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Iron in PDB 4nji: Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+

Enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+

All present enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+:
4.3.99.3;

Protein crystallography data

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+, PDB code: 4nji 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) 28.89 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.126, 119.126, 104.310, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18

Other elements in 4nji:

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ (pdb code 4nji). 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, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+, PDB code: 4nji:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4nji

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Iron binding site 1 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:33.8
occ:1.00
 FE1 A:SF4301 0.0 33.8 1.0
S2 A:SF4301 2.3 34.6 1.0
S3 A:SF4301 2.3 34.4 1.0
S4 A:SF4301 2.3 34.1 1.0
SG A:CYS46 2.3 36.6 1.0
FE2 A:SF4301 2.7 35.6 1.0
FE4 A:SF4301 2.7 36.5 1.0
FE3 A:SF4301 2.8 35.7 1.0
CB A:CYS46 3.2 32.9 1.0
CE A:LYS135 3.6 37.2 1.0
S1 A:SF4301 3.9 35.1 1.0
O A:SAM302 4.2 39.0 1.0
CB A:CYS49 4.4 40.5 1.0
SG A:CYS49 4.4 40.7 1.0
CD A:LYS135 4.6 38.5 1.0
CA A:CYS46 4.6 35.9 1.0
NZ A:LYS135 4.6 35.6 1.0
CG A:LYS135 4.7 38.8 1.0
SG A:CYS31 4.8 40.5 1.0
O A:CYS46 4.8 37.2 1.0
N A:SAM302 4.9 35.6 1.0
C A:CYS46 4.9 36.5 1.0
CB A:LEU33 4.9 36.5 1.0
CA A:CYS49 5.0 39.0 1.0

Iron binding site 2 out of 8 in 4nji

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Iron binding site 2 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:35.6
occ:1.00
 FE2 A:SF4301 0.0 35.6 1.0
SG A:CYS49 2.2 40.7 1.0
S1 A:SF4301 2.3 35.1 1.0
S4 A:SF4301 2.3 34.1 1.0
S3 A:SF4301 2.3 34.4 1.0
FE1 A:SF4301 2.7 33.8 1.0
FE4 A:SF4301 2.7 36.5 1.0
FE3 A:SF4301 2.8 35.7 1.0
CB A:CYS49 3.2 40.5 1.0
CE A:SAM302 3.6 39.5 1.0
S2 A:SF4301 3.9 34.6 1.0
CE1 A:PHE53 3.9 38.7 1.0
CA A:CYS49 4.1 39.0 1.0
SD A:SAM302 4.3 43.2 1.0
CD1 A:PHE53 4.4 41.5 1.0
N A:SAM302 4.6 35.6 1.0
SG A:CYS46 4.6 36.6 1.0
O A:SAM302 4.8 39.0 1.0
CZ A:PHE53 4.9 40.0 1.0
CG A:SAM302 4.9 26.9 1.0
CE3 A:TRP34 4.9 33.2 1.0
SG A:CYS31 5.0 40.5 1.0

Iron binding site 3 out of 8 in 4nji

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Iron binding site 3 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:35.7
occ:1.00
 FE3 A:SF4301 0.0 35.7 1.0
O A:SAM302 2.2 39.0 1.0
N A:SAM302 2.3 35.6 1.0
S1 A:SF4301 2.3 35.1 1.0
S4 A:SF4301 2.3 34.1 1.0
S2 A:SF4301 2.3 34.6 1.0
FE4 A:SF4301 2.7 36.5 1.0
FE2 A:SF4301 2.8 35.6 1.0
FE1 A:SF4301 2.8 33.8 1.0
C A:SAM302 3.0 37.4 1.0
CA A:SAM302 3.1 36.8 1.0
SD A:SAM302 3.3 43.2 1.0
CG A:SAM302 3.6 26.9 1.0
CE A:SAM302 3.9 39.5 1.0
S3 A:SF4301 3.9 34.4 1.0
CB A:SAM302 3.9 29.6 1.0
OXT A:SAM302 4.2 32.9 1.0
CE A:LYS135 4.2 37.2 1.0
NZ A:LYS135 4.3 35.6 1.0
O A:GLY92 4.4 37.2 1.0
SG A:CYS31 4.6 40.5 1.0
CB A:ASN118 4.7 31.8 1.0
SG A:CYS49 4.8 40.7 1.0
C2' A:SAM302 4.8 35.6 1.0
ND2 A:ASN118 4.9 34.1 1.0
SG A:CYS46 5.0 36.6 1.0

Iron binding site 4 out of 8 in 4nji

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Iron binding site 4 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:36.5
occ:1.00
 FE4 A:SF4301 0.0 36.5 1.0
S3 A:SF4301 2.3 34.4 1.0
S2 A:SF4301 2.3 34.6 1.0
S1 A:SF4301 2.3 35.1 1.0
SG A:CYS31 2.3 40.5 1.0
FE1 A:SF4301 2.7 33.8 1.0
FE2 A:SF4301 2.7 35.6 1.0
FE3 A:SF4301 2.7 35.7 1.0
CB A:CYS31 3.3 36.6 1.0
N A:SAM302 3.8 35.6 1.0
S4 A:SF4301 3.9 34.1 1.0
CE1 A:PHE53 4.3 38.7 1.0
CZ A:PHE53 4.5 40.0 1.0
CB A:LEU33 4.6 36.5 1.0
SG A:CYS49 4.7 40.7 1.0
ND2 A:ASN118 4.7 34.1 1.0
O A:SAM302 4.7 39.0 1.0
CA A:CYS31 4.7 40.8 1.0
O A:GLY92 4.8 37.2 1.0
SG A:CYS46 4.8 36.6 1.0
C A:GLY92 4.8 40.8 1.0
N A:TRP34 4.8 41.4 1.0
CB A:CYS46 4.9 32.9 1.0
N A:LEU33 4.9 37.8 1.0
CB A:TRP34 5.0 35.1 1.0

Iron binding site 5 out of 8 in 4nji

Go back to Iron Binding Sites List in 4nji
Iron binding site 5 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:34.8
occ:1.00
 FE1 B:SF4301 0.0 34.8 1.0
SG B:CYS46 2.2 35.8 1.0
S2 B:SF4301 2.3 35.5 1.0
S3 B:SF4301 2.3 36.8 1.0
S4 B:SF4301 2.3 32.7 1.0
FE4 B:SF4301 2.7 35.9 1.0
FE2 B:SF4301 2.7 35.1 1.0
FE3 B:SF4301 2.8 32.6 1.0
CB B:CYS46 3.2 33.9 1.0
CE B:LYS135 3.4 44.9 1.0
S1 B:SF4301 3.9 33.7 1.0
O B:SAM302 4.2 37.6 1.0
CB B:CYS49 4.3 41.0 1.0
NZ B:LYS135 4.4 36.7 1.0
CD B:LYS135 4.5 43.8 1.0
SG B:CYS49 4.5 41.6 1.0
N B:SAM302 4.5 26.1 1.0
CA B:CYS46 4.6 36.5 1.0
SG B:CYS31 4.7 39.6 1.0
CG B:LYS135 4.8 41.8 1.0
O B:CYS46 4.9 44.6 1.0
C B:CYS46 4.9 39.4 1.0
CA B:CYS49 5.0 35.8 1.0

Iron binding site 6 out of 8 in 4nji

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Iron binding site 6 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:35.1
occ:1.00
 FE2 B:SF4301 0.0 35.1 1.0
S1 B:SF4301 2.3 33.7 1.0
SG B:CYS49 2.3 41.6 1.0
S4 B:SF4301 2.3 32.7 1.0
S3 B:SF4301 2.3 36.8 1.0
FE4 B:SF4301 2.7 35.9 1.0
FE1 B:SF4301 2.7 34.8 1.0
FE3 B:SF4301 2.8 32.6 1.0
CB B:CYS49 3.2 41.0 1.0
CE B:SAM302 3.7 44.5 1.0
S2 B:SF4301 3.9 35.5 1.0
CE1 B:PHE53 3.9 41.6 1.0
CA B:CYS49 4.2 35.8 1.0
N B:SAM302 4.3 26.1 1.0
SD B:SAM302 4.3 40.4 1.0
CD1 B:PHE53 4.4 40.1 1.0
SG B:CYS46 4.6 35.8 1.0
O B:SAM302 4.9 37.6 1.0
CG B:SAM302 4.9 27.1 1.0
CE3 B:TRP34 4.9 40.2 1.0
CZ B:PHE53 4.9 47.0 1.0
SG B:CYS31 4.9 39.6 1.0

Iron binding site 7 out of 8 in 4nji

Go back to Iron Binding Sites List in 4nji
Iron binding site 7 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:32.6
occ:1.00
 FE3 B:SF4301 0.0 32.6 1.0
N B:SAM302 1.9 26.1 1.0
S4 B:SF4301 2.3 32.7 1.0
O B:SAM302 2.3 37.6 1.0
S1 B:SF4301 2.3 33.7 1.0
S2 B:SF4301 2.3 35.5 1.0
FE2 B:SF4301 2.8 35.1 1.0
FE4 B:SF4301 2.8 35.9 1.0
FE1 B:SF4301 2.8 34.8 1.0
CA B:SAM302 2.9 29.2 1.0
C B:SAM302 3.0 34.2 1.0
SD B:SAM302 3.3 40.4 1.0
CG B:SAM302 3.5 27.1 1.0
CB B:SAM302 3.8 31.8 1.0
S3 B:SF4301 3.9 36.8 1.0
CE B:SAM302 3.9 44.5 1.0
CE B:LYS135 4.1 44.9 1.0
NZ B:LYS135 4.2 36.7 1.0
OXT B:SAM302 4.2 34.3 1.0
O B:GLY92 4.5 37.2 1.0
SG B:CYS31 4.6 39.6 1.0
CB B:ASN118 4.7 37.1 1.0
C2' B:SAM302 4.9 36.7 1.0
SG B:CYS46 4.9 35.8 1.0
ND2 B:ASN118 4.9 37.4 1.0
SG B:CYS49 4.9 41.6 1.0

Iron binding site 8 out of 8 in 4nji

Go back to Iron Binding Sites List in 4nji
Iron binding site 8 out of 8 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:35.9
occ:1.00
 FE4 B:SF4301 0.0 35.9 1.0
S3 B:SF4301 2.3 36.8 1.0
S2 B:SF4301 2.3 35.5 1.0
S1 B:SF4301 2.3 33.7 1.0
SG B:CYS31 2.3 39.6 1.0
FE1 B:SF4301 2.7 34.8 1.0
FE2 B:SF4301 2.7 35.1 1.0
FE3 B:SF4301 2.8 32.6 1.0
CB B:CYS31 3.3 33.5 1.0
N B:SAM302 3.6 26.1 1.0
S4 B:SF4301 3.9 32.7 1.0
CE1 B:PHE53 4.3 41.6 1.0
CZ B:PHE53 4.6 47.0 1.0
CA B:CYS31 4.7 38.0 1.0
ND2 B:ASN118 4.7 37.4 1.0
CB B:LEU33 4.7 34.9 1.0
SG B:CYS46 4.7 35.8 1.0
SG B:CYS49 4.8 41.6 1.0
O B:SAM302 4.9 37.6 1.0
CB B:CYS46 4.9 33.9 1.0
CB B:TRP34 4.9 36.2 1.0
C B:GLY92 4.9 39.1 1.0
N B:TRP34 5.0 37.9 1.0
O B:GLY92 5.0 37.2 1.0
N B:LEU33 5.0 37.2 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 07:39:50 2024

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