Iron in PDB 4wzc: Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao

Enzymatic activity of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao

All present enzymatic activity of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao:
1.13.11.6;

Protein crystallography data

The structure of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao, PDB code: 4wzc was solved by F.Liu, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.05 / 1.84
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.282, 58.282, 230.605, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 25.8

Iron Binding Sites:

The binding sites of Iron atom in the Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao (pdb code 4wzc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao, PDB code: 4wzc:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4wzc

Go back to Iron Binding Sites List in 4wzc
Iron binding site 1 out of 2 in the Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:23.2
occ:1.00
 O A:1UC203 1.7 26.3 0.9
NE2 A:HIS95 2.0 19.0 1.0
O3 A:1UC203 2.1 53.8 1.0
OE2 A:GLU57 2.2 24.6 1.0
ND1 A:HIS51 2.2 27.9 1.0
OE1 A:GLU57 2.6 23.6 1.0
C1 A:1UC203 2.7 51.1 1.0
CD A:GLU57 2.7 28.9 1.0
C6 A:1UC203 2.8 45.2 1.0
CE1 A:HIS95 2.9 21.6 1.0
HE1 A:HIS95 3.0 25.9 1.0
HB3 A:HIS51 3.0 33.9 1.0
CD2 A:HIS95 3.2 24.8 1.0
CG A:HIS51 3.2 28.4 1.0
CE1 A:HIS51 3.2 30.5 1.0
C2 A:1UC203 3.3 48.2 1.0
O1 A:1UC203 3.3 39.5 0.8
HE1 A:HIS51 3.4 36.6 1.0
HD2 A:HIS95 3.4 29.8 1.0
CB A:HIS51 3.5 28.3 1.0
HB2 A:HIS51 3.6 33.9 1.0
HB2 A:ASP53 3.7 34.8 1.0
O4 A:1UC203 3.8 59.9 1.0
C A:1UC203 3.8 51.7 1.0
ND1 A:HIS95 4.1 20.7 1.0
CG A:HIS95 4.2 19.8 1.0
CG A:GLU57 4.2 21.4 1.0
NE2 A:HIS51 4.3 30.9 1.0
CD2 A:HIS51 4.3 28.4 1.0
OD2 A:ASP53 4.4 24.2 1.0
OE1 A:GLU110 4.4 47.6 1.0
HG3 A:GLU57 4.5 25.7 1.0
HZ A:PHE59 4.5 30.7 1.0
CB A:ASP53 4.6 29.0 1.0
HG2 A:GLU57 4.6 25.7 1.0
C3 A:1UC203 4.7 44.0 1.0
N A:1UC203 4.7 42.5 0.3
HD1 A:HIS95 4.8 24.9 1.0
HB3 A:ASP53 4.9 34.8 1.0
HD23 A:LEU89 4.9 37.3 1.0
CA A:HIS51 4.9 25.6 1.0
C4 A:1UC203 5.0 47.2 1.0
CG A:ASP53 5.0 25.4 1.0

Iron binding site 2 out of 2 in 4wzc

Go back to Iron Binding Sites List in 4wzc
Iron binding site 2 out of 2 in the Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Understanding Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Catalytic Intermediates - 2,3-Cis-4,5-Trans Acms Bound to I142A Mutant Hao within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:40.2
occ:1.00
 SG A:CYS128 2.2 48.9 1.0
SG A:CYS125 2.3 40.8 1.0
SG A:CYS162 2.3 42.5 1.0
SG A:CYS165 2.4 47.5 1.0
HB3 A:CYS165 2.9 57.5 1.0
HB3 A:CYS125 2.9 50.4 1.0
CB A:CYS125 3.0 42.0 1.0
HB3 A:CYS162 3.0 43.5 1.0
H A:CYS128 3.0 51.0 1.0
HB2 A:CYS125 3.0 50.4 1.0
CB A:CYS162 3.1 36.3 1.0
HB2 A:CYS162 3.1 43.5 1.0
CB A:CYS165 3.2 47.9 1.0
HB3 A:CYS128 3.4 57.5 1.0
CB A:CYS128 3.4 47.9 1.0
HB3 A:ALA127 3.5 52.3 1.0
H A:CYS165 3.6 62.2 1.0
HB3 A:GLN167 3.6 53.0 1.0
N A:CYS128 3.7 42.5 1.0
HB2 A:CYS165 3.9 57.5 1.0
N A:CYS165 4.0 51.9 1.0
HD1 A:HIS164 4.0 73.7 1.0
CA A:CYS128 4.1 44.8 1.0
HB3 A:HIS164 4.1 70.1 1.0
CA A:CYS165 4.1 51.1 1.0
HB3 A:HIS130 4.1 55.0 1.0
H A:HIS130 4.1 50.9 1.0
HB2 A:CYS128 4.2 57.5 1.0
H A:GLN167 4.2 50.1 1.0
CB A:ALA127 4.5 43.5 1.0
CA A:CYS125 4.5 31.9 1.0
H A:ALA127 4.5 55.5 1.0
H A:GLY129 4.5 52.4 1.0
HB2 A:HIS130 4.5 55.0 1.0
CB A:GLN167 4.5 44.2 1.0
H A:HIS164 4.5 65.0 1.0
CA A:CYS162 4.6 40.4 1.0
C A:CYS165 4.7 47.2 1.0
HG2 A:GLN167 4.7 55.2 1.0
C A:ALA127 4.7 48.3 1.0
C A:CYS128 4.7 47.1 1.0
HB1 A:ALA127 4.8 52.3 1.0
CB A:HIS130 4.8 45.8 1.0
ND1 A:HIS164 4.8 61.4 1.0
O A:HOH396 4.8 37.8 1.0
H A:GLY166 4.8 50.0 1.0
N A:GLY129 4.8 43.7 1.0
HA A:CYS125 4.8 38.3 1.0
C A:HIS164 4.9 54.4 1.0
HB2 A:GLN167 4.9 53.0 1.0
HA A:CYS128 4.9 53.7 1.0
N A:GLN167 4.9 41.8 1.0
N A:HIS130 4.9 42.4 1.0
N A:GLY166 4.9 41.7 1.0
HA A:CYS165 4.9 61.3 1.0
HA A:CYS162 4.9 48.5 1.0
CA A:ALA127 4.9 50.9 1.0
CB A:HIS164 5.0 58.5 1.0
HG22 A:VAL132 5.0 39.9 1.0

Reference:

F.Liu, A.Liu. Probing Extradiol Dioxygenase Mechanism in Nad+ Biosynthesis By Viewing Reaction Cycle Intermediates To Be Published.
Page generated: Sun Dec 13 15:51:33 2020

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