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Magnesium in PDB 4x7z: Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate)

Enzymatic activity of Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate)

All present enzymatic activity of Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate):
2.1.1.237;

Protein crystallography data

The structure of Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate), PDB code: 4x7z was solved by S.M.Bernard, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.85 / 1.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.354, 92.516, 127.798, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 16.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate) (pdb code 4x7z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate), PDB code: 4x7z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4x7z

Go back to Magnesium Binding Sites List in 4x7z
Magnesium binding site 1 out of 5 in the Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate)


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 (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:10.3
occ:1.00
 OD2 A:ASP216 1.9 10.1 1.0
OD1 A:ASP217 2.0 10.2 1.0
OD1 A:ASP189 2.1 9.6 1.0
O A:HOH755 2.1 10.0 1.0
O10 A:ZM3305 2.1 11.6 1.0
O9 A:ZM3305 2.2 12.4 1.0
C33 A:ZM3305 3.0 12.7 1.0
C35 A:ZM3305 3.0 12.1 1.0
CG A:ASP216 3.0 9.2 1.0
CG A:ASP189 3.0 9.6 1.0
CG A:ASP217 3.1 9.6 1.0
OD2 A:ASP189 3.4 9.9 1.0
OD2 A:ASP217 3.6 9.6 1.0
CB A:ASP216 3.7 9.0 1.0
C36 A:ZM3305 3.8 12.9 1.0
OD1 A:ASP191 3.9 14.4 1.0
OD1 A:ASP216 4.0 9.9 1.0
O A:HOH494 4.1 10.7 1.0
CB A:ASP217 4.3 9.3 1.0
C A:ASP216 4.4 8.9 1.0
CB A:ASP189 4.4 9.4 1.0
C31 A:ZM3305 4.4 14.0 1.0
NH2 A:ARG61 4.4 9.7 1.0
O A:ASP216 4.5 9.5 1.0
OE1 A:GLN246 4.5 13.1 1.0
N A:ASP217 4.5 8.9 1.0
C37 A:ZM3305 4.6 13.5 1.0
CA A:ASP217 4.6 9.1 1.0
CG A:ASP191 4.6 13.1 1.0
CA A:ASP189 4.7 9.3 1.0
OD2 A:ASP191 4.7 14.5 1.0
CA A:ASP216 4.7 8.6 1.0
O8 A:ZM3305 4.9 15.5 1.0
O11 A:ZM3305 4.9 14.2 1.0
O A:ASP189 4.9 10.0 1.0
C A:ASP189 5.0 9.8 1.0
C30 A:ZM3305 5.0 14.5 1.0
CB A:SAH301 5.0 10.1 1.0

Magnesium binding site 2 out of 5 in 4x7z

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Magnesium binding site 2 out of 5 in the Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate)


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 (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:18.2
occ:1.00
 O A:HOH405 2.0 20.1 1.0
O A:HOH471 2.1 19.0 1.0
O A:HOH425 2.2 16.9 1.0
O A:HOH498 4.1 13.5 1.0
O A:HOH582 4.1 21.7 1.0
O A:HOH472 4.1 34.1 1.0
OD1 A:ASP125 4.3 14.9 1.0
O A:HOH508 4.3 17.0 1.0
OD1 A:ASP198 4.4 13.2 1.0
CA A:GLY194 4.4 10.1 1.0
OD2 A:ASP198 4.5 14.0 1.0
O A:ASP124 4.5 17.0 1.0
O A:HOH443 4.6 26.7 1.0
O A:HOH591 4.7 6.5 1.0
CG A:ASP198 4.9 12.3 1.0
C A:GLY194 5.0 9.7 1.0

Magnesium binding site 3 out of 5 in 4x7z

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Magnesium binding site 3 out of 5 in the Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate)


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 (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:45.9
occ:1.00
 OD1 A:ASP123 2.2 17.3 1.0
O A:HOH403 2.4 26.7 1.0
O A:HOH410 2.4 43.2 1.0
CG A:ASP123 3.2 17.1 1.0
OD2 A:ASP123 3.5 19.4 1.0
O A:HOH476 3.7 28.6 1.0
OD2 A:ASP124 4.0 30.7 1.0
OD1 A:ASP124 4.2 26.5 1.0
CG A:ASP124 4.2 23.5 1.0
OG1 A:THR122 4.5 15.1 1.0
CB A:ASP123 4.6 15.4 1.0
N A:ASP124 4.6 15.1 1.0
N A:ASP123 4.7 13.4 1.0
CB A:THR122 4.8 13.8 1.0
CA A:ASP123 5.0 14.0 1.0

Magnesium binding site 4 out of 5 in 4x7z

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Magnesium binding site 4 out of 5 in the Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate)


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 (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:10.1
occ:1.00
 OD2 B:ASP216 1.9 10.2 1.0
OD1 B:ASP217 2.0 10.5 1.0
OD1 B:ASP189 2.0 8.9 1.0
O10 B:ZM3304 2.1 11.2 1.0
O B:HOH765 2.1 9.8 1.0
O9 B:ZM3304 2.3 12.2 1.0
C33 B:ZM3304 3.0 12.5 1.0
C35 B:ZM3304 3.0 11.9 1.0
CG B:ASP189 3.0 9.2 1.0
CG B:ASP216 3.0 9.5 1.0
CG B:ASP217 3.1 10.1 1.0
OD2 B:ASP189 3.4 9.4 1.0
OD2 B:ASP217 3.6 10.1 1.0
CB B:ASP216 3.7 9.3 1.0
C36 B:ZM3304 3.8 12.7 1.0
OD1 B:ASP191 3.9 14.2 1.0
OD1 B:ASP216 3.9 9.9 1.0
O B:HOH508 4.1 10.6 1.0
CB B:ASP189 4.3 8.9 1.0
C B:ASP216 4.4 9.4 1.0
CB B:ASP217 4.4 9.8 1.0
C31 B:ZM3304 4.4 14.3 1.0
NH2 B:ARG61 4.4 10.1 1.0
OE1 B:GLN246 4.5 13.6 1.0
O B:ASP216 4.5 9.8 1.0
N B:ASP217 4.5 9.5 1.0
C37 B:ZM3304 4.6 13.0 1.0
CA B:ASP217 4.6 9.6 1.0
CA B:ASP189 4.6 8.8 1.0
CG B:ASP191 4.7 13.2 1.0
CA B:ASP216 4.7 9.0 1.0
OD2 B:ASP191 4.8 14.6 1.0
O8 B:ZM3304 4.9 15.5 1.0
O11 B:ZM3304 4.9 13.9 1.0
O B:ASP189 4.9 9.5 1.0
C B:ASP189 5.0 9.3 1.0
C30 B:ZM3304 5.0 14.3 1.0
CB B:SAH301 5.0 9.6 1.0

Magnesium binding site 5 out of 5 in 4x7z

Go back to Magnesium Binding Sites List in 4x7z
Magnesium binding site 5 out of 5 in the Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mycf Mycinamicin III 3'-O-Methyltransferase (E35Q, M56A, E139A Variant) in Complex with Mg, Sah and Mycinamicin III (Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:29.9
occ:1.00
 O B:HOH410 2.1 31.6 1.0
O B:HOH477 2.1 31.9 1.0
O B:HOH433 2.6 18.1 1.0
OD1 B:ASP125 4.0 17.7 1.0
O B:HOH509 4.1 15.4 1.0
O B:HOH521 4.3 20.4 1.0
O B:HOH445 4.5 24.7 1.0
OD1 B:ASP198 4.5 13.8 1.0
CA B:GLY194 4.5 10.2 1.0
OD2 B:ASP198 4.7 14.3 1.0
O B:HOH495 4.8 10.8 1.0
O B:ASP124 4.9 25.2 1.0
CG B:ASP125 5.0 17.5 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 15:22:48 2024

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