Atomistry » Iron » PDB 5kts-5lg8 » 5ktt
Atomistry »
  Iron »
    PDB 5kts-5lg8 »
      5ktt »

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

Go back to Iron Binding Sites List in 5ktt
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy