Atomistry » Iron » PDB 1yev-1yqo » 1ykk
Atomistry »
  Iron »
    PDB 1yev-1yqo »
      1ykk »

Iron in PDB 1ykk: Protocatechuate 3,4-Dioxygenase Y408C Mutant

Enzymatic activity of Protocatechuate 3,4-Dioxygenase Y408C Mutant

All present enzymatic activity of Protocatechuate 3,4-Dioxygenase Y408C Mutant:
1.13.11.3;

Protein crystallography data

The structure of Protocatechuate 3,4-Dioxygenase Y408C Mutant, PDB code: 1ykk was solved by C.K.Brown, D.H.Ohlendorf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.09 / 2.06
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 194.870, 126.961, 132.764, 90.00, 96.39, 90.00
R / Rfree (%) 21 / 21.9

Iron Binding Sites:

The binding sites of Iron atom in the Protocatechuate 3,4-Dioxygenase Y408C Mutant (pdb code 1ykk). 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 Y408C Mutant, PDB code: 1ykk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1ykk

Go back to Iron Binding Sites List in 1ykk
Iron binding site 1 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:41.6
occ:1.00
 OH B:TYR447 1.9 42.4 1.0
NE2 B:HIS462 2.2 29.2 1.0
NE2 B:HIS460 2.4 24.2 1.0
O B:HOH680 2.5 31.5 1.0
CZ B:TYR447 2.8 37.6 1.0
CE1 B:HIS462 3.0 25.3 1.0
CE2 B:TYR447 3.1 38.1 1.0
CE1 B:HIS460 3.3 23.5 1.0
CD2 B:HIS462 3.3 23.9 1.0
O B:HOH686 3.3 42.3 1.0
CD2 B:HIS460 3.4 22.6 1.0
O B:HOH623 4.1 25.7 1.0
CE1 B:TYR447 4.1 37.2 1.0
ND1 B:HIS462 4.2 23.6 1.0
O B:HOH678 4.2 27.8 1.0
O A:HOH204 4.3 19.9 1.0
CG B:HIS462 4.3 24.8 1.0
ND1 B:HIS460 4.4 21.1 1.0
CG B:HIS460 4.5 22.9 1.0
CD2 B:TYR447 4.5 35.5 1.0
NH1 B:ARG457 4.7 29.8 1.0
O B:HOH685 5.0 61.0 1.0
CD2 A:TYR16 5.0 37.0 1.0

Iron binding site 2 out of 6 in 1ykk

Go back to Iron Binding Sites List in 1ykk
Iron binding site 2 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe600

b:38.2
occ:1.00
 OH D:TYR447 1.9 40.6 1.0
NE2 D:HIS462 2.1 23.1 1.0
NE2 D:HIS460 2.4 25.3 1.0
O D:HOH682 2.4 35.2 1.0
CE1 D:HIS462 2.9 23.1 1.0
CZ D:TYR447 3.0 35.5 1.0
CE1 D:HIS460 3.2 24.5 1.0
CD2 D:HIS462 3.2 21.4 1.0
O D:HOH688 3.3 47.1 1.0
CE2 D:TYR447 3.3 35.4 1.0
CD2 D:HIS460 3.4 24.3 1.0
ND1 D:HIS462 4.1 20.4 1.0
O C:HOH205 4.1 17.9 1.0
O D:HOH624 4.2 22.4 1.0
O D:HOH679 4.2 29.1 1.0
CE1 D:TYR447 4.2 34.2 1.0
CG D:HIS462 4.3 22.5 1.0
ND1 D:HIS460 4.4 26.1 1.0
CG D:HIS460 4.5 24.5 1.0
NH1 D:ARG457 4.6 23.5 1.0
CD2 D:TYR447 4.8 33.2 1.0
O D:HOH687 4.8 64.0 1.0
SG D:CYS408 4.9 38.8 0.5
CD2 C:TYR16 4.9 35.7 1.0

Iron binding site 3 out of 6 in 1ykk

Go back to Iron Binding Sites List in 1ykk
Iron binding site 3 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe600

b:44.9
occ:1.00
 OH F:TYR447 2.1 42.6 1.0
NE2 F:HIS460 2.2 25.6 1.0
NE2 F:HIS462 2.3 28.3 1.0
O F:HOH682 2.5 31.4 1.0
CZ F:TYR447 3.1 37.5 1.0
CE1 F:HIS460 3.1 26.3 1.0
CD2 F:HIS460 3.2 24.5 1.0
CD2 F:HIS462 3.3 25.1 1.0
CE1 F:HIS462 3.3 26.3 1.0
CE2 F:TYR447 3.4 37.2 1.0
O F:HOH689 3.5 46.5 1.0
O F:HOH621 3.9 25.5 1.0
O F:HOH679 4.2 33.8 1.0
ND1 F:HIS460 4.3 26.9 1.0
O E:HOH270 4.3 24.3 1.0
CG F:HIS460 4.4 24.8 1.0
CE1 F:TYR447 4.4 35.1 1.0
ND1 F:HIS462 4.4 25.1 1.0
CG F:HIS462 4.4 25.1 1.0
NH1 F:ARG457 4.4 26.8 1.0
O F:HOH688 4.6 66.0 1.0
CD2 F:TYR447 4.8 33.4 1.0
SG F:CYS408 4.9 41.5 0.5
OE1 F:GLN477 5.0 22.1 1.0

Iron binding site 4 out of 6 in 1ykk

Go back to Iron Binding Sites List in 1ykk
Iron binding site 4 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe600

b:45.0
occ:1.00
 OH H:TYR447 1.9 43.0 1.0
NE2 H:HIS462 2.3 27.6 1.0
NE2 H:HIS460 2.4 24.8 1.0
O H:HOH680 2.9 32.4 1.0
CZ H:TYR447 2.9 38.6 1.0
CE2 H:TYR447 3.1 38.4 1.0
CE1 H:HIS460 3.2 24.8 1.0
CE1 H:HIS462 3.3 26.2 1.0
O H:HOH686 3.3 44.4 1.0
CD2 H:HIS462 3.3 23.9 1.0
CD2 H:HIS460 3.4 23.2 1.0
O H:HOH623 4.1 31.1 1.0
CE1 H:TYR447 4.2 37.1 1.0
O G:HOH402 4.2 22.7 1.0
ND1 H:HIS460 4.3 23.6 1.0
ND1 H:HIS462 4.4 24.8 1.0
CG H:HIS460 4.5 23.3 1.0
CG H:HIS462 4.5 23.9 1.0
CD2 H:TYR447 4.5 35.8 1.0
O H:HOH685 4.7 68.1 1.0
NH1 H:ARG457 4.7 30.6 1.0
O H:HOH678 4.7 29.6 1.0
CD2 G:TYR16 4.9 38.4 1.0
SG H:CYS408 4.9 36.7 0.5

Iron binding site 5 out of 6 in 1ykk

Go back to Iron Binding Sites List in 1ykk
Iron binding site 5 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe600

b:51.1
occ:1.00
 OH J:TYR447 2.0 41.4 1.0
NE2 J:HIS460 2.2 26.7 1.0
NE2 J:HIS462 2.3 25.4 1.0
O J:HOH680 2.3 32.3 1.0
CZ J:TYR447 3.0 38.3 1.0
CE1 J:HIS462 3.1 25.8 1.0
CE2 J:TYR447 3.1 37.4 1.0
CE1 J:HIS460 3.1 26.7 1.0
CD2 J:HIS460 3.2 26.9 1.0
CD2 J:HIS462 3.3 23.6 1.0
O J:HOH686 3.5 42.2 1.0
O J:HOH623 3.9 26.3 1.0
O J:HOH685 4.3 65.8 1.0
ND1 J:HIS462 4.3 23.2 1.0
CE1 J:TYR447 4.3 36.4 1.0
ND1 J:HIS460 4.3 27.5 1.0
O J:HOH677 4.3 33.8 1.0
CG J:HIS460 4.3 25.6 1.0
CG J:HIS462 4.4 25.0 1.0
O I:HOH534 4.4 25.9 1.0
CD2 J:TYR447 4.5 35.2 1.0
NH1 J:ARG457 4.6 31.7 1.0
CD2 I:TYR16 4.8 38.1 1.0
SG J:CYS408 4.9 41.5 0.5

Iron binding site 6 out of 6 in 1ykk

Go back to Iron Binding Sites List in 1ykk
Iron binding site 6 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe600

b:46.3
occ:1.00
 OH L:TYR447 2.1 40.5 1.0
NE2 L:HIS462 2.2 28.2 1.0
NE2 L:HIS460 2.2 27.5 1.0
O L:HOH784 2.4 32.1 1.0
CE1 L:HIS462 3.1 26.6 1.0
CE1 L:HIS460 3.1 27.6 1.0
CD2 L:HIS460 3.2 26.7 1.0
CZ L:TYR447 3.2 36.9 1.0
CD2 L:HIS462 3.2 25.4 1.0
O L:HOH792 3.3 47.0 1.0
CE2 L:TYR447 3.5 36.9 1.0
O L:HOH700 4.1 24.1 1.0
O K:HOH666 4.2 26.0 1.0
ND1 L:HIS462 4.2 24.2 1.0
ND1 L:HIS460 4.2 26.8 1.0
CG L:HIS460 4.3 26.2 1.0
O L:HOH780 4.3 32.2 1.0
CG L:HIS462 4.3 26.7 1.0
O L:HOH791 4.4 71.2 1.0
CE1 L:TYR447 4.4 35.9 1.0
NH1 L:ARG457 4.5 27.6 1.0
CD2 L:TYR447 4.8 34.1 1.0
CD2 K:TYR16 4.9 38.0 1.0

Reference:

M.P.Valley, C.K.Brown, D.L.Burk, M.W.Vetting, D.H.Ohlendorf, J.D.Lipscomb. Roles of the Equatorial Tyrosyl Iron Ligand of Protocatechuate 3,4-Dioxygenase in Catalysis Biochemistry V. 44 11024 2005.
ISSN: ISSN 0006-2960
PubMed: 16101286
DOI: 10.1021/BI050902I
Page generated: Sun Dec 13 14:37:53 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy