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Magnesium in PDB 6vcw: Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A)

Enzymatic activity of Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A)

All present enzymatic activity of Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A):
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A), PDB code: 6vcw 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) 48.99 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.602, 62.042, 102.284, 90.00, 90.02, 90.00
R / Rfree (%) 11.5 / 15.9

Other elements in 6vcw:

The structure of Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A) (pdb code 6vcw). 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 Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A), PDB code: 6vcw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6vcw

Go back to Magnesium Binding Sites List in 6vcw
Magnesium binding site 1 out of 4 in the Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A)


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 Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:27.7
occ:1.00
 O A:HOH579 2.0 26.5 1.0
OD1 A:ASP279 2.1 20.9 1.0
O A:HOH570 2.1 29.8 1.0
O A:HOH567 2.1 31.1 1.0
O A:HOH841 2.1 35.6 1.0
O A:HOH512 2.2 27.6 1.0
CG A:ASP279 2.9 17.1 1.0
OD2 A:ASP279 3.1 25.4 1.0
OD2 A:ASP122 3.9 61.5 1.0
OD1 A:ASP122 4.0 42.3 1.0
O A:HOH652 4.1 15.8 1.0
O A:GLN123 4.3 15.4 1.0
CG A:ASP122 4.3 42.9 1.0
CB A:ASP279 4.4 13.1 1.0
O A:HOH799 4.4 18.6 1.0
O A:HOH678 4.4 15.0 1.0
CA A:GLY268 4.4 13.5 1.0
O A:HOH697 4.5 29.3 1.0
OE1 B:GLU9 4.5 33.9 1.0
O A:HOH894 4.5 40.2 1.0
CA A:GLY124 4.7 12.9 1.0
CE A:MET126 4.7 12.6 1.0
CA A:ASP279 4.9 10.2 1.0
N A:GLY268 5.0 12.5 1.0

Magnesium binding site 2 out of 4 in 6vcw

Go back to Magnesium Binding Sites List in 6vcw
Magnesium binding site 2 out of 4 in the Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A)


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 Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:27.1
occ:1.00
 O A:HOH914 2.0 37.0 1.0
O A:HOH566 2.1 24.8 1.0
O A:HOH980 2.1 29.3 1.0
O A:HOH557 2.1 24.7 1.0
O A:HOH902 2.1 41.1 1.0
O A:HOH525 2.1 28.1 1.0
OD2 A:ASP86 3.8 21.5 1.0
OD2 A:ASP88 4.1 25.6 1.0
OD1 A:ASP86 4.2 20.4 1.0
CG A:ASP86 4.4 20.9 1.0
O A:VAL79 4.4 23.3 1.0
O A:HOH636 4.6 30.9 1.0
CB A:ASP88 4.6 15.8 1.0
CG A:ASP88 4.8 17.9 1.0

Magnesium binding site 3 out of 4 in 6vcw

Go back to Magnesium Binding Sites List in 6vcw
Magnesium binding site 3 out of 4 in the Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A)


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 Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:31.8
occ:1.00
 O B:HOH547 2.0 28.6 1.0
OD1 B:ASP279 2.1 20.9 1.0
O B:HOH610 2.1 43.4 1.0
O B:HOH640 2.1 39.4 1.0
O B:HOH539 2.1 30.9 1.0
O B:HOH841 2.1 36.6 1.0
CG B:ASP279 2.9 21.8 1.0
OD2 B:ASP279 3.1 28.6 1.0
O B:HOH843 4.0 59.4 1.0
O B:HOH719 4.2 15.0 1.0
OD2 B:ASP122 4.2 70.2 1.0
O B:GLN123 4.3 20.4 1.0
O B:HOH804 4.3 18.8 1.0
CB B:ASP279 4.3 18.2 1.0
O B:HOH709 4.4 17.4 1.0
O A:HOH645 4.4 36.2 1.0
O B:HOH918 4.5 44.5 1.0
CA B:GLY268 4.5 16.8 1.0
OE1 A:GLU9 4.6 35.1 1.0
CA B:GLY124 4.8 15.8 1.0
CA B:ASP279 4.8 14.2 1.0
CE B:MET126 4.8 14.6 1.0
CG B:ASP122 4.9 53.5 1.0
N B:GLY268 5.0 13.9 1.0

Magnesium binding site 4 out of 4 in 6vcw

Go back to Magnesium Binding Sites List in 6vcw
Magnesium binding site 4 out of 4 in the Crystal Structure of Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A)


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 Medicago Truncatula S-Adenosylmethionine Synthase 3A (MTMAT3A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:26.5
occ:1.00
 O B:HOH915 2.0 32.1 1.0
O B:HOH883 2.0 24.2 1.0
O B:HOH971 2.1 29.6 1.0
O B:HOH563 2.1 29.8 1.0
O B:HOH974 2.1 32.1 1.0
O B:HOH977 2.1 28.3 1.0
O B:ALA390 4.2 32.9 1.0
O B:HOH979 4.3 45.9 1.0
C B:ALA390 4.7 25.4 1.0
OXT B:ALA390 4.8 27.7 1.0
CB B:ALA390 5.0 23.8 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 21:59:10 2024

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