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Iron in PDB 5t8y: Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.

Enzymatic activity of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.

All present enzymatic activity of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.:
1.17.99.6;

Protein crystallography data

The structure of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site., PDB code: 5t8y was solved by D.P.Dowling, Z.D.Miles, C.Kohrer, S.J.Maiocco, S.J.Elliott, V.Bandarian, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.90 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.763, 111.030, 95.971, 90.00, 99.13, 90.00
R / Rfree (%) 23.8 / 26.7

Other elements in 5t8y:

The structure of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. (pdb code 5t8y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site., PDB code: 5t8y:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 5t8y

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Iron binding site 1 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:77.0
occ:1.00
FE1 A:SF4501 0.0 77.0 1.0
S4 A:SF4501 2.3 76.4 1.0
S3 A:SF4501 2.3 79.0 1.0
SG A:CYS194 2.3 75.4 1.0
S2 A:SF4501 2.3 75.0 1.0
FE2 A:SF4501 2.7 82.2 1.0
FE3 A:SF4501 2.7 79.0 1.0
FE4 A:SF4501 2.7 76.5 1.0
CB A:CYS194 3.3 72.3 1.0
S1 A:SF4501 3.9 80.3 1.0
N A:CYS194 3.9 74.3 1.0
CA A:CYS194 4.2 73.2 1.0
CB A:LYS154 4.3 72.2 1.0
ND2 A:ASN155 4.4 67.0 1.0
CG A:ASN155 4.4 68.0 1.0
N A:ASN155 4.5 68.5 1.0
CB A:ASN155 4.6 68.2 1.0
N A:LYS193 4.7 76.6 1.0
SG A:CYS191 4.8 81.6 1.0
OD1 A:ASN155 4.8 68.0 1.0
SG A:CYS247 4.8 74.5 1.0
SG A:CYS188 4.8 74.7 1.0
N A:LYS154 4.9 70.2 1.0
C A:LYS154 5.0 69.8 1.0
CA A:LYS154 5.0 70.6 1.0

Iron binding site 2 out of 16 in 5t8y

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Iron binding site 2 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:82.2
occ:1.00
FE2 A:SF4501 0.0 82.2 1.0
S4 A:SF4501 2.3 76.4 1.0
S1 A:SF4501 2.3 80.3 1.0
S3 A:SF4501 2.3 79.0 1.0
SG A:CYS191 2.3 81.6 1.0
FE1 A:SF4501 2.7 77.0 1.0
FE3 A:SF4501 2.7 79.0 1.0
FE4 A:SF4501 2.7 76.5 1.0
CB A:CYS191 3.3 79.9 1.0
S2 A:SF4501 3.9 75.0 1.0
C A:CYS191 4.0 78.9 1.0
CD A:PRO248 4.1 73.7 1.0
O A:CYS191 4.2 78.1 1.0
N A:LYS193 4.2 76.6 1.0
CA A:CYS191 4.3 79.3 1.0
N A:THR192 4.3 78.4 1.0
CB A:LYS193 4.6 75.4 1.0
SG A:CYS194 4.7 75.4 1.0
CG A:PRO248 4.7 74.2 1.0
SG A:CYS247 4.8 74.5 1.0
SG A:CYS188 4.8 74.7 1.0
CA A:THR192 4.9 77.5 1.0
N A:CYS194 4.9 74.3 1.0
O A:CYS188 5.0 79.2 1.0
CA A:LYS193 5.0 75.4 1.0
C A:THR192 5.0 76.7 1.0

Iron binding site 3 out of 16 in 5t8y

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Iron binding site 3 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:79.0
occ:1.00
FE3 A:SF4501 0.0 79.0 1.0
SG A:CYS247 2.3 74.5 1.0
S2 A:SF4501 2.3 75.0 1.0
S1 A:SF4501 2.3 80.3 1.0
S4 A:SF4501 2.3 76.4 1.0
FE2 A:SF4501 2.7 82.2 1.0
FE4 A:SF4501 2.7 76.5 1.0
FE1 A:SF4501 2.7 77.0 1.0
CB A:CYS247 3.3 70.5 1.0
CD A:PRO248 3.8 73.7 1.0
CA A:CYS247 3.8 71.0 1.0
S3 A:SF4501 3.9 79.0 1.0
N A:PRO248 4.4 72.4 1.0
C A:CYS247 4.5 71.7 1.0
ND2 A:ASN155 4.7 67.0 1.0
SG A:CYS188 4.8 74.7 1.0
SG A:CYS194 4.8 75.4 1.0
SG A:CYS191 4.8 81.6 1.0
N A:LEU249 4.9 72.1 1.0
CG A:LEU249 4.9 73.0 1.0
CD1 A:LEU249 5.0 72.5 1.0
CG A:PRO248 5.0 74.2 1.0

Iron binding site 4 out of 16 in 5t8y

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Iron binding site 4 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:76.5
occ:1.00
FE4 A:SF4501 0.0 76.5 1.0
S2 A:SF4501 2.3 75.0 1.0
S1 A:SF4501 2.3 80.3 1.0
S3 A:SF4501 2.3 79.0 1.0
SG A:CYS188 2.3 74.7 1.0
FE3 A:SF4501 2.7 79.0 1.0
FE2 A:SF4501 2.7 82.2 1.0
FE1 A:SF4501 2.7 77.0 1.0
CB A:CYS188 3.4 75.8 1.0
S4 A:SF4501 3.9 76.4 1.0
CA A:CYS188 4.0 77.3 1.0
N A:LYS154 4.1 70.2 1.0
CB A:LYS154 4.3 72.2 1.0
CB A:ALA153 4.3 68.6 1.0
CG A:LYS154 4.4 72.0 1.0
SG A:CYS247 4.8 74.5 1.0
CD A:LYS154 4.8 74.3 1.0
SG A:CYS191 4.8 81.6 1.0
SG A:CYS194 4.8 75.4 1.0
CA A:LYS154 4.8 70.6 1.0
O A:CYS188 4.9 79.2 1.0
C A:CYS188 4.9 78.4 1.0
O A:CYS191 5.0 78.1 1.0
CA A:ALA153 5.0 68.4 1.0

Iron binding site 5 out of 16 in 5t8y

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Iron binding site 5 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:64.4
occ:1.00
FE1 A:SF4502 0.0 64.4 1.0
S4 A:SF4502 2.3 63.3 1.0
S3 A:SF4502 2.3 63.1 1.0
SG A:CYS198 2.3 66.8 1.0
S2 A:SF4502 2.3 63.1 1.0
FE2 A:SF4502 2.7 64.4 1.0
FE4 A:SF4502 2.7 59.9 1.0
FE3 A:SF4502 2.7 62.5 1.0
CB A:CYS198 3.4 68.2 1.0
S1 A:SF4502 3.9 61.1 1.0
CA A:CYS198 4.0 69.0 1.0
CD A:PRO199 4.1 67.8 1.0
CB A:ALA202 4.2 64.3 1.0
C A:CYS198 4.7 69.3 1.0
N A:PRO199 4.7 68.5 1.0
SG A:CYS243 4.8 63.5 1.0
SG A:CYS214 4.8 58.0 1.0
OG1 A:THR200 4.8 65.8 1.0
N A:ALA202 4.9 66.7 1.0
SG A:CYS240 4.9 62.1 1.0

Iron binding site 6 out of 16 in 5t8y

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Iron binding site 6 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:64.4
occ:1.00
FE2 A:SF4502 0.0 64.4 1.0
S1 A:SF4502 2.3 61.1 1.0
S4 A:SF4502 2.3 63.3 1.0
SG A:CYS243 2.3 63.5 1.0
S3 A:SF4502 2.3 63.1 1.0
FE3 A:SF4502 2.7 62.5 1.0
FE1 A:SF4502 2.7 64.4 1.0
FE4 A:SF4502 2.7 59.9 1.0
CB A:CYS243 3.3 65.5 1.0
N45 A:B12503 3.6 62.7 1.0
S2 A:SF4502 3.9 63.1 1.0
N A:CYS243 4.0 65.8 1.0
CA A:CYS243 4.3 66.0 1.0
C42 A:B12503 4.5 62.0 1.0
C43 A:B12503 4.5 61.9 1.0
SG A:CYS240 4.7 62.1 1.0
O A:CYS240 4.8 62.7 1.0
SG A:CYS198 4.8 66.8 1.0
SG A:CYS214 4.8 58.0 1.0

Iron binding site 7 out of 16 in 5t8y

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Iron binding site 7 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:62.5
occ:1.00
FE3 A:SF4502 0.0 62.5 1.0
SG A:CYS240 2.3 62.1 1.0
S4 A:SF4502 2.3 63.3 1.0
S1 A:SF4502 2.3 61.1 1.0
S2 A:SF4502 2.3 63.1 1.0
FE2 A:SF4502 2.7 64.4 1.0
FE1 A:SF4502 2.7 64.4 1.0
FE4 A:SF4502 2.7 59.9 1.0
CB A:CYS240 3.2 62.0 1.0
S3 A:SF4502 3.9 63.1 1.0
O A:CYS240 4.3 62.7 1.0
CB A:THR242 4.3 64.7 1.0
C A:CYS240 4.3 62.1 1.0
CA A:CYS240 4.4 62.5 1.0
OG1 A:THR242 4.4 64.6 1.0
N A:THR242 4.5 64.9 1.0
CD A:PRO199 4.6 67.8 1.0
CB A:ILE215 4.6 62.8 1.0
SG A:CYS243 4.7 63.5 1.0
SG A:CYS214 4.7 58.0 1.0
CD1 A:ILE215 4.8 64.2 1.0
N A:ILE215 4.8 62.3 1.0
CG1 A:ILE215 4.8 62.9 1.0
N A:CYS243 4.8 65.8 1.0
SG A:CYS198 4.8 66.8 1.0
CA A:THR242 5.0 65.4 1.0
N A:SER216 5.0 61.4 1.0
N A:ASP241 5.0 62.3 1.0

Iron binding site 8 out of 16 in 5t8y

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Iron binding site 8 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:59.9
occ:1.00
FE4 A:SF4502 0.0 59.9 1.0
S1 A:SF4502 2.3 61.1 1.0
S2 A:SF4502 2.3 63.1 1.0
SG A:CYS214 2.3 58.0 1.0
S3 A:SF4502 2.3 63.1 1.0
FE1 A:SF4502 2.7 64.4 1.0
FE3 A:SF4502 2.7 62.5 1.0
FE2 A:SF4502 2.7 64.4 1.0
CB A:CYS214 3.4 62.2 1.0
CA A:CYS214 3.8 62.7 1.0
S4 A:SF4502 3.9 63.3 1.0
N A:ILE215 4.0 62.3 1.0
C A:CYS214 4.2 62.2 1.0
N A:SER216 4.4 61.4 1.0
C42 A:B12503 4.5 62.0 1.0
CB A:ALA202 4.6 64.3 1.0
N45 A:B12503 4.6 62.7 1.0
CB A:SER216 4.6 61.7 1.0
CD1 A:LEU209 4.7 63.4 1.0
SG A:CYS240 4.7 62.1 1.0
SG A:CYS198 4.8 66.8 1.0
CB A:CYS240 4.8 62.0 1.0
SG A:CYS243 4.9 63.5 1.0
C43 A:B12503 4.9 61.9 1.0
CA A:ILE215 5.0 62.6 1.0

Iron binding site 9 out of 16 in 5t8y

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Iron binding site 9 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:84.6
occ:0.80
FE1 B:SF4501 0.0 84.6 0.8
S3 B:SF4501 2.3 86.3 0.8
SG B:CYS194 2.3 84.1 1.0
S4 B:SF4501 2.3 84.5 0.8
S2 B:SF4501 2.3 83.1 0.8
FE2 B:SF4501 2.7 91.9 0.8
FE3 B:SF4501 2.7 86.5 0.8
FE4 B:SF4501 2.7 85.3 0.8
CB B:CYS194 3.3 81.6 1.0
S1 B:SF4501 3.9 85.2 0.8
N B:CYS194 3.9 84.5 1.0
CA B:CYS194 4.2 83.2 1.0
ND2 B:ASN155 4.3 78.0 1.0
CG B:ASN155 4.4 78.1 1.0
CB B:LYS154 4.4 81.2 1.0
N B:ASN155 4.4 78.2 1.0
CB B:ASN155 4.5 78.0 1.0
SG B:CYS191 4.7 91.3 1.0
N B:LYS193 4.7 87.1 1.0
SG B:CYS247 4.8 82.4 1.0
SG B:CYS188 4.8 86.3 1.0
OD1 B:ASN155 4.8 77.3 1.0
N B:LYS154 4.9 79.6 1.0
C B:LYS154 5.0 78.8 1.0
CA B:LYS154 5.0 79.9 1.0

Iron binding site 10 out of 16 in 5t8y

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Iron binding site 10 out of 16 in the Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Epoxyqueuosine Reductase From Bacillus Subtilis with the ASP134 Catalytic Loop Swung Out of the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:91.9
occ:0.80
FE2 B:SF4501 0.0 91.9 0.8
S4 B:SF4501 2.3 84.5 0.8
S3 B:SF4501 2.3 86.3 0.8
S1 B:SF4501 2.3 85.2 0.8
SG B:CYS191 2.3 91.3 1.0
FE1 B:SF4501 2.7 84.6 0.8
FE3 B:SF4501 2.7 86.5 0.8
FE4 B:SF4501 2.7 85.3 0.8
CB B:CYS191 3.3 89.7 1.0
S2 B:SF4501 3.9 83.1 0.8
C B:CYS191 4.0 89.0 1.0
O B:CYS191 4.1 89.0 1.0
N B:LYS193 4.2 87.1 1.0
CD B:PRO248 4.2 83.7 1.0
CA B:CYS191 4.3 89.1 1.0
N B:THR192 4.3 88.7 1.0
CB B:LYS193 4.7 86.6 1.0
SG B:CYS194 4.7 84.1 1.0
SG B:CYS188 4.8 86.3 1.0
SG B:CYS247 4.8 82.4 1.0
CA B:THR192 4.8 87.1 1.0
N B:CYS194 4.8 84.5 1.0
O B:CYS188 4.8 88.2 1.0
CG B:PRO248 4.9 84.4 1.0
CA B:LYS193 5.0 86.2 1.0
C B:THR192 5.0 87.0 1.0

Reference:

D.P.Dowling, Z.D.Miles, C.Kohrer, S.J.Maiocco, S.J.Elliott, V.Bandarian, C.L.Drennan. Molecular Basis of Cobalamin-Dependent Rna Modification. Nucleic Acids Res. V. 44 9965 2016.
ISSN: ESSN 1362-4962
PubMed: 27638883
DOI: 10.1093/NAR/GKW806
Page generated: Tue Aug 6 08:54:52 2024

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