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Iron in PDB 4njh: Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin

Enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin

All present enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin:
4.3.99.3;

Protein crystallography data

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin, PDB code: 4njh 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) 39.01 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.129, 119.129, 103.363, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.4

Other elements in 4njh:

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin (pdb code 4njh). 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-Carboxy-5,6,7,8-Tetrahydropterin, PDB code: 4njh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4njh

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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-Carboxy-5,6,7,8-Tetrahydropterin


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-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:21.8
occ:1.00
 FE1 A:SF4301 0.0 21.8 1.0
S2 A:SF4301 2.3 21.3 1.0
S3 A:SF4301 2.3 21.0 1.0
S4 A:SF4301 2.3 22.1 1.0
SG A:CYS46 2.3 22.8 1.0
FE2 A:SF4301 2.7 22.9 1.0
FE4 A:SF4301 2.7 22.6 1.0
FE3 A:SF4301 2.8 22.4 1.0
CB A:CYS46 3.2 20.3 1.0
CE A:LYS135 3.7 29.9 1.0
S1 A:SF4301 3.9 23.1 1.0
O A:SAM302 4.3 24.2 1.0
CB A:CYS49 4.3 23.6 1.0
SG A:CYS49 4.5 26.6 1.0
CD A:LYS135 4.6 27.3 1.0
CA A:CYS46 4.6 23.1 1.0
NZ A:LYS135 4.6 24.8 1.0
SG A:CYS31 4.7 25.0 1.0
CG A:LYS135 4.7 26.6 1.0
O A:CYS46 4.9 26.6 1.0
CB A:LEU33 4.9 21.5 1.0
C A:CYS46 4.9 21.4 1.0
CA A:CYS49 5.0 21.8 1.0
N A:SAM302 5.0 30.2 1.0

Iron binding site 2 out of 8 in 4njh

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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-Carboxy-5,6,7,8-Tetrahydropterin


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-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:22.9
occ:1.00
 FE2 A:SF4301 0.0 22.9 1.0
S1 A:SF4301 2.3 23.1 1.0
S4 A:SF4301 2.3 22.1 1.0
SG A:CYS49 2.3 26.6 1.0
S3 A:SF4301 2.3 21.0 1.0
FE1 A:SF4301 2.7 21.8 1.0
FE4 A:SF4301 2.7 22.6 1.0
FE3 A:SF4301 2.8 22.4 1.0
CB A:CYS49 3.1 23.6 1.0
CE1 A:PHE53 3.9 23.9 1.0
S2 A:SF4301 3.9 21.3 1.0
CE A:SAM302 4.0 29.8 1.0
CA A:CYS49 4.1 21.8 1.0
SD A:SAM302 4.3 27.8 1.0
CD1 A:PHE53 4.4 27.3 1.0
SG A:CYS46 4.6 22.8 1.0
N A:SAM302 4.7 30.2 1.0
O A:SAM302 4.8 24.2 1.0
CZ A:PHE53 4.9 27.4 1.0
CE3 A:TRP34 4.9 21.2 1.0
CG A:SAM302 4.9 25.6 1.0
SG A:CYS31 4.9 25.0 1.0

Iron binding site 3 out of 8 in 4njh

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Iron binding site 3 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin


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-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:22.4
occ:1.00
 FE3 A:SF4301 0.0 22.4 1.0
O A:SAM302 2.2 24.2 1.0
S1 A:SF4301 2.3 23.1 1.0
S4 A:SF4301 2.3 22.1 1.0
S2 A:SF4301 2.3 21.3 1.0
N A:SAM302 2.4 30.2 1.0
FE4 A:SF4301 2.7 22.6 1.0
FE1 A:SF4301 2.8 21.8 1.0
FE2 A:SF4301 2.8 22.9 1.0
C A:SAM302 3.1 19.3 1.0
CA A:SAM302 3.2 25.6 1.0
SD A:SAM302 3.3 27.8 1.0
CG A:SAM302 3.5 25.6 1.0
S3 A:SF4301 3.9 21.0 1.0
CB A:SAM302 3.9 19.5 1.0
CE A:SAM302 4.2 29.8 1.0
NZ A:LYS135 4.2 24.8 1.0
CE A:LYS135 4.2 29.9 1.0
OXT A:SAM302 4.3 22.9 1.0
O A:GLY92 4.5 23.9 1.0
SG A:CYS31 4.5 25.0 1.0
CB A:ASN118 4.7 18.5 1.0
C2' A:SAM302 4.8 19.6 1.0
ND2 A:ASN118 4.9 22.4 1.0
SG A:CYS46 4.9 22.8 1.0
SG A:CYS49 5.0 26.6 1.0
C5' A:SAM302 5.0 32.3 1.0

Iron binding site 4 out of 8 in 4njh

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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-Carboxy-5,6,7,8-Tetrahydropterin


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-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:22.6
occ:1.00
 FE4 A:SF4301 0.0 22.6 1.0
S3 A:SF4301 2.2 21.0 1.0
S2 A:SF4301 2.3 21.3 1.0
SG A:CYS31 2.3 25.0 1.0
S1 A:SF4301 2.3 23.1 1.0
FE1 A:SF4301 2.7 21.8 1.0
FE3 A:SF4301 2.7 22.4 1.0
FE2 A:SF4301 2.7 22.9 1.0
CB A:CYS31 3.3 25.6 1.0
S4 A:SF4301 3.8 22.1 1.0
N A:SAM302 3.9 30.2 1.0
CE1 A:PHE53 4.2 23.9 1.0
CZ A:PHE53 4.5 27.4 1.0
CB A:LEU33 4.6 21.5 1.0
CA A:CYS31 4.7 24.0 1.0
O A:SAM302 4.8 24.2 1.0
ND2 A:ASN118 4.8 22.4 1.0
SG A:CYS49 4.8 26.6 1.0
C A:GLY92 4.8 22.6 1.0
SG A:CYS46 4.8 22.8 1.0
N A:TRP34 4.9 26.5 1.0
CB A:CYS46 4.9 20.3 1.0
O A:GLY92 4.9 23.9 1.0
N A:LEU33 4.9 24.4 1.0
CD1 A:PHE53 5.0 27.3 1.0
CB A:TRP34 5.0 25.1 1.0

Iron binding site 5 out of 8 in 4njh

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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-Carboxy-5,6,7,8-Tetrahydropterin


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-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:20.8
occ:1.00
 FE1 B:SF4301 0.0 20.8 1.0
SG B:CYS46 2.2 22.9 1.0
S2 B:SF4301 2.3 22.1 1.0
S3 B:SF4301 2.3 23.0 1.0
S4 B:SF4301 2.3 20.1 1.0
FE4 B:SF4301 2.7 21.7 1.0
FE2 B:SF4301 2.7 21.6 1.0
FE3 B:SF4301 2.8 21.3 1.0
CB B:CYS46 3.1 23.4 1.0
CE B:LYS135 3.6 28.7 1.0
S1 B:SF4301 3.9 21.8 1.0
O B:SAM302 4.2 21.3 1.0
CB B:CYS49 4.3 26.6 1.0
NZ B:LYS135 4.5 20.6 1.0
SG B:CYS49 4.5 25.8 1.0
CA B:CYS46 4.5 25.4 1.0
CD B:LYS135 4.5 27.3 1.0
N B:SAM302 4.6 26.3 1.0
CG B:LYS135 4.7 28.4 1.0
SG B:CYS31 4.7 25.3 1.0
O B:CYS46 4.8 26.3 1.0
C B:CYS46 4.9 22.9 1.0
CA B:CYS49 4.9 26.2 1.0
CB B:LEU33 4.9 21.3 1.0

Iron binding site 6 out of 8 in 4njh

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Iron binding site 6 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin


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-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:21.6
occ:1.00
 FE2 B:SF4301 0.0 21.6 1.0
S1 B:SF4301 2.2 21.8 1.0
SG B:CYS49 2.3 25.8 1.0
S4 B:SF4301 2.3 20.1 1.0
S3 B:SF4301 2.3 23.0 1.0
FE1 B:SF4301 2.7 20.8 1.0
FE4 B:SF4301 2.7 21.7 1.0
FE3 B:SF4301 2.8 21.3 1.0
CB B:CYS49 3.1 26.6 1.0
CE1 B:PHE53 3.8 23.5 1.0
S2 B:SF4301 3.9 22.1 1.0
CE B:SAM302 4.0 29.6 1.0
CA B:CYS49 4.1 26.2 1.0
N B:SAM302 4.3 26.3 1.0
SD B:SAM302 4.3 23.8 1.0
CD1 B:PHE53 4.4 26.1 1.0
SG B:CYS46 4.5 22.9 1.0
O B:SAM302 4.8 21.3 1.0
CZ B:PHE53 4.8 28.4 1.0
CE3 B:TRP34 4.9 26.8 1.0
CG B:SAM302 4.9 18.4 1.0
SG B:CYS31 5.0 25.3 1.0
N B:CYS49 5.0 25.5 1.0

Iron binding site 7 out of 8 in 4njh

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Iron binding site 7 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin


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-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:21.3
occ:1.00
 FE3 B:SF4301 0.0 21.3 1.0
N B:SAM302 1.9 26.3 1.0
O B:SAM302 2.2 21.3 1.0
S4 B:SF4301 2.3 20.1 1.0
S2 B:SF4301 2.3 22.1 1.0
S1 B:SF4301 2.3 21.8 1.0
FE4 B:SF4301 2.7 21.7 1.0
FE1 B:SF4301 2.8 20.8 1.0
FE2 B:SF4301 2.8 21.6 1.0
CA B:SAM302 3.0 18.6 1.0
C B:SAM302 3.0 20.3 1.0
SD B:SAM302 3.3 23.8 1.0
CG B:SAM302 3.6 18.4 1.0
CB B:SAM302 3.9 21.6 1.0
S3 B:SF4301 4.0 23.0 1.0
NZ B:LYS135 4.1 20.6 1.0
CE B:LYS135 4.1 28.7 1.0
CE B:SAM302 4.1 29.6 1.0
OXT B:SAM302 4.2 22.8 1.0
O B:GLY92 4.5 20.9 1.0
SG B:CYS31 4.5 25.3 1.0
CB B:ASN118 4.6 18.6 1.0
ND2 B:ASN118 4.8 21.6 1.0
SG B:CYS46 4.9 22.9 1.0
C2' B:SAM302 4.9 19.4 1.0
SG B:CYS49 5.0 25.8 1.0

Iron binding site 8 out of 8 in 4njh

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Iron binding site 8 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin


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-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:21.7
occ:1.00
 FE4 B:SF4301 0.0 21.7 1.0
S3 B:SF4301 2.2 23.0 1.0
S2 B:SF4301 2.3 22.1 1.0
S1 B:SF4301 2.3 21.8 1.0
SG B:CYS31 2.3 25.3 1.0
FE1 B:SF4301 2.7 20.8 1.0
FE2 B:SF4301 2.7 21.6 1.0
FE3 B:SF4301 2.7 21.3 1.0
CB B:CYS31 3.3 24.6 1.0
N B:SAM302 3.6 26.3 1.0
S4 B:SF4301 3.8 20.1 1.0
CE1 B:PHE53 4.2 23.5 1.0
CZ B:PHE53 4.5 28.4 1.0
CB B:LEU33 4.6 21.3 1.0
SG B:CYS46 4.7 22.9 1.0
ND2 B:ASN118 4.7 21.6 1.0
CA B:CYS31 4.7 28.6 1.0
SG B:CYS49 4.8 25.8 1.0
CB B:CYS46 4.8 23.4 1.0
O B:SAM302 4.8 21.3 1.0
N B:TRP34 4.9 23.6 1.0
C B:GLY92 4.9 23.2 1.0
N B:LEU33 4.9 26.2 1.0
CB B:TRP34 5.0 24.2 1.0
CD1 B:PHE53 5.0 26.1 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 07:39:22 2024

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