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Magnesium in PDB 6vcz: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2)

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2)

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

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2), PDB code: 6vcz 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) 42.44 / 1.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.798, 99.276, 86.930, 90.00, 109.74, 90.00
R / Rfree (%) 16 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2) (pdb code 6vcz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2), PDB code: 6vcz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6vcz

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Magnesium binding site 1 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:14.1
occ:1.00
 O1 A:PO4402 2.0 14.9 1.0
OD2 A:ASP17 2.0 13.5 1.0
O3 A:PO4401 2.1 15.8 1.0
O A:HOH699 2.1 16.9 1.0
O A:HOH579 2.1 15.6 1.0
O A:HOH687 2.1 17.2 1.0
CG A:ASP17 3.0 12.3 1.0
P A:PO4402 3.3 16.8 1.0
OD1 A:ASP17 3.4 12.7 1.0
P A:PO4401 3.4 16.1 1.0
O2 A:PO4402 3.5 18.6 1.0
NZ A:LYS253 3.6 13.1 1.0
O2 A:PO4401 3.7 17.3 1.0
NH2 A:ARG252 4.0 14.6 1.0
O4 A:PO4402 4.1 21.4 1.0
O A:HOH522 4.1 21.5 1.0
CE1 A:HIS15 4.2 13.2 1.0
O1 A:PO4401 4.3 17.4 1.0
O B:HOH622 4.3 25.3 1.0
O4 A:PO4401 4.4 16.5 1.0
O A:HOH837 4.4 36.0 1.0
CB A:ASP17 4.4 12.6 1.0
O3 A:PO4402 4.4 18.2 1.0
O A:ALA247 4.5 16.7 1.0
CZ A:ARG252 4.6 13.2 1.0
OE2 B:GLU43 4.6 16.3 1.0
CB A:ARG252 4.7 11.2 1.0
NE A:ARG252 4.7 13.2 1.0
NE2 A:HIS15 4.8 13.7 1.0
CE A:LYS253 4.8 12.6 1.0
MG B:MG408 4.8 19.2 0.8

Magnesium binding site 2 out of 7 in 6vcz

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Magnesium binding site 2 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:20.9
occ:1.00
 O A:HOH574 2.0 22.5 1.0
O A:HOH534 2.1 23.3 1.0
O A:HOH538 2.1 23.3 1.0
O1 A:PO4401 2.1 17.4 1.0
O A:HOH805 2.1 21.9 1.0
O A:HOH522 2.2 21.5 1.0
P A:PO4401 3.3 16.1 1.0
O2 A:PO4401 3.5 17.3 1.0
OD2 A:ASP246 3.7 36.4 1.0
OD2 B:ASP122 3.9 22.4 1.0
O A:HOH837 4.0 36.0 1.0
O3 A:PO4401 4.0 15.8 1.0
NE2 A:HIS15 4.0 13.7 1.0
O A:HOH956 4.2 34.2 1.0
OD1 A:ASP246 4.2 31.9 1.0
NZ A:LYS169 4.3 18.3 1.0
O2 A:PO4403 4.4 33.0 0.8
CG A:ASP246 4.4 27.8 1.0
O A:HOH687 4.4 17.2 1.0
CE A:LYS169 4.5 21.6 1.0
O4 A:PO4401 4.5 16.5 1.0
O A:HOH578 4.6 20.9 1.0
O A:HOH543 4.6 37.4 1.0
O A:HOH539 4.8 21.8 1.0
O B:HOH974 4.8 34.8 1.0
CE1 A:HIS15 4.9 13.2 1.0
CD2 A:HIS15 4.9 13.6 1.0
CG B:ASP122 4.9 18.7 1.0

Magnesium binding site 3 out of 7 in 6vcz

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Magnesium binding site 3 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:16.6
occ:0.80
 O A:HOH608 2.0 23.0 1.0
O1 B:PO4402 2.0 16.3 1.0
O1 B:PO4401 2.1 15.8 1.0
OD2 A:ASP279 2.1 15.7 1.0
O A:HOH725 2.3 23.2 1.0
O B:HOH510 2.4 17.3 1.0
P B:PO4402 3.2 15.4 1.0
P B:PO4401 3.3 14.4 1.0
CG A:ASP279 3.3 14.7 1.0
O2 B:PO4401 3.4 13.9 1.0
O2 B:PO4402 3.4 18.3 1.0
NZ A:LYS273 3.5 14.6 1.0
O A:HOH516 3.7 28.7 1.0
OD1 A:ASP279 3.8 16.7 1.0
O A:HOH503 3.8 18.9 0.5
O4 B:PO4401 4.0 13.5 1.0
O B:HOH722 4.0 15.7 1.0
O A:HOH797 4.1 17.9 1.0
O3 B:PO4402 4.2 16.8 1.0
OD2 A:ASP122 4.2 21.8 1.0
O4 B:PO4402 4.2 14.4 1.0
O A:HOH503 4.3 16.6 0.5
O B:HOH606 4.3 20.5 1.0
CE A:LYS273 4.4 14.1 1.0
CB A:ASP279 4.5 14.6 1.0
O3 B:PO4401 4.5 15.4 1.0
O B:HOH660 4.7 19.3 1.0
O A:HOH946 4.7 23.2 1.0
MG B:MG405 4.9 12.7 1.0
O B:HOH580 5.0 20.4 1.0

Magnesium binding site 4 out of 7 in 6vcz

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Magnesium binding site 4 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:12.7
occ:1.00
 O4 B:PO4401 2.0 13.5 1.0
O4 B:PO4402 2.1 14.4 1.0
OD2 B:ASP17 2.1 12.0 1.0
O B:HOH722 2.1 15.7 1.0
O B:HOH603 2.1 14.3 1.0
O B:HOH689 2.1 15.8 1.0
CG B:ASP17 3.0 11.4 1.0
P B:PO4402 3.3 15.4 1.0
OD1 B:ASP17 3.4 11.4 1.0
P B:PO4401 3.4 14.4 1.0
NZ B:LYS253 3.5 12.7 1.0
O1 B:PO4402 3.5 16.3 1.0
O1 B:PO4401 3.8 15.8 1.0
NH2 B:ARG252 4.0 14.4 1.0
O2 B:PO4402 4.1 18.3 1.0
O B:HOH538 4.1 21.5 1.0
CE1 B:HIS15 4.2 12.0 1.0
O B:HOH890 4.2 31.0 1.0
O3 B:PO4401 4.3 15.4 1.0
O2 B:PO4401 4.3 13.9 1.0
CB B:ASP17 4.4 11.1 1.0
O A:HOH613 4.4 22.8 1.0
O3 B:PO4402 4.4 16.8 1.0
O B:ALA247 4.5 14.9 1.0
CZ B:ARG252 4.6 12.6 1.0
OE2 A:GLU43 4.6 15.9 1.0
NE B:ARG252 4.7 13.0 1.0
CB B:ARG252 4.7 10.5 1.0
CE B:LYS253 4.8 12.2 1.0
NE2 B:HIS15 4.8 12.7 1.0
MG A:MG407 4.9 16.6 0.8

Magnesium binding site 5 out of 7 in 6vcz

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Magnesium binding site 5 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:17.1
occ:1.00
 O B:HOH639 2.0 20.8 1.0
O3 B:PO4401 2.1 15.4 1.0
O B:HOH606 2.1 20.5 1.0
O B:HOH536 2.1 22.4 1.0
O B:HOH538 2.1 21.5 1.0
O B:HOH818 2.2 21.5 1.0
P B:PO4401 3.3 14.4 1.0
O1 B:PO4401 3.6 15.8 1.0
OD2 A:ASP122 4.0 21.8 1.0
O B:HOH890 4.0 31.0 1.0
O4 B:PO4401 4.0 13.5 1.0
NE2 B:HIS15 4.0 12.7 1.0
OD2 B:ASP246 4.1 29.2 1.0
O B:HOH932 4.2 34.5 1.0
NZ B:LYS169 4.2 16.1 1.0
OD1 B:ASP246 4.2 24.4 1.0
O B:HOH689 4.4 15.8 1.0
O1 B:PO4403 4.5 27.1 0.8
O2 B:PO4401 4.5 13.9 1.0
CE B:LYS169 4.5 17.7 1.0
CG B:ASP246 4.5 22.0 1.0
O B:HOH558 4.6 19.0 1.0
O B:HOH521 4.7 39.3 1.0
O B:HOH609 4.7 22.8 1.0
O A:HOH964 4.8 30.0 1.0
CE1 B:HIS15 4.8 12.0 1.0
CD2 B:HIS15 4.9 12.5 1.0
CG A:ASP122 4.9 18.4 1.0
O B:HOH518 5.0 50.1 1.0

Magnesium binding site 6 out of 7 in 6vcz

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Magnesium binding site 6 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:18.2
occ:1.00
 O B:HOH535 2.0 22.4 1.0
O B:HOH556 2.1 19.2 1.0
O1 B:PO4404 2.1 19.7 0.8
P B:PO4404 3.3 33.1 0.8
O3 B:PO4404 3.5 34.6 0.8
OE1 B:GLU66 4.1 21.1 1.0
OE2 B:GLU66 4.2 20.0 1.0
O4 B:PO4404 4.2 27.8 0.8
O B:HOH507 4.2 23.1 1.0
O B:HOH742 4.4 45.1 1.0
O2 B:PO4404 4.5 35.6 0.8
CD B:GLU66 4.5 20.1 1.0
O1 B:MPO409 4.7 28.7 0.7

Magnesium binding site 7 out of 7 in 6vcz

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Magnesium binding site 7 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 2 (ATMAT2)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:19.2
occ:0.80
 O2 A:PO4402 2.0 18.6 1.0
O B:HOH601 2.0 25.6 1.0
OD2 B:ASP279 2.1 17.1 1.0
O2 A:PO4401 2.2 17.3 1.0
O B:HOH763 2.3 26.3 1.0
O A:HOH508 2.6 19.4 1.0
CG B:ASP279 3.3 16.7 1.0
P A:PO4402 3.3 16.8 1.0
P A:PO4401 3.3 16.1 1.0
O4 A:PO4401 3.4 16.5 1.0
O4 A:PO4402 3.5 21.4 1.0
NZ B:LYS273 3.5 15.0 1.0
O B:HOH549 3.8 24.0 0.5
OD1 B:ASP279 3.8 19.4 1.0
O B:HOH544 3.9 30.3 1.0
O A:HOH699 4.0 16.9 1.0
O3 A:PO4401 4.0 15.8 1.0
OD2 B:ASP122 4.1 22.4 1.0
O B:HOH796 4.2 19.0 1.0
O3 A:PO4402 4.2 18.2 1.0
O1 A:PO4402 4.2 14.9 1.0
O A:HOH538 4.3 23.3 1.0
O B:HOH549 4.3 17.1 0.5
CE B:LYS273 4.4 15.1 1.0
O1 A:PO4401 4.5 17.4 1.0
CB B:ASP279 4.5 15.7 1.0
O A:HOH627 4.6 20.6 1.0
O B:HOH955 4.7 22.8 1.0
MG A:MG405 4.8 14.1 1.0
O A:HOH548 5.0 22.4 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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