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Iron in PDB 5ktt: Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound L-Malate and FE4S4 Cluster

Enzymatic activity of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound L-Malate and FE4S4 Cluster

All present enzymatic activity of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound L-Malate and FE4S4 Cluster:
2.5.1.72;

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound L-Malate and FE4S4 Cluster, PDB code: 5ktt 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) 29.94 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.333, 54.639, 55.613, 90.00, 90.79, 90.00
R / Rfree (%) 14.6 / 19.3

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound L-Malate and FE4S4 Cluster (pdb code 5ktt). 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 L-Malate and FE4S4 Cluster, PDB code: 5ktt:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5ktt

Go back to Iron Binding Sites List in 5ktt
Iron binding site 1 out of 4 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound L-Malate 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 L-Malate and FE4S4 Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:12.8
occ:1.00
 FE1 A:SF4401 0.0 12.8 1.0
S4 A:SF4401 2.3 13.7 1.0
S2 A:SF4401 2.3 12.8 1.0
S3 A:SF4401 2.3 13.0 1.0
SG A:CYS83 2.4 14.4 1.0
FE4 A:SF4401 2.6 13.6 1.0
FE3 A:SF4401 2.6 12.6 1.0
FE2 A:SF4401 2.7 13.0 1.0
CB A:CYS83 3.3 14.6 1.0
CA A:CYS83 3.7 14.1 1.0
S1 A:SF4401 3.8 12.3 1.0
C A:CYS83 4.2 14.3 1.0
N A:ALA84 4.2 15.4 1.0
O4B A:LMR402 4.3 18.8 1.0
N A:MET85 4.3 14.8 0.4
N A:MET85 4.4 13.8 0.6
CB A:MET85 4.4 14.5 0.4
CB A:MET85 4.5 13.6 0.6
CE2 A:PHE60 4.7 13.9 1.0
SG A:CYS256 4.8 14.2 1.0
SG A:CYS170 4.9 11.6 1.0
O4A A:LMR402 5.0 20.4 1.0
N A:CYS83 5.0 15.3 1.0
CA A:MET85 5.0 14.2 0.4

Iron binding site 2 out of 4 in 5ktt

Go back to Iron Binding Sites List in 5ktt
Iron binding site 2 out of 4 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound L-Malate 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 L-Malate and FE4S4 Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:13.0
occ:1.00
 FE2 A:SF4401 0.0 13.0 1.0
S1 A:SF4401 2.2 12.3 1.0
S3 A:SF4401 2.3 13.0 1.0
S4 A:SF4401 2.3 13.7 1.0
SG A:CYS256 2.4 14.2 1.0
FE4 A:SF4401 2.7 13.6 1.0
FE1 A:SF4401 2.7 12.8 1.0
FE3 A:SF4401 2.7 12.6 1.0
CB A:CYS256 3.4 12.3 1.0
S2 A:SF4401 3.9 12.8 1.0
CA A:CYS256 4.5 11.7 1.0
CG2 A:VAL172 4.5 13.1 1.0
O4B A:LMR402 4.5 18.8 1.0
CG A:MET259 4.8 14.6 1.0
SG A:CYS170 4.9 11.6 1.0
SG A:CYS83 4.9 14.4 1.0

Iron binding site 3 out of 4 in 5ktt

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Iron binding site 3 out of 4 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound L-Malate 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 L-Malate and FE4S4 Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:12.6
occ:1.00
 FE3 A:SF4401 0.0 12.6 1.0
S2 A:SF4401 2.2 12.8 1.0
S1 A:SF4401 2.3 12.3 1.0
S4 A:SF4401 2.3 13.7 1.0
SG A:CYS170 2.4 11.6 1.0
FE4 A:SF4401 2.6 13.6 1.0
FE1 A:SF4401 2.6 12.8 1.0
FE2 A:SF4401 2.7 13.0 1.0
CB A:CYS170 3.4 12.1 1.0
S3 A:SF4401 3.9 13.0 1.0
CA A:CYS170 4.3 12.2 1.0
OE1 A:GLU198 4.3 19.6 1.0
CG2 A:VAL172 4.3 13.1 1.0
O4A A:LMR402 4.4 20.4 1.0
CB A:VAL172 4.4 11.9 1.0
ND1 A:HIS173 4.6 11.0 1.0
O4B A:LMR402 4.7 18.8 1.0
SG A:CYS83 4.8 14.4 1.0
C A:CYS170 4.9 11.8 1.0
CB A:MET85 4.9 14.5 0.4
N A:VAL172 4.9 12.0 1.0
SG A:CYS256 4.9 14.2 1.0
CB A:MET85 4.9 13.6 0.6
CE1 A:HIS173 5.0 10.8 1.0
C4 A:LMR402 5.0 19.7 1.0

Iron binding site 4 out of 4 in 5ktt

Go back to Iron Binding Sites List in 5ktt
Iron binding site 4 out of 4 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound L-Malate 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 L-Malate and FE4S4 Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:13.6
occ:1.00
 FE4 A:SF4401 0.0 13.6 1.0
O4B A:LMR402 2.1 18.8 1.0
S1 A:SF4401 2.2 12.3 1.0
S3 A:SF4401 2.3 13.0 1.0
S2 A:SF4401 2.3 12.8 1.0
FE1 A:SF4401 2.6 12.8 1.0
FE3 A:SF4401 2.6 12.6 1.0
FE2 A:SF4401 2.7 13.0 1.0
O4A A:LMR402 2.7 20.4 1.0
C4 A:LMR402 2.8 19.7 1.0
S4 A:SF4401 3.8 13.7 1.0
C3 A:LMR402 4.2 16.9 1.0
CE2 A:TYR23 4.3 13.3 1.0
OE1 A:GLU198 4.6 19.6 1.0
SG A:CYS83 4.6 14.4 1.0
SG A:CYS170 4.7 11.6 1.0
SG A:CYS256 4.8 14.2 1.0
CD2 A:TYR23 4.8 14.0 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 04:01:15 2024

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