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

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

All present enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II):
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 Manganese(II), PDB code: 4njj 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) 48.16 / 2.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.174, 119.174, 105.310, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20

Other elements in 4njj:

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

Manganese (Mn) 4 atoms

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 Manganese(II) (pdb code 4njj). 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 Manganese(II), PDB code: 4njj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4njj

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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 Manganese(II)


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 Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:48.1
occ:1.00
 FE1 A:SF4301 0.0 48.1 1.0
S2 A:SF4301 2.3 50.6 1.0
S4 A:SF4301 2.3 49.1 1.0
S3 A:SF4301 2.3 48.7 1.0
SG A:CYS46 2.3 53.0 1.0
FE4 A:SF4301 2.7 46.9 1.0
FE2 A:SF4301 2.7 47.6 1.0
FE3 A:SF4301 2.7 46.8 1.0
CB A:CYS46 3.2 47.9 1.0
CE A:LYS135 3.5 59.6 1.0
S1 A:SF4301 3.9 52.2 1.0
O A:SAM302 4.3 50.8 1.0
CB A:CYS49 4.3 40.8 1.0
CD A:LYS135 4.4 50.7 1.0
SG A:CYS49 4.6 51.7 1.0
CA A:CYS46 4.6 42.9 1.0
N A:SAM302 4.7 48.3 1.0
NZ A:LYS135 4.7 44.1 1.0
SG A:CYS31 4.7 47.6 1.0
CG A:LYS135 4.8 45.7 1.0
O A:CYS46 4.9 47.3 1.0
C A:CYS46 4.9 51.1 1.0
CB A:LEU33 4.9 38.5 1.0

Iron binding site 2 out of 8 in 4njj

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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 Manganese(II)


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 Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:47.6
occ:1.00
 FE2 A:SF4301 0.0 47.6 1.0
S1 A:SF4301 2.3 52.2 1.0
S4 A:SF4301 2.3 49.1 1.0
S3 A:SF4301 2.3 48.7 1.0
SG A:CYS49 2.3 51.7 1.0
FE1 A:SF4301 2.7 48.1 1.0
FE4 A:SF4301 2.7 46.9 1.0
FE3 A:SF4301 2.7 46.8 1.0
CB A:CYS49 3.1 40.8 1.0
CE1 A:PHE53 3.8 65.5 1.0
S2 A:SF4301 3.9 50.6 1.0
CE A:SAM302 3.9 51.8 1.0
CA A:CYS49 4.1 49.7 1.0
N A:SAM302 4.4 48.3 1.0
SD A:SAM302 4.5 54.0 1.0
CD1 A:PHE53 4.5 62.8 1.0
SG A:CYS46 4.6 53.0 1.0
CZ A:PHE53 4.7 59.3 1.0
O A:SAM302 4.9 50.8 1.0
SG A:CYS31 5.0 47.6 1.0
CE3 A:TRP34 5.0 60.9 1.0
C8 A:SAM302 5.0 54.4 1.0
CG A:SAM302 5.0 45.1 1.0

Iron binding site 3 out of 8 in 4njj

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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 Manganese(II)


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 Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:46.8
occ:1.00
 FE3 A:SF4301 0.0 46.8 1.0
N A:SAM302 2.1 48.3 1.0
S1 A:SF4301 2.3 52.2 1.0
S2 A:SF4301 2.3 50.6 1.0
S4 A:SF4301 2.3 49.1 1.0
O A:SAM302 2.4 50.8 1.0
FE1 A:SF4301 2.7 48.1 1.0
FE2 A:SF4301 2.7 47.6 1.0
FE4 A:SF4301 2.7 46.9 1.0
CA A:SAM302 3.1 48.1 1.0
C A:SAM302 3.1 49.4 1.0
SD A:SAM302 3.4 54.0 1.0
CG A:SAM302 3.7 45.1 1.0
S3 A:SF4301 3.9 48.7 1.0
CB A:SAM302 4.0 41.4 1.0
CE A:LYS135 4.0 59.6 1.0
CE A:SAM302 4.1 51.8 1.0
NZ A:LYS135 4.3 44.1 1.0
OXT A:SAM302 4.3 46.0 1.0
O A:GLY92 4.4 53.8 1.0
SG A:CYS31 4.5 47.6 1.0
CB A:ASN118 4.8 46.3 1.0
SG A:CYS46 4.8 53.0 1.0
C2' A:SAM302 4.9 47.3 1.0
SG A:CYS49 4.9 51.7 1.0
ND2 A:ASN118 4.9 40.6 1.0

Iron binding site 4 out of 8 in 4njj

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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 Manganese(II)


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 Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:46.9
occ:1.00
 FE4 A:SF4301 0.0 46.9 1.0
S3 A:SF4301 2.3 48.7 1.0
S2 A:SF4301 2.3 50.6 1.0
S1 A:SF4301 2.3 52.2 1.0
SG A:CYS31 2.3 47.6 1.0
FE1 A:SF4301 2.7 48.1 1.0
FE2 A:SF4301 2.7 47.6 1.0
FE3 A:SF4301 2.7 46.8 1.0
CB A:CYS31 3.3 46.7 1.0
N A:SAM302 3.7 48.3 1.0
S4 A:SF4301 3.9 49.1 1.0
CE1 A:PHE53 4.3 65.5 1.0
CZ A:PHE53 4.4 59.3 1.0
CB A:LEU33 4.6 38.5 1.0
CA A:CYS31 4.7 55.1 1.0
ND2 A:ASN118 4.8 40.6 1.0
SG A:CYS49 4.8 51.7 1.0
SG A:CYS46 4.8 53.0 1.0
O A:GLY92 4.8 53.8 1.0
C A:GLY92 4.8 49.8 1.0
N A:TRP34 4.9 42.5 1.0
CB A:CYS46 4.9 47.9 1.0
CB A:TRP34 4.9 46.5 1.0
O A:SAM302 5.0 50.8 1.0
N A:LEU33 5.0 51.8 1.0

Iron binding site 5 out of 8 in 4njj

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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 Manganese(II)


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 Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:44.6
occ:1.00
 FE1 B:SF4301 0.0 44.6 1.0
S2 B:SF4301 2.3 47.6 1.0
S3 B:SF4301 2.3 51.3 1.0
S4 B:SF4301 2.3 46.1 1.0
SG B:CYS46 2.3 45.0 1.0
FE4 B:SF4301 2.7 46.9 1.0
FE2 B:SF4301 2.7 44.5 1.0
FE3 B:SF4301 2.7 46.6 1.0
CB B:CYS46 3.2 46.0 1.0
CE B:LYS135 3.6 45.7 1.0
S1 B:SF4301 3.9 49.5 1.0
O B:SAM302 4.2 45.4 1.0
NZ B:LYS135 4.4 43.1 1.0
CB B:CYS49 4.4 39.8 1.0
CD B:LYS135 4.5 48.1 1.0
CA B:CYS46 4.6 47.4 1.0
SG B:CYS49 4.6 52.0 1.0
N B:SAM302 4.6 40.0 1.0
SG B:CYS31 4.7 46.5 1.0
CG B:LYS135 4.7 42.9 1.0
CB B:LEU33 4.9 45.1 1.0
C B:CYS46 4.9 50.2 1.0
O B:CYS46 4.9 47.5 1.0

Iron binding site 6 out of 8 in 4njj

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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 Manganese(II)


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 Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:44.5
occ:1.00
 FE2 B:SF4301 0.0 44.5 1.0
S1 B:SF4301 2.3 49.5 1.0
SG B:CYS49 2.3 52.0 1.0
S3 B:SF4301 2.3 51.3 1.0
S4 B:SF4301 2.3 46.1 1.0
FE4 B:SF4301 2.7 46.9 1.0
FE1 B:SF4301 2.7 44.6 1.0
FE3 B:SF4301 2.7 46.6 1.0
CB B:CYS49 3.1 39.8 1.0
CE B:SAM302 3.9 51.4 1.0
S2 B:SF4301 3.9 47.6 1.0
CE1 B:PHE53 3.9 51.4 1.0
CA B:CYS49 4.1 50.0 1.0
N B:SAM302 4.4 40.0 1.0
SD B:SAM302 4.5 52.0 1.0
CD1 B:PHE53 4.5 59.0 1.0
SG B:CYS46 4.6 45.0 1.0
CZ B:PHE53 4.7 50.1 1.0
O B:SAM302 4.8 45.4 1.0
CE3 B:TRP34 4.8 56.1 1.0
SG B:CYS31 4.9 46.5 1.0
N B:CYS49 5.0 46.1 1.0

Iron binding site 7 out of 8 in 4njj

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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 Manganese(II)


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 Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:46.6
occ:1.00
 FE3 B:SF4301 0.0 46.6 1.0
N B:SAM302 2.1 40.0 1.0
O B:SAM302 2.3 45.4 1.0
S4 B:SF4301 2.3 46.1 1.0
S1 B:SF4301 2.3 49.5 1.0
S2 B:SF4301 2.3 47.6 1.0
FE2 B:SF4301 2.7 44.5 1.0
FE4 B:SF4301 2.7 46.9 1.0
FE1 B:SF4301 2.7 44.6 1.0
CA B:SAM302 3.0 44.3 1.0
C B:SAM302 3.0 46.9 1.0
SD B:SAM302 3.4 52.0 1.0
CG B:SAM302 3.7 42.5 1.0
S3 B:SF4301 3.9 51.3 1.0
CB B:SAM302 3.9 50.4 1.0
CE B:SAM302 4.0 51.4 1.0
NZ B:LYS135 4.0 43.1 1.0
CE B:LYS135 4.2 45.7 1.0
OXT B:SAM302 4.2 44.6 1.0
SG B:CYS31 4.6 46.5 1.0
O B:GLY92 4.6 47.8 1.0
CB B:ASN118 4.8 45.8 1.0
SG B:CYS49 4.9 52.0 1.0
SG B:CYS46 4.9 45.0 1.0
ND2 B:ASN118 4.9 46.3 1.0
C2' B:SAM302 4.9 45.7 1.0

Iron binding site 8 out of 8 in 4njj

Go back to Iron Binding Sites List in 4njj
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 Manganese(II)


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 Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:46.9
occ:1.00
 FE4 B:SF4301 0.0 46.9 1.0
S3 B:SF4301 2.3 51.3 1.0
S2 B:SF4301 2.3 47.6 1.0
S1 B:SF4301 2.3 49.5 1.0
SG B:CYS31 2.3 46.5 1.0
FE1 B:SF4301 2.7 44.6 1.0
FE2 B:SF4301 2.7 44.5 1.0
FE3 B:SF4301 2.7 46.6 1.0
CB B:CYS31 3.3 44.0 1.0
N B:SAM302 3.6 40.0 1.0
S4 B:SF4301 3.9 46.1 1.0
CE1 B:PHE53 4.4 51.4 1.0
CZ B:PHE53 4.5 50.1 1.0
CB B:LEU33 4.6 45.1 1.0
CA B:CYS31 4.7 45.1 1.0
ND2 B:ASN118 4.7 46.3 1.0
SG B:CYS46 4.8 45.0 1.0
SG B:CYS49 4.8 52.0 1.0
O B:SAM302 4.8 45.4 1.0
CB B:TRP34 4.9 49.3 1.0
N B:TRP34 4.9 47.2 1.0
C B:GLY92 4.9 47.6 1.0
CB B:CYS46 4.9 46.0 1.0
N B:LEU33 5.0 50.3 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 07:55:25 2024

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