
CE1 M:HIS460 3.0 18.0 1.0
CE1 M:HIS462 3.0 17.7 1.0
CZ M:TYR447 3.1 23.5 1.0
O M:HOH719 3.2 22.5 0.7
CE2 M:TYR408 3.4 23.1 1.0
CD2 M:HIS460 3.5 18.6 1.0
CD2 M:HIS462 3.5 17.6 1.0
CE2 M:TYR447 3.6 23.0 1.0
CE1 M:TYR408 3.9 23.0 1.0
O M:HOH718 4.2 21.0 0.9
ND1 M:HIS460 4.2 17.6 1.0
O M:HOH620 4.2 19.3 1.0
ND1 M:HIS462 4.3 17.3 1.0
O A:HOH205 4.3 20.1 0.9
CE1 M:TYR447 4.3 22.4 1.0
CG M:HIS460 4.5 18.0 1.0
CG M:HIS462 4.5 17.4 1.0
NH1 M:ARG457 4.5 19.1 1.0
CD2 M:TYR408 4.8 23.6 1.0
CD2 A:TYR16 4.9 27.7 1.0
OE1 M:GLN477 5.0 19.0 1.0

Iron binding site 2 out of 6 in 2pcd

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Iron binding site 2 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:34.0
occ:1.00
 OH N:TYR408 1.7 22.3 1.0
OH N:TYR447 2.0 23.4 1.0
O N:HOH749 2.2 21.6 0.7
NE2 N:HIS460 2.3 18.7 1.0
NE2 N:HIS462 2.3 18.7 1.0
CZ N:TYR408 2.8 22.9 1.0
CE1 N:HIS460 3.1 17.5 1.0
CE1 N:HIS462 3.2 17.9 1.0
CZ N:TYR447 3.3 23.4 1.0
O N:HOH733 3.3 22.5 0.7
CD2 N:HIS462 3.3 17.4 1.0
CD2 N:HIS460 3.4 18.6 1.0
CE2 N:TYR408 3.4 23.3 1.0
CE2 N:TYR447 3.8 23.0 1.0
CE1 N:TYR408 3.9 23.1 1.0
O N:HOH629 4.1 19.1 1.0
O B:HOH245 4.1 20.2 0.9
O N:HOH731 4.2 20.8 0.9
ND1 N:HIS460 4.3 17.9 1.0
ND1 N:HIS462 4.3 17.6 1.0
CE1 N:TYR447 4.4 22.6 1.0
CG N:HIS462 4.4 17.3 1.0
CG N:HIS460 4.5 18.0 1.0
NH1 N:ARG457 4.6 18.7 1.0
CD2 N:TYR408 4.7 23.8 1.0
CD2 B:TYR16 4.9 27.8 1.0

Iron binding site 3 out of 6 in 2pcd

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Iron binding site 3 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:33.6
occ:1.00
 OH O:TYR408 1.9 22.7 1.0
NE2 O:HIS462 2.1 18.8 1.0
OH O:TYR447 2.1 23.2 1.0
O O:HOH748 2.1 21.7 0.7
NE2 O:HIS460 2.2 18.5 1.0
CE1 O:HIS460 2.9 17.6 1.0
CZ O:TYR408 3.0 23.0 1.0
CE1 O:HIS462 3.0 17.8 1.0
CD2 O:HIS462 3.2 18.1 1.0
CD2 O:HIS460 3.3 18.7 1.0
CZ O:TYR447 3.4 23.3 1.0
O O:HOH733 3.4 22.6 0.7
CE1 O:TYR408 3.7 23.5 1.0
CE2 O:TYR408 3.9 23.1 1.0
CE2 O:TYR447 3.9 23.3 1.0
ND1 O:HIS460 4.1 18.5 1.0
O C:HOH205 4.2 20.5 0.9
ND1 O:HIS462 4.2 18.0 1.0
O O:HOH629 4.2 19.3 1.0
CG O:HIS462 4.3 17.5 1.0
O O:HOH731 4.3 21.2 0.9
CG O:HIS460 4.4 18.4 1.0
CE1 O:TYR447 4.5 22.4 1.0
NH1 O:ARG457 4.6 19.3 1.0
CD2 C:TYR16 4.9 27.8 1.0
OE1 O:GLN477 4.9 18.8 1.0
CD1 O:TYR408 4.9 23.6 1.0

Iron binding site 4 out of 6 in 2pcd

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Iron binding site 4 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe600

b:33.6
occ:1.00
 OH P:TYR408 1.8 22.5 1.0
OH P:TYR447 2.1 23.1 1.0
O P:HOH746 2.2 21.6 0.7
NE2 P:HIS462 2.2 18.1 1.0
NE2 P:HIS460 2.3 18.7 1.0
CZ P:TYR408 2.9 22.8 1.0
CE1 P:HIS460 3.0 18.3 1.0
CE1 P:HIS462 3.1 17.7 1.0
O P:HOH731 3.2 22.6 0.7
CD2 P:HIS462 3.3 17.4 1.0
CZ P:TYR447 3.3 23.2 1.0
CD2 P:HIS460 3.4 18.7 1.0
CE2 P:TYR408 3.5 23.2 1.0
CE2 P:TYR447 3.8 22.9 1.0
CE1 P:TYR408 3.9 22.7 1.0
O P:HOH630 4.2 19.3 1.0
O D:HOH723 4.2 20.4 0.9
ND1 P:HIS460 4.2 18.7 1.0
O P:HOH730 4.3 21.1 0.9
ND1 P:HIS462 4.3 17.9 1.0
CG P:HIS462 4.4 17.3 1.0
CG P:HIS460 4.4 18.6 1.0
CE1 P:TYR447 4.5 22.5 1.0
NH1 P:ARG457 4.6 19.9 1.0
CD2 P:TYR408 4.8 23.7 1.0

Iron binding site 5 out of 6 in 2pcd

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Iron binding site 5 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe600

b:35.3
occ:1.00
 OH Q:TYR408 1.8 22.9 1.0
OH Q:TYR447 2.0 23.7 1.0
NE2 Q:HIS460 2.2 19.9 1.0
NE2 Q:HIS462 2.2 18.8 1.0
O Q:HOH1183 2.2 21.7 0.7
CZ Q:TYR408 3.0 23.3 1.0
CE1 Q:HIS462 3.0 18.0 1.0
CE1 Q:HIS460 3.0 18.7 1.0
O Q:HOH1157 3.2 22.6 0.7
CD2 Q:HIS462 3.3 18.1 1.0
CZ Q:TYR447 3.3 23.5 1.0
CD2 Q:HIS460 3.3 19.0 1.0
CE1 Q:TYR408 3.7 23.4 1.0
CE2 Q:TYR408 3.8 23.3 1.0
CE2 Q:TYR447 3.8 23.1 1.0
O Q:HOH1155 4.0 21.3 0.9
O E:HOH208 4.1 20.7 0.9
O Q:HOH999 4.2 19.5 1.0
ND1 Q:HIS462 4.2 17.7 1.0
ND1 Q:HIS460 4.2 18.4 1.0
CG Q:HIS462 4.3 17.9 1.0
CG Q:HIS460 4.3 18.6 1.0
CE1 Q:TYR447 4.4 22.8 1.0
NH1 Q:ARG457 4.4 19.9 1.0
CD2 E:TYR16 4.9 28.0 1.0
OE1 Q:GLN477 4.9 19.3 1.0

Iron binding site 6 out of 6 in 2pcd

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Iron binding site 6 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe600

b:34.2
occ:1.00
 OH R:TYR408 1.8 22.8 1.0
OH R:TYR447 2.0 23.6 1.0
O R:HOH1422 2.0 21.5 0.7
NE2 R:HIS460 2.3 19.3 1.0
NE2 R:HIS462 2.3 18.7 1.0
CZ R:TYR408 2.9 23.4 1.0
O R:HOH1396 3.0 22.4 0.7
CE1 R:HIS460 3.1 18.3 1.0
CE1 R:HIS462 3.2 18.4 1.0
CZ R:TYR447 3.2 22.9 1.0
CD2 R:HIS460 3.4 19.0 1.0
CD2 R:HIS462 3.4 17.9 1.0
CE2 R:TYR408 3.6 23.1 1.0
CE2 R:TYR447 3.7 23.1 1.0
CE1 R:TYR408 4.0 23.2 1.0
O R:HOH1394 4.1 20.9 0.9
O R:HOH1238 4.1 19.1 1.0
O F:HOH1201 4.2 20.6 0.9
ND1 R:HIS460 4.3 18.6 1.0
CE1 R:TYR447 4.4 22.4 1.0
ND1 R:HIS462 4.4 17.8 1.0
NH1 R:ARG457 4.4 19.9 1.0
CG R:HIS460 4.4 18.8 1.0
CG R:HIS462 4.5 17.8 1.0
CD2 R:TYR408 4.9 23.1 1.0
OE1 R:GLN477 4.9 19.9 1.0

Reference:

D.H.Ohlendorf, A.M.Orville, J.D.Lipscomb. Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa at 2.15 A Resolution. J.Mol.Biol. V. 244 586 1994.
ISSN: ISSN 0022-2836
PubMed: 7990141
DOI: 10.1006/JMBI.1994.1754
Page generated: Sun Aug 4 01:15:47 2024

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