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Iron in PDB 3cb8: 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate

Enzymatic activity of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate

All present enzymatic activity of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate:
1.97.1.4;

Protein crystallography data

The structure of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate, PDB code: 3cb8 was solved by J.L.Vey, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.95 / 2.77
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 74.494, 74.494, 187.737, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 25.4

Other elements in 3cb8:

The structure of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate (pdb code 3cb8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate, PDB code: 3cb8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3cb8

Go back to Iron Binding Sites List in 3cb8
Iron binding site 1 out of 4 in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:61.5
occ:1.00
 FE1 A:SF4500 0.0 61.5 1.0
SG A:CYS33 2.3 57.8 1.0
S3 A:SF4500 2.3 56.9 1.0
S2 A:SF4500 2.3 56.9 1.0
S4 A:SF4500 2.3 59.5 1.0
FE4 A:SF4500 2.7 58.1 1.0
FE3 A:SF4500 2.7 59.1 1.0
FE2 A:SF4500 2.7 65.9 1.0
CB A:CYS33 3.2 58.1 1.0
S1 A:SF4500 3.8 58.3 1.0
O A:SAM501 3.9 65.9 1.0
N A:CYS33 3.9 56.8 1.0
NZ A:LYS131 4.0 51.1 1.0
CE A:LYS131 4.1 54.4 1.0
CA A:CYS33 4.2 58.1 1.0
CB A:MET31 4.3 65.6 1.0
N A:SAM501 4.5 65.8 1.0
CB A:CYS36 4.7 61.2 1.0
SG A:CYS29 4.7 58.3 1.0
SG A:CYS36 4.7 57.6 1.0
CD A:LYS131 4.9 56.4 1.0
C A:SAM501 5.0 67.2 1.0

Iron binding site 2 out of 4 in 3cb8

Go back to Iron Binding Sites List in 3cb8
Iron binding site 2 out of 4 in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:65.9
occ:1.00
 FE2 A:SF4500 0.0 65.9 1.0
O A:SAM501 2.1 65.9 1.0
N A:SAM501 2.2 65.8 1.0
S4 A:SF4500 2.3 59.5 1.0
S3 A:SF4500 2.3 56.9 1.0
S1 A:SF4500 2.3 58.3 1.0
FE1 A:SF4500 2.7 61.5 1.0
FE4 A:SF4500 2.7 58.1 1.0
FE3 A:SF4500 2.9 59.1 1.0
C A:SAM501 2.9 67.2 1.0
CA A:SAM501 3.0 68.7 1.0
SD A:SAM501 3.2 78.4 1.0
CG A:SAM501 3.4 74.5 1.0
CE A:SAM501 3.5 78.4 1.0
CB A:SAM501 3.8 70.5 1.0
S2 A:SF4500 4.0 56.9 1.0
OXT A:SAM501 4.2 65.4 1.0
NZ A:LYS131 4.3 51.1 1.0
O A:GLY78 4.6 65.5 1.0
SG A:CYS29 4.6 58.3 1.0
C2' A:SAM501 4.7 77.9 1.0
SG A:CYS33 4.8 57.8 1.0
CE A:LYS131 4.8 54.4 1.0
C5' A:SAM501 5.0 78.5 1.0
ND2 A:ASN106 5.0 64.6 1.0

Iron binding site 3 out of 4 in 3cb8

Go back to Iron Binding Sites List in 3cb8
Iron binding site 3 out of 4 in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:59.1
occ:1.00
 FE3 A:SF4500 0.0 59.1 1.0
S2 A:SF4500 2.3 56.9 1.0
S4 A:SF4500 2.3 59.5 1.0
S1 A:SF4500 2.3 58.3 1.0
SG A:CYS36 2.3 57.6 1.0
FE1 A:SF4500 2.7 61.5 1.0
FE4 A:SF4500 2.8 58.1 1.0
FE2 A:SF4500 2.9 65.9 1.0
CB A:CYS36 3.2 61.2 1.0
NE1 A:TRP42 3.7 73.1 1.0
S3 A:SF4500 4.0 56.9 1.0
CA A:CYS36 4.0 63.7 1.0
CE A:SAM501 4.1 78.4 1.0
CD1 A:TRP42 4.5 74.0 1.0
SG A:CYS33 4.7 57.8 1.0
N A:SAM501 4.7 65.8 1.0
CE2 A:TRP42 4.7 72.4 1.0
CB A:CYS33 4.7 58.1 1.0
O A:SAM501 4.8 65.9 1.0
SG A:CYS29 4.8 58.3 1.0
C A:CYS36 4.9 64.4 1.0
O A:ASN38 5.0 67.1 1.0
SD A:SAM501 5.0 78.4 1.0
N A:CYS36 5.0 63.4 1.0

Iron binding site 4 out of 4 in 3cb8

Go back to Iron Binding Sites List in 3cb8
Iron binding site 4 out of 4 in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:58.1
occ:1.00
 FE4 A:SF4500 0.0 58.1 1.0
SG A:CYS29 2.2 58.3 1.0
S3 A:SF4500 2.3 56.9 1.0
S1 A:SF4500 2.3 58.3 1.0
S2 A:SF4500 2.3 56.9 1.0
FE1 A:SF4500 2.7 61.5 1.0
FE2 A:SF4500 2.7 65.9 1.0
FE3 A:SF4500 2.8 59.1 1.0
CB A:CYS29 3.4 59.8 1.0
N A:SAM501 3.5 65.8 1.0
S4 A:SF4500 3.9 59.5 1.0
CB A:MET31 4.2 65.6 1.0
O A:MET31 4.4 60.3 1.0
NE1 A:TRP42 4.4 73.1 1.0
ND2 A:ASN106 4.5 64.6 1.0
C A:MET31 4.6 61.1 1.0
O A:SAM501 4.6 65.9 1.0
N A:MET31 4.7 62.5 1.0
SG A:CYS33 4.7 57.8 1.0
CD1 A:TRP42 4.7 74.0 1.0
CA A:MET31 4.7 63.0 1.0
CA A:CYS29 4.8 60.8 1.0
SG A:CYS36 4.8 57.6 1.0
C A:GLY78 4.9 65.0 1.0
CA A:GLY78 4.9 65.0 1.0
CA A:SAM501 4.9 68.7 1.0
O A:GLY78 5.0 65.5 1.0
CG A:MET31 5.0 68.7 1.0

Reference:

J.L.Vey, J.Yang, M.Li, W.E.Broderick, J.B.Broderick, C.L.Drennan. Structural Basis For Glycyl Radical Formation By Pyruvate Formate-Lyase Activating Enzyme. Proc.Natl.Acad.Sci.Usa V. 105 16137 2008.
ISSN: ISSN 0027-8424
PubMed: 18852451
DOI: 10.1073/PNAS.0806640105
Page generated: Sun Aug 4 08:16:45 2024

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