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Magnesium in PDB 4pio: Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah

Enzymatic activity of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah

All present enzymatic activity of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah:
2.1.1.44;

Protein crystallography data

The structure of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah, PDB code: 4pio was solved by A.Vit, F.P.Seebeck, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.709, 67.511, 79.679, 90.00, 110.98, 90.00
R / Rfree (%) 14.8 / 18

Other elements in 4pio:

The structure of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah (pdb code 4pio). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah, PDB code: 4pio:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4pio

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Magnesium binding site 1 out of 6 in the Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:33.9
occ:1.00
 O A:HOH851 2.1 22.8 1.0
O A:HOH922 2.1 35.2 1.0
O A:HOH875 2.1 26.1 1.0
O A:HOH973 2.2 37.3 1.0
O A:HOH885 2.3 29.2 1.0
O A:HIS239 4.0 11.2 1.0
OE2 A:GLU238 4.2 24.3 1.0
OD1 A:ASP207 4.2 13.9 1.0
OD2 A:ASP207 4.3 19.1 1.0
O A:HOH810 4.6 23.5 1.0
CG A:ASP207 4.7 12.4 1.0
HG2 A:GLU238 4.7 20.3 1.0
HG3 A:GLU238 4.8 20.3 1.0
CL A:CL407 5.0 26.2 1.0

Magnesium binding site 2 out of 6 in 4pio

Go back to Magnesium Binding Sites List in 4pio
Magnesium binding site 2 out of 6 in the Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:36.9
occ:1.00
 O A:HOH505 2.0 30.1 1.0
OD2 A:ASP233 2.0 27.2 1.0
O A:HOH556 2.1 28.7 1.0
O A:HOH633 2.2 35.9 1.0
CG A:ASP233 3.1 21.7 1.0
HB2 A:ASP233 3.3 17.1 1.0
CB A:ASP233 3.6 14.2 1.0
HE22 A:GLN260 3.6 19.0 1.0
HB3 A:ASP233 3.6 17.1 1.0
HB2 A:ALA236 4.1 21.0 1.0
OD1 A:ASP233 4.2 21.1 1.0
O A:HOH928 4.2 30.7 1.0
NE2 A:GLN260 4.4 15.8 1.0
HE21 A:GLN260 4.9 19.0 1.0
CB A:ALA236 5.0 17.5 1.0

Magnesium binding site 3 out of 6 in 4pio

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Magnesium binding site 3 out of 6 in the Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:32.7
occ:1.00
 O A:HOH856 2.0 29.7 1.0
OD1 A:ASP233 2.1 21.1 1.0
O A:HOH625 2.2 35.9 1.0
O A:HOH502 2.3 38.0 1.0
OD1 A:ASP235 2.5 40.6 1.0
OD2 A:ASP235 2.9 42.5 1.0
CG A:ASP235 2.9 32.2 1.0
CG A:ASP233 3.1 21.7 1.0
H A:ASP235 3.2 18.4 1.0
OD2 A:ASP233 3.5 27.2 1.0
O A:HOH769 3.9 19.5 1.0
N A:ASP235 4.0 15.3 1.0
O B:HOH621 4.0 34.6 1.0
CB A:ASP235 4.2 25.6 1.0
HA A:ASP233 4.2 18.1 1.0
H A:LEU234 4.3 15.8 1.0
CB A:ASP233 4.4 14.2 1.0
HB3 A:ASP235 4.4 30.8 1.0
N A:LEU234 4.5 13.2 1.0
C A:ASP233 4.6 12.4 1.0
CA A:ASP233 4.6 15.1 1.0
CA A:ASP235 4.6 19.3 1.0
H A:ALA236 4.8 17.5 1.0
HB2 A:ASP235 4.9 30.8 1.0
HB2 A:ASP233 4.9 17.1 1.0
HB3 A:ASP233 5.0 17.1 1.0

Magnesium binding site 4 out of 6 in 4pio

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Magnesium binding site 4 out of 6 in the Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:40.7
occ:1.00
 O A:HOH689 2.4 32.7 1.0
O A:HOH685 2.5 41.0 1.0
O A:HOH531 3.8 30.8 1.0
O A:HOH546 4.1 21.3 1.0
HG2 A:ARG101 4.9 14.7 1.0
HD2 A:ARG101 4.9 17.5 1.0

Magnesium binding site 5 out of 6 in 4pio

Go back to Magnesium Binding Sites List in 4pio
Magnesium binding site 5 out of 6 in the Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:19.9
occ:1.00
 O B:HOH680 2.1 19.0 1.0
O B:HOH966 3.7 37.4 1.0
O B:HOH508 3.7 33.4 1.0
HG3 B:GLU91 4.4 20.3 1.0
O B:HOH630 4.6 30.7 1.0
HB2 B:GLU91 5.0 15.5 1.0

Magnesium binding site 6 out of 6 in 4pio

Go back to Magnesium Binding Sites List in 4pio
Magnesium binding site 6 out of 6 in the Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ergothioneine-Biosynthetic Methyltransferase Egtd in Complex with N,N- Dimethylhistidine and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:40.8
occ:1.00
 O B:HOH513 2.1 27.0 1.0
O B:HOH951 2.2 40.3 1.0
O B:HOH891 2.3 32.6 1.0
O B:HOH597 2.5 30.5 1.0
HA B:ARG226 3.7 14.2 1.0
HG B:SER229 3.7 26.7 1.0
O B:HOH777 4.0 26.1 1.0
O B:HOH904 4.1 34.1 1.0
HA B:SER229 4.2 19.7 1.0
O B:ARG226 4.3 14.5 1.0
O B:ASN225 4.4 13.6 1.0
OG B:SER229 4.5 22.3 1.0
HG3 B:ARG226 4.6 19.7 1.0
CA B:ARG226 4.6 11.9 1.0
C B:ARG226 4.9 13.9 1.0

Reference:

A.Vit, L.Misson, W.Blankenfeldt, F.P.Seebeck. Ergothioneine Biosynthetic Methyltransferase Egtd Reveals the Structural Basis of Aromatic Amino Acid Betaine Biosynthesis. Chembiochem 2014.
ISSN: ESSN 1439-7633
PubMed: 25404173
DOI: 10.1002/CBIC.201402522
Page generated: Tue Aug 20 01:22:36 2024

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