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:
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
Go back to
Magnesium Binding Sites List in 6vd1
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
|