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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: Sun Dec 13 16:46:40 2020

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