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Magnesium in PDB 6vd1: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp, PDB code: 6vd1 was solved by B.Sekula, M.Ruszkowski, Z.Dauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.09 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.205, 101.484, 84.334, 90.00, 99.37, 90.00
R / Rfree (%) 14.2 / 17.3

Other elements in 6vd1:

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp (pdb code 6vd1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp, PDB code: 6vd1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6vd1

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Magnesium binding site 1 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:12.6
occ:1.00
 OD2 A:ASP17 2.0 10.1 1.0
O2A A:PPK401 2.1 11.4 1.0
O3G A:PPK401 2.1 10.9 1.0
O2B A:PPK401 2.1 11.0 1.0
O A:HOH583 2.1 13.2 1.0
O A:HOH568 2.1 12.1 1.0
CG A:ASP17 3.0 10.0 1.0
PB A:PPK401 3.1 11.2 1.0
OD1 A:ASP17 3.3 10.3 1.0
PG A:PPK401 3.3 11.5 1.0
PA A:PPK401 3.3 10.3 1.0
O3A A:PPK401 3.4 11.9 1.0
N3B A:PPK401 3.5 9.6 1.0
NZ A:LYS253 3.6 10.4 1.0
K A:K405 3.7 13.2 1.0
NH2 A:ARG252 4.0 13.3 1.0
O1A A:PPK401 4.2 9.4 1.0
O2G A:PPK401 4.3 11.8 1.0
CE1 A:HIS15 4.3 11.2 1.0
O1G A:PPK401 4.3 12.1 1.0
OD2 A:ASP246 4.3 13.6 1.0
CB A:ASP17 4.3 9.9 1.0
O4A A:PPK401 4.4 11.1 1.0
O A:ALA247 4.4 10.4 1.0
O1B A:PPK401 4.5 11.8 1.0
CB A:ARG252 4.5 10.1 1.0
CZ A:ARG252 4.6 11.8 1.0
NE A:ARG252 4.6 12.7 1.0
CE A:LYS253 4.6 11.2 1.0
OE2 B:GLU43 4.8 14.4 1.0
NE2 A:HIS15 4.8 10.4 1.0
O A:ARG252 4.9 10.6 1.0

Magnesium binding site 2 out of 4 in 6vd1

Go back to Magnesium Binding Sites List in 6vd1
Magnesium binding site 2 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:11.8
occ:1.00
 O1A A:PPK401 1.9 9.4 1.0
O B:HOH619 2.1 13.2 1.0
O2G A:PPK401 2.1 11.8 1.0
O A:HOH655 2.1 12.5 1.0
O B:HOH575 2.1 11.3 1.0
O A:HOH661 2.2 12.0 1.0
PA A:PPK401 3.3 10.3 1.0
PG A:PPK401 3.4 11.5 1.0
N3B A:PPK401 3.5 9.6 1.0
NZ A:LYS253 3.8 10.4 1.0
O3A A:PPK401 3.8 11.9 1.0
OD2 B:ASP279 4.0 13.3 1.0
O2A A:PPK401 4.1 11.4 1.0
OE1 A:GLU9 4.1 10.2 1.0
OD2 B:ASP122 4.1 12.4 1.0
O A:HOH598 4.1 12.9 1.0
OD1 B:ASP279 4.2 12.6 1.0
NZ A:LYS169 4.2 10.4 1.0
O3G A:PPK401 4.3 10.9 1.0
O4A A:PPK401 4.3 11.1 1.0
O B:HOH678 4.4 10.7 1.0
PB A:PPK401 4.4 11.2 1.0
O1G A:PPK401 4.5 12.1 1.0
CG B:ASP279 4.5 12.4 1.0
CE A:LYS253 4.5 11.2 1.0
O B:GLN123 4.5 10.9 1.0
OE2 A:GLU9 4.6 11.8 1.0
CA B:GLY268 4.6 11.5 1.0
CD A:GLU9 4.7 10.9 1.0
O B:HOH702 4.8 12.8 1.0

Magnesium binding site 3 out of 4 in 6vd1

Go back to Magnesium Binding Sites List in 6vd1
Magnesium binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:12.0
occ:1.00
 O4A B:PPK401 1.9 9.5 1.0
O2G B:PPK401 2.1 11.6 1.0
O A:HOH588 2.1 12.6 1.0
O B:HOH638 2.1 11.9 1.0
O A:HOH585 2.1 11.2 1.0
O B:HOH653 2.2 11.6 1.0
PA B:PPK401 3.3 10.1 1.0
PG B:PPK401 3.4 11.5 1.0
N3B B:PPK401 3.5 9.5 1.0
NZ B:LYS253 3.8 10.2 1.0
O3A B:PPK401 3.8 11.8 1.0
OD2 A:ASP279 3.9 13.5 1.0
OE1 B:GLU9 4.0 10.0 1.0
O1A B:PPK401 4.0 11.3 1.0
OD2 A:ASP122 4.1 12.1 1.0
O A:HOH595 4.1 11.9 1.0
NZ B:LYS169 4.2 10.8 1.0
OD1 A:ASP279 4.2 13.3 1.0
O1G B:PPK401 4.3 10.9 1.0
O2A B:PPK401 4.4 10.5 1.0
O B:HOH671 4.4 11.0 1.0
PB B:PPK401 4.4 11.1 1.0
O3G B:PPK401 4.4 12.3 1.0
CE B:LYS253 4.5 11.6 1.0
CG A:ASP279 4.5 12.6 1.0
O A:GLN123 4.5 10.7 1.0
OE2 B:GLU9 4.6 10.9 1.0
CA A:GLY268 4.7 11.3 1.0
CD B:GLU9 4.7 10.2 1.0
O A:HOH659 4.8 12.9 1.0

Magnesium binding site 4 out of 4 in 6vd1

Go back to Magnesium Binding Sites List in 6vd1
Magnesium binding site 4 out of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine and Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:13.7
occ:1.00
 O1G B:PPK401 2.0 10.9 1.0
O1B B:PPK401 2.0 11.3 1.0
OD2 B:ASP17 2.1 9.6 1.0
O1A B:PPK401 2.1 11.3 1.0
O B:HOH565 2.1 14.2 1.0
O B:HOH586 2.2 11.7 1.0
CG B:ASP17 3.0 10.6 1.0
PB B:PPK401 3.1 11.1 1.0
PG B:PPK401 3.3 11.5 1.0
OD1 B:ASP17 3.3 10.5 1.0
PA B:PPK401 3.3 10.1 1.0
O3A B:PPK401 3.4 11.8 1.0
N3B B:PPK401 3.5 9.5 1.0
NZ B:LYS253 3.6 10.2 1.0
K B:K406 3.7 13.4 1.0
NH2 B:ARG252 4.0 13.3 1.0
O2G B:PPK401 4.2 11.6 1.0
CE1 B:HIS15 4.3 10.6 1.0
O4A B:PPK401 4.3 9.5 1.0
O3G B:PPK401 4.3 12.3 1.0
CB B:ASP17 4.3 9.8 1.0
OD2 B:ASP246 4.4 14.1 1.0
O2A B:PPK401 4.4 10.5 1.0
O B:ALA247 4.4 10.7 1.0
O2B B:PPK401 4.4 11.9 1.0
CB B:ARG252 4.5 9.6 1.0
CZ B:ARG252 4.5 13.3 1.0
CE B:LYS253 4.6 11.6 1.0
NE B:ARG252 4.6 13.2 1.0
OE2 A:GLU43 4.7 14.5 1.0
NE2 B:HIS15 4.8 10.6 1.0
O B:ARG252 4.9 10.5 1.0

Reference:

B.Sekula, M.Ruszkowski, Z.Dauter. S-Adenosylmethionine Synthases in Plants: Structural Characterization of Type I and II Isoenzymes From Arabidopsis Thaliana and Medicago Truncatula. Int.J.Biol.Macromol. 2020.
ISSN: ISSN 0141-8130
PubMed: 32057875
DOI: 10.1016/J.IJBIOMAC.2020.02.100
Page generated: Tue Oct 1 21:59:10 2024

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