Atomistry » Magnesium » PDB 6vcl-6vno » 6vcz
Atomistry »
  Magnesium »
    PDB 6vcl-6vno »
      6vcz »

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

Go back to Magnesium Binding Sites List in 6vcz
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

Go back to Magnesium Binding Sites List in 6vcz
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

Go back to Magnesium Binding Sites List in 6vcz
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

Go back to Magnesium Binding Sites List in 6vcz
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

Go back to Magnesium Binding Sites List in 6vcz
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

Go back to Magnesium Binding Sites List in 6vcz
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

Go back to Magnesium Binding Sites List in 6vcz
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy