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Sodium in PDB 6s6y: X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran

Enzymatic activity of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran

All present enzymatic activity of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran:
2.3.1.101;

Protein crystallography data

The structure of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran, PDB code: 6s6y was solved by T.Wagner, J.L.Hemmann, S.Shima, J.Vorholt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.95 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 84.974, 130.322, 172.689, 84.97, 75.91, 82.09
R / Rfree (%) 22.1 / 25.1

Other elements in 6s6y:

The structure of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran also contains other interesting chemical elements:

Potassium (K) 9 atoms
Zinc (Zn) 8 atoms
Calcium (Ca) 6 atoms
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran (pdb code 6s6y). 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 X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran, PDB code: 6s6y:

Sodium binding site 1 out of 1 in 6s6y

Go back to Sodium Binding Sites List in 6s6y
Sodium binding site 1 out of 1 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na402

b:60.1
occ:1.00
 OG J:SER39 2.5 76.0 1.0
CB J:GLU37 3.0 0.6 1.0
CB J:SER39 3.1 77.5 1.0
N J:ALA317 3.2 75.9 1.0
N J:SER39 3.4 82.5 1.0
CA J:GLY316 3.6 0.1 1.0
CG J:GLU37 3.8 0.3 1.0
CA J:SER39 3.9 79.8 1.0
C J:GLY316 3.9 0.1 1.0
N J:VAL38 4.0 83.3 1.0
CB J:ALA317 4.2 74.2 1.0
CA J:ALA317 4.2 74.3 1.0
CA J:GLU37 4.2 0.2 1.0
CG2 J:VAL38 4.2 79.9 1.0
C J:GLU37 4.4 0.6 1.0
O J:ALA317 4.4 73.2 1.0
C J:VAL38 4.5 81.3 1.0
O I:ALA533 4.6 0.1 1.0
OE1 J:GLU37 4.7 0.0 1.0
CA J:VAL38 4.7 79.0 1.0
CD J:GLU37 4.8 0.2 1.0
C J:ALA317 4.8 73.5 1.0
N J:GLY316 4.9 0.4 1.0
O J:GLY315 4.9 88.1 1.0
C J:SER39 5.0 84.0 1.0
CE1 J:TYR328 5.0 81.2 1.0
CA I:ALA533 5.0 0.2 1.0

Reference:

J.L.Hemmann, T.Wagner, S.Shima, J.Vorholt. Methylofuran Is A Prosthetic Group of the Formyltransferase/Hydrolase Complex and Shuttles One-Carbon Units Between Two Active Sites To Be Published.
Page generated: Tue Oct 8 13:23:29 2024

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