Atomistry » Iron » PDB 6nlk-6o6l » 6nsu
Atomistry »
  Iron »
    PDB 6nlk-6o6l »
      6nsu »

Iron in PDB 6nsu: Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States

Enzymatic activity of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States

All present enzymatic activity of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States:
2.5.1.72;

Protein crystallography data

The structure of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States, PDB code: 6nsu was solved by O.A.Esakova, T.L.Grove, A.Silakov, N.H.Yennawar, S.J.Booker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.73 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.258, 52.298, 53.580, 90.00, 114.56, 90.00
R / Rfree (%) 21 / 24.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States (pdb code 6nsu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States, PDB code: 6nsu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6nsu

Go back to Iron Binding Sites List in 6nsu
Iron binding site 1 out of 4 in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:50.5
occ:1.00
 FE1 A:SF4401 0.0 50.5 1.0
OD1 A:DYA402 2.0 51.5 1.0
S4 A:SF4401 2.2 41.1 1.0
S3 A:SF4401 2.2 32.3 1.0
S2 A:SF4401 2.2 31.3 1.0
CG A:DYA402 2.7 51.6 1.0
OD2 A:DYA402 2.7 52.0 1.0
FE3 A:SF4401 3.1 28.5 1.0
FE2 A:SF4401 3.1 28.6 1.0
FE4 A:SF4401 3.1 25.7 1.0
S1 A:SF4401 3.8 39.0 1.0
CE2 A:TYR23 4.0 26.7 1.0
CB A:DYA402 4.1 52.9 1.0
ND2 A:ASN111 4.1 61.7 1.0
CD2 A:TYR23 4.3 25.5 1.0
OE1 A:GLU198 4.6 38.7 1.0
SG A:CYS170 4.9 26.5 1.0
OE2 A:GLU198 5.0 38.9 1.0
CE1 A:HIS173 5.0 27.1 1.0

Iron binding site 2 out of 4 in 6nsu

Go back to Iron Binding Sites List in 6nsu
Iron binding site 2 out of 4 in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:28.6
occ:1.00
 FE2 A:SF4401 0.0 28.6 1.0
S1 A:SF4401 2.2 39.0 1.0
S3 A:SF4401 2.2 32.3 1.0
S4 A:SF4401 2.2 41.1 1.0
SG A:CYS83 2.3 37.6 1.0
FE1 A:SF4401 3.1 50.5 1.0
FE4 A:SF4401 3.1 25.7 1.0
FE3 A:SF4401 3.1 28.5 1.0
CB A:CYS83 3.1 31.2 1.0
CA A:CYS83 3.6 29.9 1.0
S2 A:SF4401 3.8 31.3 1.0
C A:CYS83 4.2 32.2 1.0
N A:ALA84 4.2 33.8 1.0
N A:MET85 4.5 41.7 1.0
ND2 A:ASN111 4.5 61.7 1.0
CB A:MET85 4.6 48.1 1.0
CE2 A:PHE60 4.6 33.0 1.0
OD1 A:DYA402 4.6 51.5 1.0
N A:CYS83 4.9 26.2 1.0
OD2 A:DYA402 5.0 52.0 1.0

Iron binding site 3 out of 4 in 6nsu

Go back to Iron Binding Sites List in 6nsu
Iron binding site 3 out of 4 in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:28.5
occ:1.00
 FE3 A:SF4401 0.0 28.5 1.0
S2 A:SF4401 2.2 31.3 1.0
S4 A:SF4401 2.2 41.1 1.0
S1 A:SF4401 2.2 39.0 1.0
SG A:CYS170 2.3 26.5 1.0
FE1 A:SF4401 3.1 50.5 1.0
FE4 A:SF4401 3.1 25.7 1.0
FE2 A:SF4401 3.1 28.6 1.0
CB A:CYS170 3.3 24.7 1.0
S3 A:SF4401 3.8 32.3 1.0
CA A:CYS170 4.2 25.6 1.0
OE1 A:GLU198 4.2 38.7 1.0
CG2 A:VAL172 4.2 27.7 1.0
CB A:VAL172 4.3 27.0 1.0
ND1 A:HIS173 4.5 27.4 1.0
N A:VAL172 4.7 26.1 1.0
C A:CYS170 4.7 25.5 1.0
N A:TYR171 4.8 25.5 1.0
CE1 A:HIS173 4.8 27.1 1.0
OD2 A:DYA402 5.0 52.0 1.0

Iron binding site 4 out of 4 in 6nsu

Go back to Iron Binding Sites List in 6nsu
Iron binding site 4 out of 4 in the Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:25.7
occ:1.00
 FE4 A:SF4401 0.0 25.7 1.0
S2 A:SF4401 2.2 31.3 1.0
S1 A:SF4401 2.2 39.0 1.0
S3 A:SF4401 2.2 32.3 1.0
SG A:CYS256 2.3 28.2 1.0
FE2 A:SF4401 3.1 28.6 1.0
FE3 A:SF4401 3.1 28.5 1.0
FE1 A:SF4401 3.1 50.5 1.0
CB A:CYS256 3.1 25.4 1.0
S4 A:SF4401 3.8 41.1 1.0
CA A:CYS256 4.3 24.5 1.0
CG2 A:VAL172 4.4 27.7 1.0
OD1 A:DYA402 4.6 51.5 1.0
CG A:MET259 4.7 26.0 1.0

Reference:

O.A.Esakova, A.Silakov, T.L.Grove, D.M.Warui, N.H.Yennawar, S.J.Booker. An Unexpected Species Determined By X-Ray Crystallography That May Represent An Intermediate in the Reaction Catalyzed By Quinolinate Synthase. J.Am.Chem.Soc. V. 141 14142 2019.
ISSN: ESSN 1520-5126
PubMed: 31390192
DOI: 10.1021/JACS.9B02513
Page generated: Wed Aug 7 03:57:53 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy