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Iron in PDB 5ul3: Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound

Protein crystallography data

The structure of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound, PDB code: 5ul3 was solved by J.Bridwell-Rabb, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.80 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.357, 99.595, 121.439, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.2

Other elements in 5ul3:

The structure of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound also contains other interesting chemical elements:

Cobalt (Co) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound (pdb code 5ul3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound, PDB code: 5ul3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5ul3

Go back to Iron Binding Sites List in 5ul3
Iron binding site 1 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:25.1
occ:1.00
FE1 A:SF4801 0.0 25.1 1.0
SG A:CYS318 2.2 24.6 1.0
S3 A:SF4801 2.2 29.8 1.0
S4 A:SF4801 2.3 27.3 1.0
S2 A:SF4801 2.3 24.2 1.0
FE3 A:SF4801 2.7 24.4 1.0
FE2 A:SF4801 2.7 28.0 1.0
FE4 A:SF4801 2.7 25.1 1.0
CB A:CYS318 3.0 24.7 1.0
NZ A:LYS448 3.8 32.0 0.5
S1 A:SF4801 3.9 26.0 1.0
N A:CYS318 4.1 28.1 1.0
CA A:CYS318 4.2 26.3 1.0
NZ A:LYS448 4.2 29.8 0.5
CD2 A:TYR315 4.3 27.6 1.0
CB A:CYS321 4.5 22.0 1.0
SG A:CYS321 4.6 24.2 1.0
S1 A:DTT803 4.6 34.5 1.0
CE A:LYS448 4.7 34.9 0.5
CE2 A:TYR315 4.8 23.4 1.0
SG A:CYS313 4.8 25.9 1.0
O A:HOH1031 4.9 38.0 1.0

Iron binding site 2 out of 4 in 5ul3

Go back to Iron Binding Sites List in 5ul3
Iron binding site 2 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:28.0
occ:1.00
FE2 A:SF4801 0.0 28.0 1.0
S4 A:SF4801 2.3 27.3 1.0
S3 A:SF4801 2.3 29.8 1.0
S1 A:SF4801 2.3 26.0 1.0
S1 A:DTT803 2.4 34.5 1.0
FE1 A:SF4801 2.7 25.1 1.0
FE4 A:SF4801 2.8 25.1 1.0
FE3 A:SF4801 2.8 24.4 1.0
O2 A:DTT803 3.1 52.4 1.0
C1 A:DTT803 3.4 30.2 1.0
C2 A:DTT803 3.7 45.3 1.0
S2 A:SF4801 4.0 24.2 1.0
C3 A:DTT803 4.2 54.1 1.0
O A:HOH1031 4.2 38.0 1.0
NZ A:LYS448 4.2 32.0 0.5
O A:HOH1227 4.3 32.5 1.0
O A:HOH1064 4.6 38.0 1.0
SG A:CYS318 4.7 24.6 1.0
SG A:CYS313 4.7 25.9 1.0
NZ A:LYS448 4.8 29.8 0.5
SG A:CYS321 4.9 24.2 1.0
O A:HOH1097 4.9 35.6 1.0
O A:GLU363 4.9 24.4 1.0
CG A:ARG399 5.0 32.8 1.0

Iron binding site 3 out of 4 in 5ul3

Go back to Iron Binding Sites List in 5ul3
Iron binding site 3 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:24.4
occ:1.00
FE3 A:SF4801 0.0 24.4 1.0
SG A:CYS321 2.3 24.2 1.0
S1 A:SF4801 2.3 26.0 1.0
S2 A:SF4801 2.3 24.2 1.0
S4 A:SF4801 2.3 27.3 1.0
FE1 A:SF4801 2.7 25.1 1.0
FE4 A:SF4801 2.7 25.1 1.0
FE2 A:SF4801 2.8 28.0 1.0
CB A:CYS321 3.1 22.0 1.0
S3 A:SF4801 3.9 29.8 1.0
NH2 A:ARG323 3.9 24.2 1.0
O A:HOH1064 4.2 38.0 1.0
N29 A:B12802 4.2 24.0 1.0
CA A:CYS321 4.6 24.2 1.0
CB A:CYS318 4.6 24.7 1.0
CZ A:ARG323 4.6 25.2 1.0
CD A:ARG323 4.7 23.4 1.0
SG A:CYS318 4.7 24.6 1.0
O2 A:DTT803 4.7 52.4 1.0
SG A:CYS313 4.9 25.9 1.0
OE2 A:GLU363 4.9 26.2 1.0
NE A:ARG323 5.0 25.4 1.0

Iron binding site 4 out of 4 in 5ul3

Go back to Iron Binding Sites List in 5ul3
Iron binding site 4 out of 4 in the Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Cobalamin-Dependent S-Adenosylmethionine Radical Enzyme Oxsb with Aqua-Cobalamin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:25.1
occ:1.00
FE4 A:SF4801 0.0 25.1 1.0
S2 A:SF4801 2.3 24.2 1.0
S3 A:SF4801 2.3 29.8 1.0
SG A:CYS313 2.3 25.9 1.0
S1 A:SF4801 2.3 26.0 1.0
FE3 A:SF4801 2.7 24.4 1.0
FE1 A:SF4801 2.7 25.1 1.0
FE2 A:SF4801 2.8 28.0 1.0
CB A:CYS313 3.3 23.7 1.0
S4 A:SF4801 3.9 27.3 1.0
N A:SER316 4.0 26.2 1.0
O A:HOH1097 4.1 35.6 1.0
CA A:SER316 4.4 25.0 1.0
CB A:TYR315 4.6 22.0 1.0
CA A:CYS313 4.7 22.7 1.0
SG A:CYS318 4.8 24.6 1.0
S1 A:DTT803 4.8 34.5 1.0
CD2 A:TYR315 4.8 27.6 1.0
SG A:CYS321 4.8 24.2 1.0
NH2 A:ARG323 4.8 24.2 1.0
CZ A:ARG323 4.9 25.2 1.0

Reference:

J.Bridwell-Rabb, A.Zhong, H.G.Sun, C.L.Drennan, H.W.Liu. A B12-Dependent Radical Sam Enzyme Involved in Oxetanocin A Biosynthesis. Nature V. 544 322 2017.
ISSN: ESSN 1476-4687
PubMed: 28346939
DOI: 10.1038/NATURE21689
Page generated: Tue Aug 6 09:52:39 2024

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