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Magnesium in PDB 4xvz: Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg

Enzymatic activity of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg

All present enzymatic activity of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg:
2.1.1.237;

Protein crystallography data

The structure of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg, PDB code: 4xvz was solved by D.L.Akey, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.60 / 2.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.864, 148.587, 66.855, 90.00, 120.23, 90.00
R / Rfree (%) 17.8 / 21.7

Other elements in 4xvz:

The structure of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg (pdb code 4xvz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg, PDB code: 4xvz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4xvz

Go back to Magnesium Binding Sites List in 4xvz
Magnesium binding site 1 out of 4 in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:27.3
occ:1.00
O A:HOH453 2.0 49.9 1.0
O A:HOH455 2.1 43.9 1.0
OD2 A:ASP216 2.2 36.7 1.0
O A:HOH454 2.2 36.5 1.0
OD1 A:ASP189 2.3 45.0 1.0
OD2 A:ASP217 2.3 41.0 1.0
OD1 A:ASP217 2.4 41.9 1.0
CG A:ASP217 2.7 40.4 1.0
CG A:ASP216 3.4 37.2 1.0
CG A:ASP189 3.4 45.3 1.0
OD2 A:ASP189 3.8 53.6 1.0
OE1 A:GLN246 4.0 46.1 1.0
CB A:ASP216 4.1 35.1 1.0
CB A:ASP217 4.2 39.5 1.0
N A:GLY190 4.3 46.5 1.0
O A:HOH437 4.3 52.8 1.0
OD1 A:ASP216 4.4 36.1 1.0
NH2 A:ARG61 4.6 55.6 1.0
O A:HOH447 4.6 47.5 1.0
CB A:ASP189 4.6 41.7 1.0
C A:ASP216 4.7 33.4 1.0
CA A:ASP189 4.8 42.2 1.0
O A:ASP216 4.8 32.9 1.0
C A:ASP189 4.8 44.1 1.0
N A:ASP217 4.8 35.9 1.0
CA A:ASP217 4.9 37.9 1.0

Magnesium binding site 2 out of 4 in 4xvz

Go back to Magnesium Binding Sites List in 4xvz
Magnesium binding site 2 out of 4 in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:43.2
occ:1.00
O B:HOH408 1.8 50.6 1.0
O B:HOH409 1.9 54.7 1.0
OD2 B:ASP216 1.9 63.7 1.0
OD1 B:ASP189 2.2 55.3 1.0
O B:HOH407 2.4 54.7 1.0
OD2 B:ASP217 2.4 57.1 1.0
OD1 B:ASP217 2.5 62.7 1.0
CG B:ASP217 2.8 63.9 1.0
CG B:ASP216 3.0 62.3 1.0
CG B:ASP189 3.2 56.9 1.0
OD2 B:ASP189 3.6 63.0 1.0
CB B:ASP216 3.8 58.0 1.0
OE1 B:GLN246 3.9 76.8 1.0
OD1 B:ASP216 4.0 66.2 1.0
NH2 B:ARG61 4.3 68.1 1.0
N B:GLY190 4.3 61.5 1.0
CB B:ASP217 4.3 64.2 1.0
CB B:ASP189 4.5 54.8 1.0
C B:ASP216 4.6 58.2 1.0
CA B:ASP189 4.7 54.5 1.0
O B:ASP216 4.7 54.8 1.0
N B:ASP217 4.8 62.3 1.0
C B:ASP189 4.8 56.0 1.0
CA B:ASP216 4.9 56.9 1.0
CA B:ASP217 5.0 63.8 1.0

Magnesium binding site 3 out of 4 in 4xvz

Go back to Magnesium Binding Sites List in 4xvz
Magnesium binding site 3 out of 4 in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:25.3
occ:1.00
O C:HOH452 1.9 44.8 1.0
OD2 C:ASP216 2.1 38.1 1.0
O C:HOH453 2.2 36.7 1.0
O C:HOH451 2.2 35.9 1.0
OD1 C:ASP189 2.3 41.1 1.0
OD2 C:ASP217 2.3 40.5 1.0
OD1 C:ASP217 2.3 38.8 1.0
CG C:ASP217 2.7 38.9 1.0
CG C:ASP216 3.3 35.0 1.0
CG C:ASP189 3.4 43.9 1.0
OD2 C:ASP189 3.8 53.5 1.0
OE1 C:GLN246 3.9 51.3 1.0
CB C:ASP216 4.0 32.9 1.0
CB C:ASP217 4.2 39.1 1.0
OD1 C:ASP216 4.3 31.9 1.0
N C:GLY190 4.3 40.2 1.0
NH2 C:ARG61 4.5 51.7 1.0
CB C:ASP189 4.7 40.2 1.0
C C:ASP216 4.7 34.2 1.0
O C:ASP216 4.8 36.4 1.0
N C:ASP217 4.8 35.8 1.0
CA C:ASP189 4.8 38.5 1.0
O C:HOH444 4.8 47.8 1.0
C C:ASP189 4.9 38.5 1.0
CA C:ASP217 4.9 38.3 1.0

Magnesium binding site 4 out of 4 in 4xvz

Go back to Magnesium Binding Sites List in 4xvz
Magnesium binding site 4 out of 4 in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:36.3
occ:1.00
O D:HOH417 1.9 45.0 1.0
OD2 D:ASP216 2.0 51.1 1.0
O D:HOH416 2.0 55.1 1.0
OD1 D:ASP189 2.2 62.9 1.0
OD2 D:ASP217 2.2 54.3 1.0
OD1 D:ASP217 2.4 57.8 1.0
O D:HOH418 2.4 45.0 1.0
CG D:ASP217 2.6 58.6 1.0
CG D:ASP216 3.1 57.0 1.0
CG D:ASP189 3.2 63.0 1.0
OD2 D:ASP189 3.7 66.2 1.0
CB D:ASP216 3.7 55.8 1.0
OE1 D:GLN246 3.9 71.1 1.0
OD1 D:ASP216 4.1 52.9 1.0
CB D:ASP217 4.1 60.5 1.0
N D:GLY190 4.1 58.6 1.0
NH2 D:ARG61 4.4 72.9 1.0
CB D:ASP189 4.5 57.8 1.0
C D:ASP216 4.5 58.4 1.0
CA D:ASP189 4.6 56.6 1.0
N D:ASP217 4.6 60.9 1.0
O D:ASP216 4.6 59.9 1.0
C D:ASP189 4.7 54.2 1.0
CA D:ASP217 4.8 61.7 1.0
CA D:ASP216 4.8 55.8 1.0

Reference:

S.M.Bernard, D.L.Akey, A.Tripathi, S.R.Park, J.R.Konwerski, Y.Anzai, S.Li, F.Kato, D.H.Sherman, J.L.Smith. Structural Basis of Substrate Specificity and Regiochemistry in the Mycf/Tylf Family of Sugar O-Methyltransferases. Acs Chem.Biol. 2015.
ISSN: ESSN 1554-8937
PubMed: 25692963
DOI: 10.1021/CB5009348
Page generated: Mon Dec 14 19:48:36 2020

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