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Iron in PDB 4njg: Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin

Enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin

All present enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin:
4.3.99.3;

Protein crystallography data

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin, PDB code: 4njg was solved by D.P.Dowling, N.A.Bruender, A.P.Young, R.M.Mccarty, V.Bandarian, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.16 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.956, 118.956, 101.952, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin (pdb code 4njg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin, PDB code: 4njg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4njg

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Iron binding site 1 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin


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 Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:46.1
occ:1.00
 FE1 A:SF4301 0.0 46.1 1.0
S3 A:SF4301 2.3 48.3 1.0
SG A:CYS46 2.3 55.5 1.0
S2 A:SF4301 2.3 48.2 1.0
S4 A:SF4301 2.3 46.7 1.0
FE4 A:SF4301 2.7 47.4 1.0
FE2 A:SF4301 2.7 51.2 1.0
FE3 A:SF4301 2.7 49.0 1.0
CB A:CYS46 3.1 47.4 1.0
CE A:LYS135 3.7 48.6 1.0
S1 A:SF4301 3.9 50.4 1.0
CB A:CYS49 4.2 52.2 1.0
O A:SAM302 4.3 45.4 1.0
SG A:CYS49 4.5 47.5 1.0
CD A:LYS135 4.5 47.1 1.0
CA A:CYS46 4.5 47.9 1.0
SG A:CYS31 4.7 58.5 1.0
NZ A:LYS135 4.8 49.0 1.0
CG A:LYS135 4.8 46.9 1.0
O A:CYS46 4.8 46.8 1.0
C A:CYS46 4.9 47.6 1.0
N A:SAM302 4.9 39.3 1.0
CB A:LEU33 4.9 49.9 1.0

Iron binding site 2 out of 8 in 4njg

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Iron binding site 2 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin


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 Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:51.2
occ:1.00
 FE2 A:SF4301 0.0 51.2 1.0
S1 A:SF4301 2.3 50.4 1.0
S4 A:SF4301 2.3 46.7 1.0
S3 A:SF4301 2.3 48.3 1.0
SG A:CYS49 2.3 47.5 1.0
FE4 A:SF4301 2.7 47.4 1.0
FE1 A:SF4301 2.7 46.1 1.0
FE3 A:SF4301 2.7 49.0 1.0
CB A:CYS49 3.1 52.2 1.0
S2 A:SF4301 3.9 48.2 1.0
CE A:SAM302 3.9 55.7 1.0
CE1 A:PHE53 4.0 58.5 1.0
CA A:CYS49 4.2 53.1 1.0
SD A:SAM302 4.4 54.3 1.0
N A:SAM302 4.4 39.3 1.0
CD1 A:PHE53 4.6 58.0 1.0
SG A:CYS46 4.6 55.5 1.0
CZ A:PHE53 4.7 60.2 1.0
O A:SAM302 4.9 45.4 1.0
CE3 A:TRP34 4.9 56.0 1.0
SG A:CYS31 4.9 58.5 1.0
CG A:SAM302 5.0 35.4 1.0
C8 A:SAM302 5.0 46.3 1.0
N A:GLY92 5.0 57.9 1.0

Iron binding site 3 out of 8 in 4njg

Go back to Iron Binding Sites List in 4njg
Iron binding site 3 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin


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 Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:49.0
occ:1.00
 FE3 A:SF4301 0.0 49.0 1.0
O A:SAM302 2.3 45.4 1.0
S1 A:SF4301 2.3 50.4 1.0
S2 A:SF4301 2.3 48.2 1.0
S4 A:SF4301 2.3 46.7 1.0
N A:SAM302 2.3 39.3 1.0
FE2 A:SF4301 2.7 51.2 1.0
FE4 A:SF4301 2.7 47.4 1.0
FE1 A:SF4301 2.7 46.1 1.0
C A:SAM302 3.0 43.5 1.0
CA A:SAM302 3.1 38.5 1.0
SD A:SAM302 3.4 54.3 1.0
CG A:SAM302 3.7 35.4 1.0
S3 A:SF4301 3.9 48.3 1.0
CB A:SAM302 4.0 36.0 1.0
CE A:LYS135 4.2 48.6 1.0
CE A:SAM302 4.2 55.7 1.0
OXT A:SAM302 4.2 40.1 1.0
NZ A:LYS135 4.3 49.0 1.0
O A:GLY92 4.6 52.2 1.0
SG A:CYS31 4.6 58.5 1.0
CB A:ASN118 4.8 49.2 1.0
SG A:CYS46 4.8 55.5 1.0
C2' A:SAM302 4.8 54.9 1.0
SG A:CYS49 4.9 47.5 1.0
ND2 A:ASN118 4.9 51.8 1.0

Iron binding site 4 out of 8 in 4njg

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Iron binding site 4 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin


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 Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:47.4
occ:1.00
 FE4 A:SF4301 0.0 47.4 1.0
S3 A:SF4301 2.3 48.3 1.0
S2 A:SF4301 2.3 48.2 1.0
S1 A:SF4301 2.3 50.4 1.0
SG A:CYS31 2.3 58.5 1.0
FE1 A:SF4301 2.7 46.1 1.0
FE2 A:SF4301 2.7 51.2 1.0
FE3 A:SF4301 2.7 49.0 1.0
CB A:CYS31 3.4 55.7 1.0
N A:SAM302 3.7 39.3 1.0
S4 A:SF4301 3.9 46.7 1.0
CZ A:PHE53 4.6 60.2 1.0
CE1 A:PHE53 4.6 58.5 1.0
CB A:LEU33 4.7 49.9 1.0
O A:SAM302 4.7 45.4 1.0
CA A:CYS31 4.8 58.7 1.0
ND2 A:ASN118 4.8 51.8 1.0
SG A:CYS49 4.8 47.5 1.0
C A:GLY92 4.8 55.9 1.0
SG A:CYS46 4.9 55.5 1.0
N A:TRP34 4.9 57.2 1.0
O A:GLY92 4.9 52.2 1.0
N A:LEU33 5.0 55.4 1.0
CB A:TRP34 5.0 56.0 1.0
CB A:CYS46 5.0 47.4 1.0

Iron binding site 5 out of 8 in 4njg

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Iron binding site 5 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:42.6
occ:1.00
 FE1 B:SF4301 0.0 42.6 1.0
S2 B:SF4301 2.3 39.2 1.0
S3 B:SF4301 2.3 45.5 1.0
SG B:CYS46 2.3 46.0 1.0
S4 B:SF4301 2.3 41.6 1.0
FE4 B:SF4301 2.7 45.1 1.0
FE3 B:SF4301 2.7 45.3 1.0
FE2 B:SF4301 2.7 44.3 1.0
CB B:CYS46 3.2 45.2 1.0
CE B:LYS135 3.7 43.5 1.0
S1 B:SF4301 3.9 43.7 1.0
CB B:CYS49 4.2 48.3 1.0
O B:SAM302 4.2 41.2 1.0
CD B:LYS135 4.5 43.9 1.0
SG B:CYS49 4.5 54.4 1.0
CA B:CYS46 4.6 47.3 1.0
N B:SAM302 4.6 23.0 1.0
NZ B:LYS135 4.6 42.7 1.0
CG B:LYS135 4.7 44.6 1.0
SG B:CYS31 4.7 57.4 1.0
O B:CYS46 4.8 47.9 1.0
C B:CYS46 4.9 48.4 1.0
CB B:LEU33 4.9 52.5 1.0

Iron binding site 6 out of 8 in 4njg

Go back to Iron Binding Sites List in 4njg
Iron binding site 6 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:44.3
occ:1.00
 FE2 B:SF4301 0.0 44.3 1.0
S1 B:SF4301 2.3 43.7 1.0
S4 B:SF4301 2.3 41.6 1.0
S3 B:SF4301 2.3 45.5 1.0
SG B:CYS49 2.3 54.4 1.0
FE4 B:SF4301 2.7 45.1 1.0
FE3 B:SF4301 2.7 45.3 1.0
FE1 B:SF4301 2.7 42.6 1.0
CB B:CYS49 3.1 48.3 1.0
CE1 B:PHE53 3.7 51.3 1.0
S2 B:SF4301 3.9 39.2 1.0
CE B:SAM302 3.9 45.9 1.0
CA B:CYS49 4.2 49.0 1.0
N B:SAM302 4.3 23.0 1.0
CD1 B:PHE53 4.4 52.1 1.0
SD B:SAM302 4.4 54.3 1.0
CZ B:PHE53 4.6 51.9 1.0
SG B:CYS46 4.7 46.0 1.0
SG B:CYS31 4.9 57.4 1.0
CE3 B:TRP34 4.9 57.2 1.0
O B:SAM302 4.9 41.2 1.0
CG B:SAM302 4.9 24.7 1.0

Iron binding site 7 out of 8 in 4njg

Go back to Iron Binding Sites List in 4njg
Iron binding site 7 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:45.3
occ:1.00
 FE3 B:SF4301 0.0 45.3 1.0
N B:SAM302 2.1 23.0 1.0
S4 B:SF4301 2.3 41.6 1.0
S1 B:SF4301 2.3 43.7 1.0
S2 B:SF4301 2.3 39.2 1.0
O B:SAM302 2.3 41.2 1.0
FE4 B:SF4301 2.7 45.1 1.0
FE2 B:SF4301 2.7 44.3 1.0
FE1 B:SF4301 2.7 42.6 1.0
CA B:SAM302 3.0 27.5 1.0
C B:SAM302 3.0 38.7 1.0
SD B:SAM302 3.3 54.3 1.0
CG B:SAM302 3.6 24.7 1.0
CB B:SAM302 3.9 27.0 1.0
S3 B:SF4301 3.9 45.5 1.0
CE B:SAM302 4.0 45.9 1.0
CE B:LYS135 4.2 43.5 1.0
OXT B:SAM302 4.2 35.4 1.0
NZ B:LYS135 4.2 42.7 1.0
O B:GLY92 4.4 49.5 1.0
SG B:CYS31 4.6 57.4 1.0
C2' B:SAM302 4.8 46.5 1.0
SG B:CYS46 4.8 46.0 1.0
CB B:ASN118 4.8 40.8 1.0
SG B:CYS49 4.8 54.4 1.0

Iron binding site 8 out of 8 in 4njg

Go back to Iron Binding Sites List in 4njg
Iron binding site 8 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxypterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:45.1
occ:1.00
 FE4 B:SF4301 0.0 45.1 1.0
S3 B:SF4301 2.3 45.5 1.0
SG B:CYS31 2.3 57.4 1.0
S2 B:SF4301 2.3 39.2 1.0
S1 B:SF4301 2.3 43.7 1.0
FE1 B:SF4301 2.7 42.6 1.0
FE2 B:SF4301 2.7 44.3 1.0
FE3 B:SF4301 2.7 45.3 1.0
CB B:CYS31 3.3 47.7 1.0
N B:SAM302 3.5 23.0 1.0
S4 B:SF4301 3.9 41.6 1.0
CE1 B:PHE53 4.4 51.3 1.0
CZ B:PHE53 4.5 51.9 1.0
CB B:LEU33 4.6 52.5 1.0
O B:GLY92 4.7 49.5 1.0
CA B:CYS31 4.7 49.9 1.0
ND2 B:ASN118 4.7 43.5 1.0
C B:GLY92 4.8 50.7 1.0
O B:SAM302 4.8 41.2 1.0
SG B:CYS46 4.8 46.0 1.0
SG B:CYS49 4.9 54.4 1.0
CA B:SAM302 4.9 27.5 1.0
N B:TRP34 4.9 55.4 1.0
N B:LEU33 5.0 52.7 1.0
CB B:TRP34 5.0 57.0 1.0
CB B:CYS46 5.0 45.2 1.0

Reference:

D.P.Dowling, N.A.Bruender, A.P.Young, R.M.Mccarty, V.Bandarian, C.L.Drennan. Radical Sam Enzyme Quee Defines A New Minimal Core Fold and Metal-Dependent Mechanism. Nat.Chem.Biol. V. 10 106 2014.
ISSN: ISSN 1552-4450
PubMed: 24362703
DOI: 10.1038/NCHEMBIO.1426
Page generated: Mon Aug 5 07:38:56 2024

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