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Iron in PDB 5ktn: Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster

Enzymatic activity of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster

All present enzymatic activity of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster:
2.5.1.72;

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster, PDB code: 5ktn was solved by M.K.Fenwick, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.64 / 1.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.303, 52.522, 55.544, 90.00, 112.20, 90.00
R / Rfree (%) 12.3 / 15.5

Other elements in 5ktn:

The structure of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster (pdb code 5ktn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster, PDB code: 5ktn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5ktn

Go back to Iron Binding Sites List in 5ktn
Iron binding site 1 out of 4 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:7.6
occ:1.00
 FE1 A:SF4401 0.0 7.6 1.0
S3 A:SF4401 2.2 9.2 1.0
S2 A:SF4401 2.3 8.4 1.0
S4 A:SF4401 2.3 8.6 1.0
SG A:CYS83 2.3 9.4 1.0
FE3 A:SF4401 2.7 7.3 1.0
FE2 A:SF4401 2.7 7.6 1.0
FE4 A:SF4401 2.7 8.9 1.0
CB A:CYS83 3.3 9.4 1.0
CA A:CYS83 3.7 9.9 1.0
S1 A:SF4401 3.8 7.4 1.0
ND2 A:ASN111 4.0 15.5 1.0
N A:ALA84 4.3 11.9 1.0
C A:CYS83 4.3 9.8 1.0
O2 A:13P402 4.4 15.2 1.0
N A:MET85 4.6 13.3 0.6
CB A:MET85 4.6 12.2 0.6
N A:MET85 4.6 14.0 0.4
CE2 A:PHE60 4.7 11.8 1.0
O3 A:13P402 4.7 10.4 1.0
SG A:CYS256 4.8 7.6 1.0
SG A:CYS170 4.8 7.2 1.0

Iron binding site 2 out of 4 in 5ktn

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Iron binding site 2 out of 4 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:7.6
occ:1.00
 FE2 A:SF4401 0.0 7.6 1.0
S1 A:SF4401 2.2 7.4 1.0
S3 A:SF4401 2.3 9.2 1.0
SG A:CYS256 2.3 7.6 1.0
S4 A:SF4401 2.3 8.6 1.0
FE1 A:SF4401 2.7 7.6 1.0
FE3 A:SF4401 2.7 7.3 1.0
FE4 A:SF4401 2.9 8.9 1.0
CB A:CYS256 3.3 6.9 1.0
S2 A:SF4401 3.9 8.4 1.0
O A:HOH521 4.1 18.6 1.0
CG2 A:VAL172 4.4 8.4 1.0
CA A:CYS256 4.4 6.6 1.0
CG A:MET259 4.7 7.2 1.0
O2 A:13P402 4.8 15.2 1.0
O3 A:13P402 4.8 10.4 1.0
SG A:CYS83 4.9 9.4 1.0
SG A:CYS170 4.9 7.2 1.0

Iron binding site 3 out of 4 in 5ktn

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Iron binding site 3 out of 4 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:7.3
occ:1.00
 FE3 A:SF4401 0.0 7.3 1.0
S2 A:SF4401 2.3 8.4 1.0
S1 A:SF4401 2.3 7.4 1.0
S4 A:SF4401 2.3 8.6 1.0
SG A:CYS170 2.3 7.2 1.0
FE1 A:SF4401 2.7 7.6 1.0
FE4 A:SF4401 2.7 8.9 1.0
FE2 A:SF4401 2.7 7.6 1.0
CB A:CYS170 3.4 7.3 1.0
O3 A:13P402 3.8 10.4 1.0
S3 A:SF4401 3.8 9.2 1.0
CG2 A:VAL172 4.1 8.4 1.0
OE1 A:GLU198 4.2 11.7 1.0
CA A:CYS170 4.3 7.5 1.0
CB A:VAL172 4.3 6.4 1.0
ND1 A:HIS173 4.6 7.2 1.0
SG A:CYS83 4.8 9.4 1.0
SG A:CYS256 4.8 7.6 1.0
N A:VAL172 4.8 7.1 1.0
C A:CYS170 4.8 7.1 1.0

Iron binding site 4 out of 4 in 5ktn

Go back to Iron Binding Sites List in 5ktn
Iron binding site 4 out of 4 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Dihydroxyacetone Phosphate (Dhap) and FE4S4 Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:8.9
occ:0.96
 FE4 A:SF4401 0.0 8.9 1.0
O3 A:13P402 2.2 10.4 1.0
S2 A:SF4401 2.3 8.4 1.0
O2 A:13P402 2.3 15.2 1.0
S1 A:SF4401 2.4 7.4 1.0
S3 A:SF4401 2.4 9.2 1.0
FE3 A:SF4401 2.7 7.3 1.0
FE1 A:SF4401 2.7 7.6 1.0
FE2 A:SF4401 2.9 7.6 1.0
C3 A:13P402 3.1 11.7 1.0
C2 A:13P402 3.1 13.0 1.0
S4 A:SF4401 4.0 8.6 1.0
OE1 A:GLU198 4.1 11.7 1.0
ND2 A:ASN111 4.1 15.5 1.0
CE2 A:TYR23 4.1 6.5 1.0
SG A:CYS170 4.5 7.2 1.0
C1 A:13P402 4.6 13.0 1.0
OE2 A:GLU198 4.7 9.7 1.0
CD2 A:TYR23 4.7 6.4 1.0
O A:HOH530 4.7 32.8 1.0
SG A:CYS83 4.7 9.4 1.0
CD A:GLU198 4.8 8.5 1.0
SG A:CYS256 5.0 7.6 1.0

Reference:

M.K.Fenwick, S.E.Ealick. Crystal Structures of the Iron-Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate. Biochemistry V. 55 4135 2016.
ISSN: ISSN 0006-2960
PubMed: 27404889
DOI: 10.1021/ACS.BIOCHEM.6B00626
Page generated: Tue Aug 6 03:44:22 2024

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