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Sodium 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:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the 4FE-4S-Pyruvate Formate-Lyase Activating Enzyme in Complex with Adomet and A Peptide Substrate, PDB code: 3cb8:

Sodium binding site 1 out of 1 in 3cb8

Go back to Sodium Binding Sites List in 3cb8
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na820

b:62.5
occ:1.00
 OD1 A:ASP104 2.3 75.3 1.0
OXT A:SAM501 2.4 65.4 1.0
O A:THR105 2.6 66.1 1.0
OD1 A:ASP129 2.7 71.5 1.0
O A:MET127 3.0 64.7 1.0
C A:THR105 3.2 66.4 1.0
N A:THR105 3.2 66.3 1.0
CG A:ASP129 3.4 70.1 1.0
CG A:ASP104 3.4 73.6 1.0
C A:SAM501 3.5 67.2 1.0
C A:ASP104 3.6 67.7 1.0
CA A:THR105 3.6 65.8 1.0
CB A:ASP129 3.6 66.4 1.0
N A:ASP129 3.8 66.5 1.0
O A:ASP104 4.1 68.7 1.0
C A:MET127 4.1 66.0 1.0
CA A:SAM501 4.1 68.7 1.0
CA A:ASP104 4.1 68.2 1.0
CB A:SAM501 4.2 70.5 1.0
O3' A:SAM501 4.2 79.5 1.0
OD2 A:ASP104 4.2 76.3 1.0
CA A:ASP129 4.3 65.4 1.0
N A:ASN106 4.3 66.1 1.0
C3' A:SAM501 4.3 78.4 1.0
CB A:ASP104 4.4 70.9 1.0
C A:LEU128 4.5 64.9 1.0
OD2 A:ASP129 4.5 72.7 1.0
O A:SAM501 4.6 65.9 1.0
CA A:LEU128 4.7 63.9 1.0
CA A:ASN106 4.8 64.9 1.0
N A:LEU128 4.8 64.3 1.0
CB A:MET127 4.9 69.5 1.0
CD A:ARG166 4.9 86.4 1.0
C5' A:SAM501 5.0 78.5 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: Mon Oct 7 06:13:22 2024

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