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Magnesium in PDB 6vd0: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp

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

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

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp, PDB code: 6vd0 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) 39.83 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.941, 84.721, 119.503, 90.00, 95.67, 90.00
R / Rfree (%) 22.2 / 25.1

Other elements in 6vd0:

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

Potassium (K) 4 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 Free Methionine and Ampcpp (pdb code 6vd0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp, PDB code: 6vd0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6vd0

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Magnesium binding site 1 out of 9 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


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 Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:25.3
occ:1.00
 O1A B:APC401 2.0 18.3 1.0
O B:HOH544 2.1 16.9 1.0
O2G B:APC401 2.1 17.9 1.0
O A:HOH598 2.2 24.2 1.0
O A:HOH517 2.3 21.6 1.0
O B:HOH552 2.4 16.6 1.0
PA B:APC401 3.4 18.8 1.0
PG B:APC401 3.4 21.0 1.0
O3B B:APC401 3.6 21.5 1.0
NZ B:LYS253 3.9 21.4 1.0
OE1 B:GLU9 3.9 21.5 1.0
OD2 A:ASP279 3.9 20.5 1.0
O A:HOH581 4.0 22.0 1.0
OD2 A:ASP122 4.1 19.0 1.0
NZ B:LYS169 4.1 20.3 1.0
OD1 A:ASP279 4.1 22.6 1.0
C3A B:APC401 4.2 19.2 1.0
O1G B:APC401 4.3 20.5 1.0
O2A B:APC401 4.3 19.6 1.0
O5' B:APC401 4.3 20.6 1.0
O B:HOH632 4.4 15.3 1.0
OE2 B:GLU9 4.5 22.8 1.0
CE B:LYS253 4.5 21.0 1.0
O A:GLN123 4.5 20.4 1.0
CG A:ASP279 4.5 21.7 1.0
O3G B:APC401 4.6 22.1 1.0
CD B:GLU9 4.6 20.7 1.0
PB B:APC401 4.6 23.2 1.0
CA A:GLY268 4.7 20.6 1.0
O A:HOH626 4.7 21.6 1.0

Magnesium binding site 2 out of 9 in 6vd0

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Magnesium binding site 2 out of 9 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


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 Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:21.0
occ:1.00
 O2G A:APC401 2.0 22.4 1.0
O A:HOH613 2.1 18.8 1.0
O A:HOH637 2.2 17.4 1.0
OD2 A:ASP17 2.2 17.8 1.0
O2A A:APC401 2.2 19.1 1.0
O2B A:APC401 2.2 19.5 1.0
CG A:ASP17 3.0 16.3 1.0
PB A:APC401 3.2 21.0 1.0
OD1 A:ASP17 3.3 16.4 1.0
PG A:APC401 3.3 21.6 1.0
PA A:APC401 3.4 18.7 1.0
O3B A:APC401 3.5 19.8 1.0
NZ A:LYS253 3.6 20.1 1.0
C3A A:APC401 3.7 19.9 1.0
K A:K406 3.8 23.7 1.0
NH2 A:ARG252 4.0 19.7 1.0
O1G A:APC401 4.2 18.2 1.0
O3G A:APC401 4.3 20.6 1.0
O1A A:APC401 4.3 18.9 1.0
CE1 A:HIS15 4.4 22.0 1.0
CB A:ASP17 4.4 17.6 1.0
O A:ALA247 4.4 19.2 1.0
OD2 A:ASP246 4.5 21.1 1.0
CB A:ARG252 4.5 18.8 1.0
CZ A:ARG252 4.5 19.2 1.0
O1B A:APC401 4.6 21.3 1.0
O5' A:APC401 4.6 22.1 1.0
OE2 B:GLU43 4.6 25.6 1.0
NE A:ARG252 4.6 18.9 1.0
CE A:LYS253 4.7 21.0 1.0
O A:ARG252 4.9 20.7 1.0
NE2 A:HIS15 5.0 21.8 1.0

Magnesium binding site 3 out of 9 in 6vd0

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Magnesium binding site 3 out of 9 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


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 Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:31.4
occ:1.00
 O A:HOH644 1.9 26.8 1.0
O A:HOH759 2.0 22.8 1.0
O A:HOH529 2.1 30.3 1.0
OE2 A:GLU66 3.9 30.4 1.0
OE1 A:GLU66 4.0 27.4 1.0
CD A:GLU66 4.4 27.0 1.0
O A:HOH750 4.4 34.6 1.0

Magnesium binding site 4 out of 9 in 6vd0

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Magnesium binding site 4 out of 9 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


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 Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:17.9
occ:1.00
 O B:HOH574 1.7 13.4 1.0
O2A B:APC401 2.0 19.6 1.0
O B:HOH571 2.0 16.7 1.0
O1G B:APC401 2.1 20.5 1.0
O2B B:APC401 2.1 21.7 1.0
OD2 B:ASP17 2.2 20.4 1.0
CG B:ASP17 3.1 19.4 1.0
PB B:APC401 3.1 23.2 1.0
PA B:APC401 3.3 18.8 1.0
OD1 B:ASP17 3.3 18.6 1.0
PG B:APC401 3.4 21.0 1.0
C3A B:APC401 3.5 19.2 1.0
O3B B:APC401 3.5 21.5 1.0
NZ B:LYS253 3.7 21.4 1.0
K B:K405 3.7 23.4 1.0
OD2 B:ASP246 4.1 23.1 1.0
O1A B:APC401 4.2 18.3 1.0
CE1 B:HIS15 4.2 17.4 1.0
NH2 B:ARG252 4.2 24.0 1.0
O B:ALA247 4.2 19.6 1.0
O2G B:APC401 4.3 17.9 1.0
CB B:ASP17 4.4 20.0 1.0
O3G B:APC401 4.4 22.1 1.0
O5' B:APC401 4.5 20.6 1.0
O1B B:APC401 4.5 21.2 1.0
OE2 A:GLU43 4.7 21.2 1.0
CE B:LYS253 4.7 21.0 1.0
CZ B:ARG252 4.8 22.8 1.0
NE2 B:HIS15 4.8 16.2 1.0
CB B:ARG252 4.8 21.9 1.0
OD1 B:ASP246 4.8 20.8 1.0
NE B:ARG252 4.8 22.7 1.0
CG B:ASP246 4.9 22.0 1.0

Magnesium binding site 5 out of 9 in 6vd0

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Magnesium binding site 5 out of 9 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:23.0
occ:1.00
 O B:HOH539 1.8 16.0 1.0
O1A A:APC401 1.9 18.9 1.0
O B:HOH603 2.1 24.6 1.0
O A:HOH589 2.2 22.5 1.0
O1G A:APC401 2.2 18.2 1.0
O A:HOH544 2.2 18.3 1.0
PA A:APC401 3.3 18.7 1.0
PG A:APC401 3.4 21.6 1.0
O3B A:APC401 3.5 19.8 1.0
OE1 A:GLU9 3.9 19.4 1.0
OD2 B:ASP279 3.9 17.8 1.0
OD2 B:ASP122 3.9 22.9 1.0
NZ A:LYS253 4.0 20.1 1.0
C3A A:APC401 4.0 19.9 1.0
NZ A:LYS169 4.1 23.2 1.0
OD1 B:ASP279 4.1 18.4 1.0
O2A A:APC401 4.2 19.1 1.0
O2G A:APC401 4.2 22.4 1.0
O A:HOH551 4.3 19.4 1.0
O B:HOH580 4.3 15.3 1.0
O5' A:APC401 4.4 22.1 1.0
OE2 A:GLU9 4.4 19.4 1.0
O B:GLN123 4.4 19.2 1.0
O3G A:APC401 4.4 20.6 1.0
CG B:ASP279 4.4 19.1 1.0
PB A:APC401 4.5 21.0 1.0
CE A:LYS253 4.6 21.0 1.0
CD A:GLU9 4.6 19.4 1.0
O B:HOH642 4.7 19.1 1.0
CA B:GLY268 4.8 19.8 1.0
CG B:ASP122 5.0 20.5 1.0

Magnesium binding site 6 out of 9 in 6vd0

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Magnesium binding site 6 out of 9 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:25.3
occ:1.00
 O2G D:APC401 2.0 20.6 1.0
O2A D:APC401 2.1 24.6 1.0
O C:HOH625 2.1 23.5 1.0
O D:HOH590 2.1 20.8 1.0
O C:HOH515 2.2 19.9 1.0
O C:HOH586 2.6 20.6 1.0
PG D:APC401 3.3 21.8 1.0
PA D:APC401 3.5 22.6 1.0
O3B D:APC401 3.5 22.1 1.0
OD2 C:ASP279 3.8 20.9 1.0
NZ D:LYS253 3.8 25.9 1.0
OE1 D:GLU9 3.9 24.0 1.0
O C:HOH562 4.1 20.7 1.0
OD2 C:ASP122 4.1 23.2 1.0
OD1 C:ASP279 4.1 22.0 1.0
C3A D:APC401 4.1 23.7 1.0
O3G D:APC401 4.2 19.1 1.0
NZ D:LYS169 4.3 27.4 1.0
O C:HOH578 4.3 24.9 1.0
CG C:ASP279 4.3 21.4 1.0
O1A D:APC401 4.4 21.4 1.0
O1G D:APC401 4.4 21.4 1.0
O5' D:APC401 4.4 28.2 1.0
CE D:LYS253 4.4 23.6 1.0
CA C:GLY268 4.6 23.1 1.0
O C:GLN123 4.6 20.8 1.0
PB D:APC401 4.6 25.2 1.0
OE2 D:GLU9 4.7 22.1 1.0
CD D:GLU9 4.8 24.5 1.0
O C:HOH556 4.8 36.3 1.0

Magnesium binding site 7 out of 9 in 6vd0

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Magnesium binding site 7 out of 9 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:25.6
occ:1.00
 OD2 C:ASP17 2.0 22.3 1.0
O1B C:APC402 2.0 20.1 1.0
O1A C:APC402 2.0 20.7 1.0
O3G C:APC402 2.0 23.1 1.0
O C:HOH504 2.1 26.2 1.0
O C:HOH653 2.4 24.0 1.0
CG C:ASP17 3.0 24.3 1.0
PB C:APC402 3.1 23.9 1.0
PA C:APC402 3.3 25.3 1.0
OD1 C:ASP17 3.3 21.2 1.0
PG C:APC402 3.4 23.4 1.0
O3B C:APC402 3.5 23.4 1.0
NZ C:LYS253 3.6 21.8 1.0
C3A C:APC402 3.7 24.0 1.0
K C:K407 3.7 32.4 1.0
O2A C:APC402 4.1 23.1 1.0
OD2 C:ASP246 4.1 27.4 1.0
NH2 C:ARG252 4.2 27.1 1.0
CE1 C:HIS15 4.2 20.0 1.0
CB C:ASP17 4.3 24.0 1.0
O2G C:APC402 4.3 21.6 1.0
O C:ALA247 4.4 25.2 1.0
O1G C:APC402 4.4 23.5 1.0
O2B C:APC402 4.5 24.9 1.0
O5' C:APC402 4.5 25.7 1.0
CB C:ARG252 4.6 22.4 1.0
NE C:ARG252 4.6 27.2 1.0
CE C:LYS253 4.7 20.9 1.0
CZ C:ARG252 4.7 28.0 1.0
OE2 D:GLU43 4.7 25.8 1.0
NE2 C:HIS15 4.9 20.3 1.0
O C:ARG252 4.9 21.5 1.0
CG C:ASP246 5.0 28.4 1.0

Magnesium binding site 8 out of 9 in 6vd0

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Magnesium binding site 8 out of 9 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg406

b:25.4
occ:1.00
 O2G C:APC402 1.9 21.6 1.0
O2A C:APC402 1.9 23.1 1.0
O C:HOH610 2.0 26.1 1.0
O D:HOH536 2.1 22.0 1.0
O D:HOH594 2.2 25.7 1.0
O C:HOH541 2.5 22.9 1.0
PG C:APC402 3.2 23.4 1.0
PA C:APC402 3.4 25.3 1.0
O3B C:APC402 3.5 23.4 1.0
NZ C:LYS253 3.8 21.8 1.0
OD2 D:ASP279 4.0 23.6 1.0
OD2 D:ASP122 4.0 28.6 1.0
C3A C:APC402 4.0 24.0 1.0
O3G C:APC402 4.0 23.1 1.0
O C:HOH596 4.1 22.2 1.0
OD1 D:ASP279 4.1 22.4 1.0
OE1 C:GLU9 4.1 25.0 1.0
NZ C:LYS169 4.1 31.1 1.0
O1A C:APC402 4.2 20.7 1.0
O1G C:APC402 4.4 23.5 1.0
O5' C:APC402 4.4 25.7 1.0
CE C:LYS253 4.4 20.9 1.0
CG D:ASP279 4.4 21.4 1.0
PB C:APC402 4.5 23.9 1.0
O C:HOH642 4.5 27.2 1.0
OE2 C:GLU9 4.6 23.6 1.0
O D:GLN123 4.6 29.0 1.0
CA D:GLY268 4.7 20.9 1.0
O D:HOH649 4.7 27.1 1.0
CD C:GLU9 4.8 24.4 1.0

Magnesium binding site 9 out of 9 in 6vd0

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Magnesium binding site 9 out of 9 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) in Complex with Free Methionine and Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:27.9
occ:1.00
 O3G D:APC401 1.9 19.1 1.0
OD2 D:ASP17 1.9 20.0 1.0
O1B D:APC401 2.1 25.5 1.0
O1A D:APC401 2.2 21.4 1.0
O D:HOH601 2.2 20.4 1.0
O D:HOH617 2.2 28.1 1.0
CG D:ASP17 2.8 19.4 1.0
OD1 D:ASP17 3.1 19.5 1.0
PB D:APC401 3.2 25.2 1.0
PG D:APC401 3.2 21.8 1.0
PA D:APC401 3.5 22.6 1.0
O3B D:APC401 3.5 22.1 1.0
NZ D:LYS253 3.6 25.9 1.0
K D:K404 3.8 26.7 1.0
C3A D:APC401 3.9 23.7 1.0
NH2 D:ARG252 4.2 24.2 1.0
CB D:ASP17 4.2 20.2 1.0
O2G D:APC401 4.2 20.6 1.0
O2A D:APC401 4.2 24.6 1.0
O1G D:APC401 4.3 21.4 1.0
CB D:ARG252 4.3 21.8 1.0
CE1 D:HIS15 4.4 22.2 1.0
O D:ALA247 4.4 21.8 1.0
NE D:ARG252 4.5 24.8 1.0
OD2 D:ASP246 4.5 35.6 1.0
O2B D:APC401 4.5 25.6 1.0
CZ D:ARG252 4.6 24.0 1.0
OE2 C:GLU43 4.7 30.0 1.0
O5' D:APC401 4.7 28.2 1.0
CE D:LYS253 4.7 23.6 1.0
O D:ARG252 4.8 18.5 1.0
CG D:ARG252 4.9 22.6 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 21:59:11 2024

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