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Iron in PDB 4zk6: 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: 4zk6 was solved by O.A.Esakova, T.L.Grove, A.H.Saunders, 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) 48.59 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.562, 51.588, 97.541, 90.00, 94.95, 90.00
R / Rfree (%) 18.4 / 23.1

Other elements in 4zk6:

The structure of Crystallographic Capture of Quinolinate Synthase (Nada) From Pyrococcus Horikoshii in Its Substrates and Product-Bound States also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 4 atoms

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 4zk6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 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: 4zk6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4zk6

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Iron binding site 1 out of 8 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:15.5
occ:1.00
 FE1 A:SF4401 0.0 15.5 1.0
S3 A:SF4401 2.2 18.6 1.0
S4 A:SF4401 2.2 21.8 1.0
S2 A:SF4401 2.2 20.0 1.0
SG A:CYS83 2.5 20.2 1.0
FE2 A:SF4401 2.8 20.6 1.0
FE3 A:SF4401 2.9 15.0 1.0
FE4 A:SF4401 2.9 16.2 1.0
CB A:CYS83 3.2 17.5 1.0
CA A:CYS83 3.6 17.9 1.0
S1 A:SF4401 3.7 18.6 1.0
CB A:MET85 4.1 29.9 1.0
N A:ALA84 4.1 24.7 1.0
C A:CYS83 4.1 22.7 1.0
N A:MET85 4.2 24.4 1.0
O1 A:NTM402 4.2 31.5 1.0
O A:HOH536 4.5 29.4 1.0
ND2 A:ASN111 4.7 38.4 0.5
CA A:MET85 4.8 29.3 1.0
CE A:MET85 4.8 33.9 1.0
N1 A:NTM402 4.8 28.5 1.0
ND2 A:ASN111 4.9 37.7 0.5
N A:CYS83 5.0 16.6 1.0

Iron binding site 2 out of 8 in 4zk6

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Iron binding site 2 out of 8 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:20.6
occ:1.00
 FE2 A:SF4401 0.0 20.6 1.0
S4 A:SF4401 2.2 21.8 1.0
S1 A:SF4401 2.2 18.6 1.0
S3 A:SF4401 2.2 18.6 1.0
N1 A:NTM402 2.3 28.5 1.0
O1 A:NTM402 2.5 31.5 1.0
FE1 A:SF4401 2.8 15.5 1.0
FE4 A:SF4401 3.0 16.2 1.0
FE3 A:SF4401 3.0 15.0 1.0
C2 A:NTM402 3.2 28.4 1.0
C6 A:NTM402 3.2 27.0 1.0
C7 A:NTM402 3.2 31.5 1.0
S2 A:SF4401 3.9 20.0 1.0
CE2 A:TYR23 4.3 16.6 1.0
O2 A:NTM402 4.4 32.3 1.0
C3 A:NTM402 4.5 29.3 1.0
C5 A:NTM402 4.5 27.4 1.0
CD2 A:TYR23 4.5 14.7 1.0
CE A:MET259 4.6 19.8 1.0
ND2 A:ASN111 4.7 38.4 0.5
SG A:CYS83 4.8 20.2 1.0
ND2 A:ASN111 4.9 37.7 0.5

Iron binding site 3 out of 8 in 4zk6

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Iron binding site 3 out of 8 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:15.0
occ:1.00
 FE3 A:SF4401 0.0 15.0 1.0
S4 A:SF4401 2.2 21.8 1.0
S1 A:SF4401 2.2 18.6 1.0
S2 A:SF4401 2.2 20.0 1.0
SG A:CYS256 2.4 14.7 1.0
FE4 A:SF4401 2.8 16.2 1.0
FE1 A:SF4401 2.9 15.5 1.0
FE2 A:SF4401 3.0 20.6 1.0
CB A:CYS256 3.3 16.1 1.0
S3 A:SF4401 3.7 18.6 1.0
O A:HOH536 3.9 29.4 1.0
CA A:CYS256 4.4 15.3 1.0
CG A:MET259 4.6 14.3 1.0
CG2 A:VAL172 4.7 26.1 1.0
O1 A:NTM402 5.0 31.5 1.0

Iron binding site 4 out of 8 in 4zk6

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Iron binding site 4 out of 8 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:16.2
occ:1.00
 FE4 A:SF4401 0.0 16.2 1.0
S3 A:SF4401 2.2 18.6 1.0
S1 A:SF4401 2.2 18.6 1.0
S2 A:SF4401 2.2 20.0 1.0
SG A:CYS170 2.5 19.9 1.0
FE3 A:SF4401 2.8 15.0 1.0
FE1 A:SF4401 2.9 15.5 1.0
FE2 A:SF4401 3.0 20.6 1.0
CB A:CYS170 3.2 19.9 1.0
S4 A:SF4401 3.7 21.8 1.0
CA A:CYS170 4.2 21.3 1.0
C6 A:NTM402 4.4 27.0 1.0
N1 A:NTM402 4.4 28.5 1.0
CG2 A:VAL172 4.4 26.1 1.0
CB A:VAL172 4.5 23.0 1.0
OE1 A:GLU198 4.6 38.0 1.0
ND1 A:HIS173 4.7 15.7 1.0
C A:CYS170 4.7 20.4 1.0
CB A:MET85 4.9 29.9 1.0
N A:VAL172 4.9 18.7 1.0
N A:TYR171 4.9 21.5 1.0

Iron binding site 5 out of 8 in 4zk6

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Iron binding site 5 out of 8 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 5 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
B:Fe401

b:32.9
occ:1.00
 FE1 B:SF4401 0.0 32.9 1.0
S3 B:SF4401 2.2 32.0 1.0
S2 B:SF4401 2.2 36.7 1.0
S4 B:SF4401 2.2 29.5 1.0
N1 B:NTM402 2.3 28.2 0.9
O2 B:NTM402 2.5 29.1 0.9
FE4 B:SF4401 2.9 25.3 1.0
FE2 B:SF4401 3.0 20.2 1.0
FE3 B:SF4401 3.0 26.2 1.0
C2 B:NTM402 3.1 29.0 0.9
C7 B:NTM402 3.1 28.7 0.9
C6 B:NTM402 3.2 29.9 0.9
S1 B:SF4401 3.8 33.7 1.0
O1 B:NTM402 4.3 29.1 0.9
CE2 B:TYR23 4.4 27.4 1.0
C3 B:NTM402 4.4 29.4 0.9
OH B:TYR109 4.4 60.4 1.0
C5 B:NTM402 4.4 29.3 0.9
CD2 B:TYR23 4.7 23.6 1.0
CE B:MET259 4.7 20.2 1.0
ND2 B:ASN111 4.8 60.5 1.0
SG B:CYS83 4.9 29.4 1.0
C4 B:NTM402 4.9 29.4 0.9

Iron binding site 6 out of 8 in 4zk6

Go back to Iron Binding Sites List in 4zk6
Iron binding site 6 out of 8 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 6 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
B:Fe401

b:20.2
occ:1.00
 FE2 B:SF4401 0.0 20.2 1.0
S4 B:SF4401 2.2 29.5 1.0
S3 B:SF4401 2.2 32.0 1.0
S1 B:SF4401 2.2 33.7 1.0
SG B:CYS170 2.5 19.4 1.0
FE3 B:SF4401 2.9 26.2 1.0
FE1 B:SF4401 3.0 32.9 1.0
FE4 B:SF4401 3.0 25.3 1.0
CB B:CYS170 3.2 20.0 1.0
S2 B:SF4401 3.7 36.7 1.0
CA B:CYS170 4.2 20.7 1.0
C6 B:NTM402 4.2 29.9 0.9
N1 B:NTM402 4.3 28.2 0.9
CG2 B:VAL172 4.4 22.3 1.0
CB B:VAL172 4.6 19.9 1.0
OE1 B:GLU198 4.6 44.6 1.0
ND1 B:HIS173 4.6 16.9 1.0
C B:CYS170 4.8 20.8 1.0
N B:TYR171 4.9 22.1 1.0
N B:VAL172 5.0 20.8 1.0

Iron binding site 7 out of 8 in 4zk6

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Iron binding site 7 out of 8 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 7 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
B:Fe401

b:26.2
occ:1.00
 FE3 B:SF4401 0.0 26.2 1.0
S2 B:SF4401 2.2 36.7 1.0
S4 B:SF4401 2.2 29.5 1.0
S1 B:SF4401 2.2 33.7 1.0
SG B:CYS256 2.5 25.6 1.0
FE2 B:SF4401 2.9 20.2 1.0
FE1 B:SF4401 3.0 32.9 1.0
FE4 B:SF4401 3.0 25.3 1.0
CB B:CYS256 3.3 27.2 1.0
S3 B:SF4401 3.8 32.0 1.0
O B:HOH540 4.1 22.8 1.0
CA B:CYS256 4.5 25.0 1.0
CG2 B:VAL172 4.5 22.3 1.0
CG B:MET259 4.6 20.4 1.0
O2 B:NTM402 4.9 29.1 0.9

Iron binding site 8 out of 8 in 4zk6

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Iron binding site 8 out of 8 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 8 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
B:Fe401

b:25.3
occ:1.00
 FE4 B:SF4401 0.0 25.3 1.0
S2 B:SF4401 2.2 36.7 1.0
S3 B:SF4401 2.2 32.0 1.0
S1 B:SF4401 2.2 33.7 1.0
SG B:CYS83 2.5 29.4 1.0
FE1 B:SF4401 2.9 32.9 1.0
FE2 B:SF4401 3.0 20.2 1.0
FE3 B:SF4401 3.0 26.2 1.0
CB B:CYS83 3.2 23.6 1.0
CA B:CYS83 3.5 24.1 1.0
S4 B:SF4401 3.8 29.5 1.0
N B:ALA84 3.8 28.2 1.0
C B:CYS83 4.0 25.6 1.0
N B:MET85 4.2 34.0 1.0
O2 B:NTM402 4.3 29.1 0.9
CB B:MET85 4.5 37.5 1.0
ND2 B:ASN111 4.6 60.5 1.0
O B:HOH540 4.7 22.8 1.0
N B:CYS83 4.8 23.0 1.0
N1 B:NTM402 4.9 28.2 0.9
O B:CYS83 4.9 25.6 1.0
CA B:ALA84 4.9 32.1 1.0
CA B:MET85 5.0 36.4 1.0

Reference:

O.A.Esakova, A.Silakov, T.L.Grove, A.H.Saunders, M.I.Mclaughlin, N.H.Yennawar, S.J.Booker. Structure of Quinolinate Synthase From Pyrococcus Horikoshii in the Presence of Its Product, Quinolinic Acid. J.Am.Chem.Soc. V. 138 7224 2016.
ISSN: ESSN 1520-5126
PubMed: 27224840
DOI: 10.1021/JACS.6B02708
Page generated: Mon Aug 5 18:14:38 2024

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