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Iron in PDB 5tgs: Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound

Enzymatic activity of Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound

All present enzymatic activity of Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound:
4.3.99.3;

Protein crystallography data

The structure of Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound, PDB code: 5tgs was solved by T.A.J.Grell, D.P.Dowling, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.01 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.182, 79.297, 122.224, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 24.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound (pdb code 5tgs). 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 Bacillus Subtilis with Methionine Bound, PDB code: 5tgs:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5tgs

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Iron binding site 1 out of 8 in the Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound


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 Bacillus Subtilis with Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:45.2
occ:1.00
 FE1 A:SF4301 0.0 45.2 1.0
SG A:CYS38 2.3 43.0 1.0
S4 A:SF4301 2.3 45.7 1.0
S3 A:SF4301 2.3 44.3 1.0
S2 A:SF4301 2.3 46.1 1.0
FE3 A:SF4301 2.7 46.4 1.0
FE2 A:SF4301 2.7 45.7 1.0
FE4 A:SF4301 2.7 46.4 1.0
CB A:CYS38 3.2 43.7 1.0
CE A:LYS129 3.7 39.6 1.0
S1 A:SF4301 3.9 50.9 1.0
CB A:TYR36 4.1 35.8 1.0
N A:CYS38 4.1 39.1 1.0
CA A:CYS38 4.3 43.0 1.0
NZ A:LYS129 4.5 39.8 1.0
CG A:LYS129 4.5 42.4 1.0
CD2 A:TYR36 4.5 36.7 1.0
CD A:LYS129 4.5 41.8 1.0
CB A:CYS41 4.7 55.1 1.0
SG A:CYS41 4.7 55.4 1.0
SG A:CYS34 4.7 39.1 1.0
CG A:TYR36 4.8 37.6 1.0
OXT A:MET302 5.0 78.5 1.0
CZ3 A:TRP40 5.0 44.5 1.0

Iron binding site 2 out of 8 in 5tgs

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Iron binding site 2 out of 8 in the Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound


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 Bacillus Subtilis with Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:45.7
occ:1.00
 FE2 A:SF4301 0.0 45.7 1.0
S1 A:SF4301 2.3 50.9 1.0
S3 A:SF4301 2.3 44.3 1.0
S4 A:SF4301 2.3 45.7 1.0
OXT A:MET302 2.4 78.5 1.0
C A:MET302 2.7 79.8 1.0
FE3 A:SF4301 2.7 46.4 1.0
FE1 A:SF4301 2.7 45.2 1.0
FE4 A:SF4301 2.7 46.4 1.0
CA A:MET302 3.0 80.7 1.0
N A:MET302 3.2 80.6 1.0
O A:MET302 3.6 80.2 1.0
S2 A:SF4301 3.9 46.1 1.0
CE A:LYS129 3.9 39.6 1.0
NZ A:LYS129 4.1 39.8 1.0
O A:HOH411 4.2 48.8 1.0
CB A:MET302 4.4 81.1 1.0
O A:GLY83 4.6 40.5 1.0
O A:HOH404 4.6 52.5 1.0
SG A:CYS34 4.8 39.1 1.0
SG A:CYS41 4.9 55.4 1.0
SG A:CYS38 4.9 43.0 1.0
N A:GLY83 5.0 42.2 1.0

Iron binding site 3 out of 8 in 5tgs

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Iron binding site 3 out of 8 in the Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound


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 Bacillus Subtilis with Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:46.4
occ:1.00
 FE3 A:SF4301 0.0 46.4 1.0
SG A:CYS41 2.3 55.4 1.0
S4 A:SF4301 2.3 45.7 1.0
S2 A:SF4301 2.3 46.1 1.0
S1 A:SF4301 2.3 50.9 1.0
FE1 A:SF4301 2.7 45.2 1.0
FE2 A:SF4301 2.7 45.7 1.0
FE4 A:SF4301 2.7 46.4 1.0
CB A:CYS41 3.0 55.1 1.0
CA A:CYS41 3.6 53.9 1.0
S3 A:SF4301 3.9 44.3 1.0
NE1 A:TRP47 4.0 38.8 1.0
C A:CYS41 4.5 56.4 1.0
CA A:MET302 4.5 80.7 1.0
SG A:CYS38 4.6 43.0 1.0
CB A:CYS38 4.7 43.7 1.0
CD1 A:TRP47 4.7 38.4 1.0
N A:ASP42 4.7 55.4 1.0
N A:CYS41 4.8 52.6 1.0
N A:MET302 4.8 80.6 1.0
SG A:CYS34 4.8 39.1 1.0
N A:SER43 4.9 52.0 1.0
C A:MET302 4.9 79.8 1.0
O A:SER43 4.9 48.0 1.0

Iron binding site 4 out of 8 in 5tgs

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Iron binding site 4 out of 8 in the Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound


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 Bacillus Subtilis with Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:46.4
occ:1.00
 FE4 A:SF4301 0.0 46.4 1.0
S2 A:SF4301 2.3 46.1 1.0
S1 A:SF4301 2.3 50.9 1.0
S3 A:SF4301 2.3 44.3 1.0
SG A:CYS34 2.3 39.1 1.0
FE3 A:SF4301 2.7 46.4 1.0
FE1 A:SF4301 2.7 45.2 1.0
FE2 A:SF4301 2.7 45.7 1.0
CB A:CYS34 3.6 39.8 1.0
S4 A:SF4301 3.9 45.7 1.0
CB A:TYR36 4.0 35.8 1.0
O A:GLY83 4.4 40.5 1.0
C A:GLY83 4.5 41.6 1.0
O A:TYR36 4.5 39.9 1.0
NE1 A:TRP47 4.5 38.8 1.0
SG A:CYS41 4.5 55.4 1.0
CD1 A:TRP47 4.6 38.4 1.0
CA A:GLY83 4.6 42.5 1.0
SG A:CYS38 4.7 43.0 1.0
OXT A:MET302 4.7 78.5 1.0
N A:GLY83 4.7 42.2 1.0
C A:TYR36 4.7 39.6 1.0
NE2 A:GLN110 4.7 46.1 1.0
CA A:TYR36 4.8 38.0 1.0
N A:TYR36 4.9 38.1 1.0
C A:MET302 4.9 79.8 1.0
CA A:CYS34 5.0 40.6 1.0

Iron binding site 5 out of 8 in 5tgs

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Iron binding site 5 out of 8 in the Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound


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 Bacillus Subtilis with Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:73.1
occ:1.00
 FE1 B:SF4301 0.0 73.1 1.0
SG B:CYS38 2.3 85.8 1.0
S4 B:SF4301 2.3 0.2 1.0
S3 B:SF4301 2.3 81.6 1.0
S2 B:SF4301 2.3 63.2 1.0
FE3 B:SF4301 2.7 73.9 1.0
FE2 B:SF4301 2.7 0.1 1.0
FE4 B:SF4301 2.7 78.2 1.0
CB B:CYS38 3.1 85.0 1.0
S1 B:SF4301 3.9 0.4 1.0
CE B:LYS129 3.9 55.5 1.0
N B:CYS38 4.1 84.0 1.0
CB B:TYR36 4.1 67.3 1.0
CA B:CYS38 4.2 84.4 1.0
CG B:LYS129 4.4 56.5 1.0
CD B:LYS129 4.5 55.9 1.0
CD2 B:TYR36 4.5 64.3 1.0
CB B:CYS41 4.6 88.6 1.0
SG B:CYS41 4.7 85.3 1.0
SG B:CYS34 4.7 54.3 1.0
NZ B:LYS129 4.7 58.3 1.0
O B:HOH425 4.8 76.0 1.0
CG B:TYR36 4.9 65.8 1.0
CZ3 B:TRP40 5.0 75.2 1.0

Iron binding site 6 out of 8 in 5tgs

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Iron binding site 6 out of 8 in the Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound


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 Bacillus Subtilis with Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:0.1
occ:1.00
 FE2 B:SF4301 0.0 0.1 1.0
O B:HOH425 2.1 76.0 1.0
S3 B:SF4301 2.3 81.6 1.0
S1 B:SF4301 2.3 0.4 1.0
S4 B:SF4301 2.3 0.2 1.0
FE1 B:SF4301 2.7 73.1 1.0
FE3 B:SF4301 2.7 73.9 1.0
FE4 B:SF4301 2.7 78.2 1.0
CE B:LYS129 3.7 55.5 1.0
S2 B:SF4301 3.9 63.2 1.0
NZ B:LYS129 4.1 58.3 1.0
O B:HOH401 4.1 59.0 1.0
O B:GLY83 4.8 69.5 1.0
SG B:CYS34 4.8 54.3 1.0
SG B:CYS38 4.9 85.8 1.0
SG B:CYS41 4.9 85.3 1.0
CD B:LYS129 5.0 55.9 1.0

Iron binding site 7 out of 8 in 5tgs

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Iron binding site 7 out of 8 in the Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound


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 Bacillus Subtilis with Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:73.9
occ:1.00
 FE3 B:SF4301 0.0 73.9 1.0
SG B:CYS41 2.3 85.3 1.0
S2 B:SF4301 2.3 63.2 1.0
S4 B:SF4301 2.3 0.2 1.0
S1 B:SF4301 2.3 0.4 1.0
FE1 B:SF4301 2.7 73.1 1.0
FE2 B:SF4301 2.7 0.1 1.0
FE4 B:SF4301 2.7 78.2 1.0
CB B:CYS41 3.0 88.6 1.0
CA B:CYS41 3.6 89.1 1.0
S3 B:SF4301 3.9 81.6 1.0
NE1 B:TRP47 4.2 78.0 1.0
O B:HOH425 4.2 76.0 1.0
C B:CYS41 4.4 91.8 1.0
CB B:CYS38 4.6 85.0 1.0
SG B:CYS38 4.7 85.8 1.0
N B:ASP42 4.7 93.4 1.0
CD1 B:TRP47 4.7 79.0 1.0
N B:CYS41 4.7 86.2 1.0
O B:SER43 4.8 92.1 1.0
N B:SER43 4.8 96.4 1.0
SG B:CYS34 4.8 54.3 1.0
OD1 B:ASP42 4.9 96.5 1.0

Iron binding site 8 out of 8 in 5tgs

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Iron binding site 8 out of 8 in the Crystal Structure of Quee From Bacillus Subtilis with Methionine Bound


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 Bacillus Subtilis with Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:78.2
occ:1.00
 FE4 B:SF4301 0.0 78.2 1.0
S2 B:SF4301 2.3 63.2 1.0
S1 B:SF4301 2.3 0.4 1.0
S3 B:SF4301 2.3 81.6 1.0
SG B:CYS34 2.3 54.3 1.0
FE3 B:SF4301 2.7 73.9 1.0
FE2 B:SF4301 2.7 0.1 1.0
FE1 B:SF4301 2.7 73.1 1.0
CB B:CYS34 3.7 55.0 1.0
S4 B:SF4301 3.9 0.2 1.0
O B:HOH425 4.0 76.0 1.0
CB B:TYR36 4.2 67.3 1.0
O B:GLY83 4.3 69.5 1.0
O B:HOH401 4.4 59.0 1.0
SG B:CYS41 4.5 85.3 1.0
C B:GLY83 4.5 68.2 1.0
NE2 B:GLN110 4.6 65.4 1.0
N B:GLY83 4.6 72.5 1.0
CA B:GLY83 4.7 70.1 1.0
SG B:CYS38 4.7 85.8 1.0
CD1 B:TRP47 4.7 79.0 1.0
NE1 B:TRP47 4.8 78.0 1.0
O B:TYR36 4.8 74.3 1.0
CA B:CYS34 5.0 55.9 1.0
C B:TYR36 5.0 74.2 1.0

Reference:

N.A.Bruender, T.A.Grell, D.P.Dowling, R.M.Mccarty, C.L.Drennan, V.Bandarian. 7-Carboxy-7-Deazaguanine Synthase: A Radical S-Adenosyl-L-Methionine Enzyme with Polar Tendencies. J. Am. Chem. Soc. V. 139 1912 2017.
ISSN: ESSN 1520-5126
PubMed: 28045519
DOI: 10.1021/JACS.6B11381
Page generated: Tue Aug 6 08:59:43 2024

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