Atomistry » Iron » PDB 4n4j-4nji » 4nji
Atomistry »
  Iron »
    PDB 4n4j-4nji »
      4nji »

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

Go back to Iron Binding Sites List in 4nji
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

Go back to Iron Binding Sites List in 4nji
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

Go back to Iron Binding Sites List in 4nji
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

Go back to Iron Binding Sites List in 4nji
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

Go back to Iron Binding Sites List in 4nji
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy