Magnesium in PDB 6vd2: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine
Enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine
All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine:
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, PDB code: 6vd2
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)
|
45.72 /
1.97
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.980,
101.354,
84.708,
90.00,
99.80,
90.00
|
R / Rfree (%)
|
19.1 /
24
|
Other elements in 6vd2:
The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine 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
(pdb code 6vd2). 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, PDB code: 6vd2:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6vd2
Go back to
Magnesium Binding Sites List in 6vd2
Magnesium binding site 1 out
of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:31.0
occ:1.00
|
O1
|
A:PO4405
|
2.0
|
37.5
|
1.0
|
O2
|
A:PO4406
|
2.1
|
35.1
|
1.0
|
O
|
A:HOH675
|
2.1
|
22.4
|
1.0
|
O
|
A:HOH613
|
2.1
|
30.4
|
1.0
|
OD2
|
A:ASP17
|
2.2
|
31.5
|
1.0
|
O
|
A:HOH536
|
2.3
|
25.9
|
1.0
|
CG
|
A:ASP17
|
3.2
|
27.7
|
1.0
|
P
|
A:PO4406
|
3.4
|
30.4
|
1.0
|
P
|
A:PO4405
|
3.4
|
37.0
|
1.0
|
OD1
|
A:ASP17
|
3.4
|
30.3
|
1.0
|
K
|
A:K404
|
3.5
|
46.7
|
1.0
|
O4
|
A:PO4406
|
3.7
|
30.5
|
1.0
|
NZ
|
A:LYS253
|
3.8
|
32.4
|
1.0
|
O4
|
A:PO4405
|
3.9
|
42.1
|
1.0
|
OD2
|
A:ASP246
|
4.1
|
35.1
|
1.0
|
NH2
|
A:ARG252
|
4.2
|
27.5
|
1.0
|
O3
|
A:PO4405
|
4.2
|
32.8
|
1.0
|
O3
|
A:PO4406
|
4.2
|
30.9
|
1.0
|
CE1
|
A:HIS15
|
4.3
|
30.8
|
1.0
|
O1
|
A:PO4406
|
4.4
|
36.7
|
1.0
|
O2
|
A:PO4405
|
4.4
|
44.5
|
1.0
|
O
|
A:ALA247
|
4.5
|
24.4
|
1.0
|
CB
|
A:ASP17
|
4.5
|
28.2
|
1.0
|
OE2
|
B:GLU43
|
4.5
|
32.7
|
1.0
|
CB
|
A:ARG252
|
4.7
|
25.0
|
1.0
|
CZ
|
A:ARG252
|
4.8
|
26.7
|
1.0
|
NE
|
A:ARG252
|
4.9
|
27.1
|
1.0
|
CG
|
A:ASP246
|
4.9
|
36.9
|
1.0
|
OD1
|
A:ASP246
|
4.9
|
36.5
|
1.0
|
NE2
|
A:HIS15
|
4.9
|
32.8
|
1.0
|
CE
|
A:LYS253
|
5.0
|
30.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6vd2
Go back to
Magnesium Binding Sites List in 6vd2
Magnesium binding site 2 out
of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:36.8
occ:1.00
|
O3
|
A:PO4405
|
2.0
|
32.8
|
1.0
|
O
|
B:HOH538
|
2.0
|
32.3
|
1.0
|
O3
|
A:PO4406
|
2.1
|
30.9
|
1.0
|
O
|
B:HOH598
|
2.3
|
27.9
|
1.0
|
O
|
A:HOH538
|
2.3
|
30.4
|
1.0
|
O
|
B:HOH558
|
2.7
|
23.0
|
1.0
|
P
|
A:PO4406
|
3.3
|
30.4
|
1.0
|
P
|
A:PO4405
|
3.5
|
37.0
|
1.0
|
O4
|
A:PO4406
|
3.5
|
30.5
|
1.0
|
OD2
|
B:ASP279
|
3.6
|
36.5
|
1.0
|
NZ
|
A:LYS253
|
3.9
|
32.4
|
1.0
|
OD1
|
B:ASP279
|
4.0
|
35.7
|
1.0
|
O4
|
A:PO4405
|
4.1
|
42.1
|
1.0
|
OD2
|
B:ASP122
|
4.1
|
38.2
|
1.0
|
OE1
|
A:GLU9
|
4.1
|
27.3
|
1.0
|
O
|
A:HOH561
|
4.1
|
26.9
|
1.0
|
O2
|
A:PO4406
|
4.1
|
35.1
|
1.0
|
O1
|
A:PO4405
|
4.1
|
37.5
|
1.0
|
CG
|
B:ASP279
|
4.2
|
37.7
|
1.0
|
NZ
|
A:LYS169
|
4.3
|
30.4
|
1.0
|
O
|
A:HOH599
|
4.3
|
30.2
|
1.0
|
O1
|
A:PO4406
|
4.4
|
36.7
|
1.0
|
O2
|
A:PO4405
|
4.5
|
44.5
|
1.0
|
CA
|
B:GLY268
|
4.5
|
28.7
|
1.0
|
O
|
B:HOH621
|
4.6
|
33.5
|
1.0
|
O
|
B:GLN123
|
4.7
|
28.4
|
1.0
|
CE
|
A:LYS253
|
4.7
|
30.8
|
1.0
|
OE2
|
A:GLU9
|
4.8
|
32.3
|
1.0
|
CD
|
A:GLU9
|
4.9
|
29.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6vd2
Go back to
Magnesium Binding Sites List in 6vd2
Magnesium binding site 3 out
of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg407
b:32.9
occ:1.00
|
O3
|
B:PO4404
|
1.8
|
27.6
|
1.0
|
O
|
A:HOH579
|
2.0
|
31.6
|
1.0
|
O
|
A:HOH590
|
2.1
|
29.6
|
1.0
|
O3
|
B:PO4405
|
2.2
|
31.4
|
1.0
|
O
|
B:HOH590
|
2.2
|
29.0
|
1.0
|
O
|
B:HOH599
|
2.5
|
33.9
|
1.0
|
P
|
B:PO4404
|
3.2
|
29.2
|
1.0
|
O1
|
B:PO4404
|
3.6
|
28.6
|
1.0
|
OD2
|
A:ASP279
|
3.6
|
37.2
|
1.0
|
P
|
B:PO4405
|
3.6
|
37.1
|
1.0
|
NZ
|
B:LYS253
|
4.0
|
29.9
|
1.0
|
O2
|
B:PO4404
|
4.0
|
29.4
|
1.0
|
OD1
|
A:ASP279
|
4.0
|
36.2
|
1.0
|
O
|
A:HOH595
|
4.1
|
32.2
|
1.0
|
OD2
|
A:ASP122
|
4.2
|
37.5
|
1.0
|
NZ
|
B:LYS169
|
4.2
|
30.6
|
1.0
|
OE1
|
B:GLU9
|
4.2
|
28.8
|
1.0
|
O4
|
B:PO4404
|
4.2
|
31.8
|
1.0
|
CG
|
A:ASP279
|
4.2
|
33.0
|
1.0
|
O2
|
B:PO4405
|
4.3
|
30.6
|
1.0
|
O1
|
B:PO4405
|
4.3
|
34.7
|
1.0
|
O
|
A:HOH585
|
4.5
|
22.6
|
1.0
|
CA
|
A:GLY268
|
4.6
|
28.0
|
1.0
|
O4
|
B:PO4405
|
4.6
|
39.2
|
1.0
|
O
|
A:HOH526
|
4.6
|
36.7
|
1.0
|
O
|
A:GLN123
|
4.8
|
27.5
|
1.0
|
CE
|
B:LYS253
|
4.8
|
29.1
|
1.0
|
OE2
|
B:GLU9
|
4.8
|
29.4
|
1.0
|
CD
|
B:GLU9
|
5.0
|
30.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6vd2
Go back to
Magnesium Binding Sites List in 6vd2
Magnesium binding site 4 out
of 4 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with S-Adenosylmethionine
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:30.7
occ:1.00
|
O2
|
B:PO4405
|
2.0
|
30.6
|
1.0
|
O2
|
B:PO4404
|
2.1
|
29.4
|
1.0
|
O
|
B:HOH574
|
2.1
|
29.7
|
1.0
|
OD2
|
B:ASP17
|
2.1
|
27.3
|
1.0
|
O
|
B:HOH658
|
2.2
|
29.1
|
1.0
|
O
|
B:HOH572
|
2.2
|
27.6
|
1.0
|
CG
|
B:ASP17
|
3.1
|
28.1
|
1.0
|
P
|
B:PO4405
|
3.4
|
37.1
|
1.0
|
P
|
B:PO4404
|
3.4
|
29.2
|
1.0
|
OD1
|
B:ASP17
|
3.4
|
26.0
|
1.0
|
K
|
B:K403
|
3.5
|
40.2
|
1.0
|
O1
|
B:PO4404
|
3.6
|
28.6
|
1.0
|
NZ
|
B:LYS253
|
3.6
|
29.9
|
1.0
|
O1
|
B:PO4405
|
3.8
|
34.7
|
1.0
|
O3
|
B:PO4405
|
4.0
|
31.4
|
1.0
|
O3
|
B:PO4404
|
4.2
|
27.6
|
1.0
|
NH2
|
B:ARG252
|
4.2
|
31.4
|
1.0
|
OD2
|
B:ASP246
|
4.2
|
39.4
|
1.0
|
CE1
|
B:HIS15
|
4.4
|
32.2
|
1.0
|
CB
|
B:ASP17
|
4.4
|
28.5
|
1.0
|
O4
|
B:PO4405
|
4.5
|
39.2
|
1.0
|
O4
|
B:PO4404
|
4.5
|
31.8
|
1.0
|
O
|
B:ALA247
|
4.6
|
31.1
|
1.0
|
OE2
|
A:GLU43
|
4.6
|
35.6
|
1.0
|
CB
|
B:ARG252
|
4.6
|
25.5
|
1.0
|
CZ
|
B:ARG252
|
4.7
|
30.4
|
1.0
|
CE
|
B:LYS253
|
4.8
|
29.1
|
1.0
|
OD1
|
B:ASP246
|
4.8
|
37.8
|
1.0
|
NE
|
B:ARG252
|
4.8
|
29.4
|
1.0
|
CG
|
B:ASP246
|
4.9
|
36.2
|
1.0
|
O
|
B:ARG252
|
4.9
|
25.8
|
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 21:59:39 2024
|