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Potassium in PDB 3bof: Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine

Enzymatic activity of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine

All present enzymatic activity of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine:
2.1.1.13;

Protein crystallography data

The structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine, PDB code: 3bof was solved by M.Koutmos, J.L.Smith, M.L.Ludwig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.68 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.067, 86.308, 125.879, 90.00, 100.03, 90.00
R / Rfree (%) 19.5 / 22.2

Other elements in 3bof:

The structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine also contains other interesting chemical elements:

Yttrium (Y) 1 atom
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine (pdb code 3bof). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine, PDB code: 3bof:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 3bof

Go back to Potassium Binding Sites List in 3bof
Potassium binding site 1 out of 2 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K703

b:12.8
occ:1.00
 O A:GLY271 2.7 13.3 1.0
O A:GLY20 2.7 14.3 1.0
OE1 A:GLU232 2.7 12.0 1.0
OD2 A:ASP19 2.8 12.5 1.0
O A:HOH714 2.9 14.0 1.0
O A:ASP19 2.9 13.0 1.0
C A:ASP19 3.5 12.6 1.0
C A:GLY20 3.5 13.6 1.0
CD1 A:LEU62 3.6 13.0 1.0
CD A:GLU232 3.9 10.2 1.0
C A:GLY271 3.9 13.6 1.0
CG A:ASP19 3.9 13.2 1.0
CA A:GLY20 4.0 12.4 1.0
N A:GLY20 4.0 13.1 1.0
CA A:ASP19 4.3 13.2 1.0
CG A:LEU62 4.3 14.1 1.0
N A:ASP19 4.3 13.9 1.0
N A:GLY271 4.4 13.3 1.0
N A:ALA21 4.5 12.5 1.0
OE2 A:GLU146 4.5 14.5 1.0
CB A:ASP19 4.6 13.3 1.0
CG A:GLU232 4.6 9.9 1.0
OE2 A:GLU232 4.7 13.6 1.0
N A:CYS272 4.7 13.9 1.0
CA A:CYS272 4.7 13.4 1.0
OD1 A:ASP19 4.8 13.7 1.0
CA A:GLY271 4.8 13.8 1.0
CA A:ALA21 4.9 12.3 1.0
CD2 A:LEU18 5.0 14.4 1.0
CB A:GLU232 5.0 10.3 1.0

Potassium binding site 2 out of 2 in 3bof

Go back to Potassium Binding Sites List in 3bof
Potassium binding site 2 out of 2 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K704

b:17.0
occ:1.00
 O B:GLY271 2.6 19.4 1.0
OE1 B:GLU232 2.7 16.3 1.0
O B:GLY20 2.8 17.5 1.0
OD2 B:ASP19 2.8 16.5 1.0
O B:HOH734 2.8 19.2 1.0
O B:ASP19 2.8 18.3 1.0
C B:ASP19 3.4 18.0 1.0
CD1 B:LEU62 3.5 18.9 1.0
C B:GLY20 3.5 18.1 1.0
CD B:GLU232 3.8 17.4 1.0
C B:GLY271 3.9 19.4 1.0
CG B:ASP19 3.9 18.3 1.0
CA B:GLY20 3.9 17.4 1.0
N B:GLY20 4.0 17.9 1.0
CA B:ASP19 4.3 18.1 1.0
N B:ASP19 4.3 18.1 1.0
N B:GLY271 4.4 18.5 1.0
CG B:LEU62 4.4 16.2 1.0
OE2 B:GLU146 4.5 18.6 1.0
N B:ALA21 4.5 16.5 1.0
CB B:ASP19 4.6 17.9 1.0
CG B:GLU232 4.6 17.1 1.0
OE2 B:GLU232 4.6 17.9 1.0
CA B:GLY271 4.7 18.9 1.0
N B:CYS272 4.8 19.4 1.0
OD1 B:ASP19 4.8 17.4 1.0
CA B:CYS272 4.8 18.8 1.0
CD2 B:LEU18 4.9 18.1 1.0
N B:HCS712 4.9 18.6 1.0
CA B:ALA21 4.9 17.4 1.0
OXT B:HCS712 4.9 19.8 1.0
CE1 B:TYR22 5.0 15.4 1.0
CB B:GLU232 5.0 17.8 1.0
CB B:LEU18 5.0 18.6 1.0

Reference:

M.Koutmos, R.Pejchal, T.M.Bomer, R.G.Matthews, J.L.Smith, M.L.Ludwig. Metal Active Site Elasticity Linked to Activation of Homocysteine in Methionine Synthases. Proc.Natl.Acad.Sci.Usa V. 105 3286 2008.
ISSN: ISSN 0027-8424
PubMed: 18296644
DOI: 10.1073/PNAS.0709960105
Page generated: Mon Aug 12 07:51:33 2024

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