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Iron in PDB 5ktm: Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with A Bound FE4S4 Cluster

Enzymatic activity of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with A Bound FE4S4 Cluster

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

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with A Bound FE4S4 Cluster, PDB code: 5ktm 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) 42.22 / 1.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.480, 52.877, 55.996, 90.00, 111.72, 90.00
R / Rfree (%) 17.1 / 21.5

Other elements in 5ktm:

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

Chlorine (Cl) 1 atom

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 5ktm

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

b:9.3
occ:1.00
 FE1 A:SF4401 0.0 9.3 1.0
S3 A:SF4401 2.2 11.1 1.0
S4 A:SF4401 2.2 8.9 1.0
S2 A:SF4401 2.2 10.3 1.0
SG A:CYS83 2.4 9.8 1.0
FE4 A:SF4401 2.6 12.3 1.0
FE3 A:SF4401 2.7 8.3 1.0
FE2 A:SF4401 2.7 9.4 1.0
CB A:CYS83 3.3 9.2 1.0
CA A:CYS83 3.7 9.3 1.0
S1 A:SF4401 3.8 9.2 1.0
N A:ALA84 4.2 9.6 1.0
C A:CYS83 4.2 10.1 1.0
N A:MET85 4.4 10.1 0.6
N A:MET85 4.4 11.2 0.4
CB A:MET85 4.4 12.9 0.6
CB A:MET85 4.4 14.5 0.4
CL A:CL402 4.6 14.3 1.0
O A:HOH613 4.6 18.0 1.0
CE2 A:PHE60 4.8 11.1 1.0
SG A:CYS256 4.8 10.5 1.0
SG A:CYS170 4.8 7.4 1.0

Iron binding site 2 out of 4 in 5ktm

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

b:9.4
occ:1.00
 FE2 A:SF4401 0.0 9.4 1.0
S3 A:SF4401 2.2 11.1 1.0
S1 A:SF4401 2.3 9.2 1.0
S4 A:SF4401 2.3 8.9 1.0
SG A:CYS256 2.4 10.5 1.0
FE1 A:SF4401 2.7 9.3 1.0
FE3 A:SF4401 2.7 8.3 1.0
FE4 A:SF4401 2.7 12.3 1.0
CB A:CYS256 3.4 8.0 1.0
S2 A:SF4401 3.9 10.3 1.0
O A:HOH613 3.9 18.0 1.0
CA A:CYS256 4.5 7.5 1.0
CG2 A:VAL172 4.6 10.5 1.0
CG A:MET259 4.6 8.6 1.0
CL A:CL402 4.8 14.3 1.0
SG A:CYS170 4.9 7.4 1.0
SG A:CYS83 4.9 9.8 1.0
CA A:CYS83 5.0 9.3 1.0

Iron binding site 3 out of 4 in 5ktm

Go back to Iron Binding Sites List in 5ktm
Iron binding site 3 out of 4 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with A Bound 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 A Bound FE4S4 Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:8.3
occ:1.00
 FE3 A:SF4401 0.0 8.3 1.0
S2 A:SF4401 2.3 10.3 1.0
S1 A:SF4401 2.3 9.2 1.0
S4 A:SF4401 2.3 8.9 1.0
SG A:CYS170 2.4 7.4 1.0
FE1 A:SF4401 2.7 9.3 1.0
FE2 A:SF4401 2.7 9.4 1.0
FE4 A:SF4401 2.8 12.3 1.0
CB A:CYS170 3.4 7.6 1.0
S3 A:SF4401 3.9 11.1 1.0
CA A:CYS170 4.3 8.7 1.0
OE1 A:GLU198 4.3 13.7 1.0
CG2 A:VAL172 4.4 10.5 1.0
CB A:VAL172 4.5 8.5 1.0
ND1 A:HIS173 4.6 11.0 1.0
SG A:CYS83 4.8 9.8 1.0
SG A:CYS256 4.8 10.5 1.0
C A:CYS170 4.9 8.2 1.0
CL A:CL402 4.9 14.3 1.0
N A:VAL172 4.9 8.4 1.0
CB A:MET85 5.0 12.9 0.6
CB A:MET85 5.0 14.5 0.4
CE1 A:HIS173 5.0 10.5 1.0

Iron binding site 4 out of 4 in 5ktm

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

b:12.3
occ:1.00
 FE4 A:SF4401 0.0 12.3 1.0
CL A:CL402 2.3 14.3 1.0
S3 A:SF4401 2.3 11.1 1.0
S2 A:SF4401 2.3 10.3 1.0
S1 A:SF4401 2.3 9.2 1.0
FE1 A:SF4401 2.6 9.3 1.0
FE2 A:SF4401 2.7 9.4 1.0
FE3 A:SF4401 2.8 8.3 1.0
S4 A:SF4401 3.9 8.9 1.0
CE2 A:TYR23 4.2 8.3 1.0
ND2 A:ASN111 4.3 26.8 1.0
CD2 A:TYR23 4.4 7.7 1.0
SG A:CYS83 4.6 9.8 1.0
CE A:MET259 4.7 8.2 1.0
SG A:CYS170 4.8 7.4 1.0
SG A:CYS256 4.8 10.5 1.0
O A:HOH680 4.9 22.7 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 03:43:10 2024

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