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Iron in PDB 2y8n: Crystal Structure of Glycyl Radical Enzyme

Enzymatic activity of Crystal Structure of Glycyl Radical Enzyme

All present enzymatic activity of Crystal Structure of Glycyl Radical Enzyme:
4.1.1.83;

Protein crystallography data

The structure of Crystal Structure of Glycyl Radical Enzyme, PDB code: 2y8n was solved by B.M.Martins, M.Blaser, M.Feliks, G.M.Ullmann, T.Selmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.18 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 132.280, 227.760, 148.010, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.8

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Glycyl Radical Enzyme (pdb code 2y8n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Glycyl Radical Enzyme, PDB code: 2y8n:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 2y8n

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Iron binding site 1 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


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 Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe87

b:38.0
occ:1.00
 FE1 B:SF487 0.0 38.0 1.0
S2 B:SF487 2.3 42.1 1.0
S4 B:SF487 2.3 41.4 1.0
S3 B:SF487 2.3 35.6 1.0
SG B:CYS6 2.5 32.6 1.0
FE3 B:SF487 2.7 44.2 1.0
FE2 B:SF487 2.7 42.2 1.0
FE4 B:SF487 2.7 40.2 1.0
CB B:CYS6 3.1 33.6 1.0
S1 B:SF487 3.9 48.2 1.0
CB B:ASN8 4.0 37.0 1.0
CA B:PHE39 4.4 41.7 1.0
ND2 B:ASN8 4.5 41.3 1.0
CA B:CYS6 4.6 29.5 1.0
CA B:HIS3 4.7 41.3 1.0
CA B:ASN8 4.7 30.9 1.0
CD2 B:PHE39 4.7 41.2 1.0
CG B:ASN8 4.7 36.2 1.0
N B:ASN8 4.7 30.3 1.0
ND1 B:HIS3 4.8 39.6 1.0
N B:TYR9 4.8 28.2 1.0
C B:ASN8 4.8 29.7 1.0
O B:HIS3 4.9 34.9 1.0
N B:PHE39 4.9 44.1 1.0
SG B:CYS19 4.9 37.7 1.0
O B:ASN38 5.0 46.6 1.0
CB B:PHE39 5.0 42.7 1.0

Iron binding site 2 out of 16 in 2y8n

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Iron binding site 2 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


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 Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe87

b:42.2
occ:1.00
 FE2 B:SF487 0.0 42.2 1.0
ND1 B:HIS3 2.1 39.6 1.0
S4 B:SF487 2.3 41.4 1.0
S1 B:SF487 2.3 48.2 1.0
S3 B:SF487 2.3 35.6 1.0
FE4 B:SF487 2.7 40.2 1.0
FE1 B:SF487 2.7 38.0 1.0
FE3 B:SF487 2.7 44.2 1.0
CG B:HIS3 3.1 41.3 1.0
CE1 B:HIS3 3.1 45.3 1.0
CB B:HIS3 3.4 40.6 1.0
CA B:HIS3 3.5 41.3 1.0
S2 B:SF487 3.9 42.1 1.0
NE2 B:HIS3 4.2 44.9 1.0
CD2 B:HIS3 4.2 41.8 1.0
N B:HIS3 4.3 39.3 1.0
N B:CYS36 4.5 45.2 1.0
CB B:CYS19 4.6 35.7 1.0
C B:HIS3 4.7 38.0 1.0
CB B:CYS6 4.8 33.6 1.0
SG B:CYS19 4.8 37.7 1.0
CA B:ALA35 4.8 45.4 1.0
O B:HIS3 4.9 34.9 1.0
CB B:CYS36 4.9 45.4 1.0
SG B:CYS6 5.0 32.6 1.0
O B:GLU34 5.0 40.5 1.0

Iron binding site 3 out of 16 in 2y8n

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Iron binding site 3 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


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 Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe87

b:44.2
occ:1.00
 FE3 B:SF487 0.0 44.2 1.0
S1 B:SF487 2.3 48.2 1.0
S2 B:SF487 2.3 42.1 1.0
S4 B:SF487 2.3 41.4 1.0
FE4 B:SF487 2.7 40.2 1.0
SG B:CYS36 2.7 48.5 1.0
FE1 B:SF487 2.7 38.0 1.0
FE2 B:SF487 2.7 42.2 1.0
CB B:CYS36 3.1 45.4 1.0
N B:CYS36 3.5 45.2 1.0
CA B:CYS36 3.8 46.9 1.0
S3 B:SF487 3.9 35.6 1.0
O B:CYS36 4.3 48.3 1.0
C B:CYS36 4.3 50.1 1.0
ND1 B:HIS3 4.4 39.6 1.0
N B:PHE39 4.5 44.1 1.0
C B:ASN38 4.6 46.5 1.0
CB B:ASN38 4.7 47.6 1.0
C B:ALA35 4.7 45.3 1.0
SG B:CYS19 4.7 37.7 1.0
CA B:PHE39 4.7 41.7 1.0
N B:ASN38 4.9 51.2 1.0
CE1 B:HIS3 4.9 45.3 1.0
SG B:CYS6 4.9 32.6 1.0
CA B:ASN38 5.0 49.7 1.0

Iron binding site 4 out of 16 in 2y8n

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Iron binding site 4 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


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 Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe87

b:40.2
occ:1.00
 FE4 B:SF487 0.0 40.2 1.0
S2 B:SF487 2.3 42.1 1.0
S3 B:SF487 2.3 35.6 1.0
S1 B:SF487 2.3 48.2 1.0
SG B:CYS19 2.4 37.7 1.0
FE2 B:SF487 2.7 42.2 1.0
FE3 B:SF487 2.7 44.2 1.0
FE1 B:SF487 2.7 38.0 1.0
CB B:CYS19 3.1 35.7 1.0
CA B:CYS19 3.9 34.3 1.0
S4 B:SF487 3.9 41.4 1.0
ND1 B:HIS3 4.5 39.6 1.0
CB B:ASN8 4.5 37.0 1.0
C B:CYS19 4.6 33.1 1.0
N B:ALA20 4.7 33.1 1.0
CD1 B:LEU21 4.8 46.1 1.0
CG B:LEU21 4.8 41.7 1.0
CB B:LEU21 4.9 40.7 1.0
SG B:CYS6 5.0 32.6 1.0
SG B:CYS36 5.0 48.5 1.0
N B:LEU21 5.0 37.1 1.0

Iron binding site 5 out of 16 in 2y8n

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Iron binding site 5 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


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 Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe88

b:30.1
occ:1.00
 FE1 B:SF488 0.0 30.1 1.0
S3 B:SF488 2.3 28.0 1.0
SG B:CYS62 2.3 26.1 1.0
S4 B:SF488 2.3 26.5 1.0
S2 B:SF488 2.3 26.8 1.0
FE4 B:SF488 2.7 28.1 1.0
FE3 B:SF488 2.7 30.1 1.0
FE2 B:SF488 2.7 28.3 1.0
CB B:CYS62 3.2 27.0 1.0
S1 B:SF488 3.9 27.8 1.0
NH1 A:ARG61 4.0 22.1 1.0
CA B:CYS62 4.2 23.6 1.0
CB B:ASN50 4.4 27.9 1.0
N B:GLY64 4.7 28.8 1.0
NH2 A:ARG61 4.7 25.9 1.0
CA B:GLY64 4.8 34.6 1.0
SG B:CYS45 4.8 24.1 1.0
SG B:CYS48 4.8 24.4 1.0
CZ A:ARG61 4.9 26.3 1.0
C B:CYS62 4.9 27.5 1.0
SG B:CYS80 4.9 26.6 1.0
O B:ASN50 5.0 29.1 1.0
CB B:ALA71 5.0 27.5 1.0

Iron binding site 6 out of 16 in 2y8n

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Iron binding site 6 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


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 Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe88

b:28.3
occ:1.00
 FE2 B:SF488 0.0 28.3 1.0
S3 B:SF488 2.3 28.0 1.0
S1 B:SF488 2.3 27.8 1.0
S4 B:SF488 2.3 26.5 1.0
SG B:CYS80 2.4 26.6 1.0
FE4 B:SF488 2.7 28.1 1.0
FE1 B:SF488 2.7 30.1 1.0
FE3 B:SF488 2.8 30.1 1.0
CB B:CYS80 3.3 21.6 1.0
S2 B:SF488 3.9 26.8 1.0
N B:TYR83 4.1 27.8 1.0
CA B:TYR83 4.4 29.3 1.0
CH2 A:TRP58 4.4 18.7 1.0
C B:SER82 4.4 32.4 1.0
CB B:SER82 4.5 34.5 1.0
CZ2 A:TRP58 4.6 19.4 1.0
SG B:CYS62 4.7 26.1 1.0
CA B:CYS80 4.7 25.7 1.0
CB B:TYR83 4.7 26.8 1.0
SG B:CYS45 4.7 24.1 1.0
CA B:SER82 4.8 27.9 1.0
O A:HOH2043 4.8 33.8 1.0
N B:SER82 4.9 31.7 1.0
SG B:CYS48 4.9 24.4 1.0
O B:SER82 4.9 27.8 1.0

Iron binding site 7 out of 16 in 2y8n

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Iron binding site 7 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


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 Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe88

b:30.1
occ:1.00
 FE3 B:SF488 0.0 30.1 1.0
S2 B:SF488 2.3 26.8 1.0
S1 B:SF488 2.3 27.8 1.0
SG B:CYS45 2.3 24.1 1.0
S4 B:SF488 2.3 26.5 1.0
FE4 B:SF488 2.7 28.1 1.0
FE1 B:SF488 2.7 30.1 1.0
FE2 B:SF488 2.8 28.3 1.0
CB B:CYS45 3.2 26.3 1.0
CA B:CYS45 3.6 24.5 1.0
S3 B:SF488 3.9 28.0 1.0
N B:CYS45 4.4 24.9 1.0
CB B:ALA71 4.6 27.5 1.0
CB B:CYS48 4.7 28.2 1.0
SG B:CYS48 4.8 24.4 1.0
CB B:ALA77 4.8 23.6 1.0
O B:HOH2058 4.8 23.1 1.0
SG B:CYS62 4.8 26.1 1.0
C B:CYS45 4.8 29.3 1.0
SG B:CYS80 4.9 26.6 1.0

Iron binding site 8 out of 16 in 2y8n

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Iron binding site 8 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


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 Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe88

b:28.1
occ:1.00
 FE4 B:SF488 0.0 28.1 1.0
S2 B:SF488 2.3 26.8 1.0
S3 B:SF488 2.3 28.0 1.0
S1 B:SF488 2.3 27.8 1.0
SG B:CYS48 2.4 24.4 1.0
FE1 B:SF488 2.7 30.1 1.0
FE2 B:SF488 2.7 28.3 1.0
FE3 B:SF488 2.7 30.1 1.0
CB B:CYS48 3.2 28.2 1.0
S4 B:SF488 3.8 26.5 1.0
CA B:TYR83 4.1 29.3 1.0
CB B:ASN50 4.2 27.9 1.0
OD1 B:ASN50 4.3 29.8 1.0
CD1 B:TYR83 4.5 28.5 1.0
N B:TYR83 4.5 27.8 1.0
O B:SER82 4.6 27.8 1.0
CB B:TYR83 4.7 26.8 1.0
CA B:CYS48 4.7 29.8 1.0
CG B:ASN50 4.7 29.9 1.0
SG B:CYS62 4.7 26.1 1.0
CA B:CYS45 4.7 24.5 1.0
C B:SER82 4.7 32.4 1.0
SG B:CYS45 4.8 24.1 1.0
N B:PHE51 4.8 28.6 1.0
N B:ASN50 4.8 31.8 1.0
CA B:ASN50 4.8 28.0 1.0
SG B:CYS80 4.8 26.6 1.0
C B:ASN50 4.9 27.6 1.0
N B:LYS84 4.9 29.9 1.0
CB B:CYS45 5.0 26.3 1.0

Iron binding site 9 out of 16 in 2y8n

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Iron binding site 9 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe87

b:38.0
occ:1.00
 FE1 D:SF487 0.0 38.0 1.0
S4 D:SF487 2.3 42.9 1.0
S3 D:SF487 2.3 40.7 1.0
S2 D:SF487 2.3 37.7 1.0
SG D:CYS6 2.4 33.7 1.0
FE3 D:SF487 2.7 47.1 1.0
FE4 D:SF487 2.7 41.8 1.0
FE2 D:SF487 2.8 44.8 1.0
CB D:CYS6 3.0 32.6 1.0
S1 D:SF487 4.0 49.3 1.0
CB D:ASN8 4.0 33.0 1.0
CA D:PHE39 4.3 44.4 1.0
ND2 D:ASN8 4.4 41.2 1.0
CA D:CYS6 4.5 33.6 1.0
CD2 D:PHE39 4.7 42.1 1.0
CA D:ASN8 4.7 32.6 1.0
N D:ASN8 4.7 34.3 1.0
C D:ASN8 4.7 29.2 1.0
N D:PHE39 4.8 47.1 1.0
CG D:ASN8 4.8 38.3 1.0
CA D:HIS3 4.8 42.3 1.0
O D:HIS3 4.8 38.7 1.0
CB D:PHE39 4.8 43.6 1.0
N D:TYR9 4.8 30.7 1.0
ND1 D:HIS3 4.9 46.0 1.0
SG D:CYS19 4.9 37.0 1.0

Iron binding site 10 out of 16 in 2y8n

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Iron binding site 10 out of 16 in the Crystal Structure of Glycyl Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Glycyl Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe87

b:44.8
occ:1.00
 FE2 D:SF487 0.0 44.8 1.0
ND1 D:HIS3 2.2 46.0 1.0
S4 D:SF487 2.3 42.9 1.0
S1 D:SF487 2.3 49.3 1.0
S3 D:SF487 2.3 40.7 1.0
FE3 D:SF487 2.7 47.1 1.0
FE4 D:SF487 2.7 41.8 1.0
FE1 D:SF487 2.8 38.0 1.0
CE1 D:HIS3 3.1 47.3 1.0
CG D:HIS3 3.1 47.8 1.0
CB D:HIS3 3.5 45.5 1.0
CA D:HIS3 3.6 42.3 1.0
S2 D:SF487 3.9 37.7 1.0
NE2 D:HIS3 4.1 47.5 1.0
CD2 D:HIS3 4.2 45.7 1.0
N D:HIS3 4.5 41.6 1.0
N D:CYS36 4.6 52.3 1.0
CA D:ALA35 4.7 50.0 1.0
SG D:CYS19 4.7 37.0 1.0
CB D:CYS19 4.8 37.1 1.0
C D:HIS3 4.8 40.7 1.0
CB D:CYS6 4.8 32.6 1.0
O D:HIS3 4.9 38.7 1.0
SG D:CYS36 5.0 47.8 1.0
SG D:CYS6 5.0 33.7 1.0

Reference:

B.M.Martins, M.Blaser, M.Feliks, G.M.Ullmann, W.Buckel, T.Selmer. Structural Basis For A Kolbe-Type Decarboxylation Catalyzed By A Glycyl Radical Enzyme. J.Am.Chem.Soc. V. 133 14666 2011.
ISSN: ISSN 0002-7863
PubMed: 21823587
DOI: 10.1021/JA203344X
Page generated: Sun Aug 4 05:09:43 2024

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