Atomistry » Magnesium » PDB 4xtr-4y2q » 4xvz
Atomistry »
  Magnesium »
    PDB 4xtr-4y2q »
      4xvz »

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: Tue Aug 20 16:01:40 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy