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Chlorine in PDB 6vcy: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine, PDB code: 6vcy 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) 49.25 / 1.82
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.280, 69.156, 210.450, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.9

Other elements in 6vcy:

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine (pdb code 6vcy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine, PDB code: 6vcy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6vcy

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Chlorine binding site 1 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:61.2
occ:1.00
 O A:HOH740 3.3 48.8 1.0
CB A:ARG373 3.7 32.4 1.0
NE A:ARG373 3.9 29.8 1.0
N A:ASP374 4.0 33.6 1.0
N A:ASP375 4.2 33.5 1.0
CA A:ARG373 4.3 31.4 1.0
CB A:ASP375 4.4 33.2 1.0
O A:HOH784 4.4 47.0 1.0
NH1 A:ARG373 4.5 29.0 1.0
C A:ARG373 4.6 31.9 1.0
CG A:ARG373 4.6 34.6 1.0
CD A:ARG373 4.7 31.5 1.0
CZ A:ARG373 4.7 27.9 1.0
CA A:ASP375 4.8 31.9 1.0

Chlorine binding site 2 out of 7 in 6vcy

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Chlorine binding site 2 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:54.5
occ:1.00
 N A:VAL239 3.1 27.6 1.0
O A:HOH593 3.2 44.9 1.0
N A:ILE240 3.4 31.8 1.0
O A:ARG237 3.9 33.9 1.0
CA A:VAL239 3.9 30.2 1.0
CB A:VAL239 4.0 31.9 1.0
C A:PHE238 4.0 29.6 1.0
CA A:PHE238 4.0 29.1 1.0
CB A:ILE240 4.1 41.2 1.0
C A:VAL239 4.2 31.0 1.0
C A:ARG237 4.3 35.8 1.0
CG1 A:ILE240 4.3 49.7 1.0
CA A:ILE240 4.3 36.2 1.0
N A:PHE238 4.4 31.9 1.0
O A:ILE240 4.4 35.7 1.0
CD1 A:ILE240 4.6 53.2 1.0
CG2 A:VAL239 4.7 31.8 1.0
N6 A:MTA406 4.8 46.1 1.0
C A:ILE240 4.9 32.9 1.0
O A:HOH543 5.0 46.5 1.0

Chlorine binding site 3 out of 7 in 6vcy

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Chlorine binding site 3 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:39.1
occ:1.00
 O A:HOH790 2.9 56.0 1.0
O A:HOH609 2.9 41.4 1.0
O A:HOH611 2.9 30.8 1.0
N A:ASP342 3.3 28.4 1.0
CE A:LYS384 3.7 48.2 1.0
CA A:PHE341 3.7 29.4 1.0
NZ A:LYS384 3.8 49.5 1.0
ND2 A:ASN351 4.0 31.9 1.0
C A:PHE341 4.0 31.3 1.0
CD2 A:PHE341 4.0 27.3 1.0
CD1 A:ILE285 4.2 33.3 1.0
O A:SER340 4.2 37.0 1.0
CB A:ASN351 4.2 29.1 1.0
CB A:ASP342 4.3 26.5 1.0
CA A:ASP342 4.3 27.2 1.0
CB A:PHE341 4.4 27.4 1.0
O A:ASP342 4.5 29.2 1.0
CG A:ASN351 4.5 33.4 1.0
CG A:PHE341 4.5 26.3 1.0
CG1 A:ILE285 4.7 32.8 1.0
C A:ASP342 4.8 28.1 1.0
CE2 A:PHE341 4.8 26.7 1.0
O A:HOH775 4.8 48.3 1.0
N A:PHE341 4.9 31.1 1.0
OE1 A:GLN288 4.9 26.0 1.0
C A:SER340 5.0 34.9 1.0

Chlorine binding site 4 out of 7 in 6vcy

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Chlorine binding site 4 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:47.5
occ:1.00
 O A:HOH719 3.1 26.0 1.0
CA A:GLY121 3.2 26.2 1.0
O A:HOH797 3.3 48.4 1.0
N A:GLY121 3.4 26.4 1.0
N A:ASP122 3.4 25.2 1.0
C A:GLY121 3.4 25.2 1.0
N A:VAL278 3.4 26.2 1.0
CA A:LYS277 3.4 24.3 1.0
O A:HOH595 3.6 35.2 1.0
O A:HOH753 3.6 41.3 1.0
CB A:LYS277 3.8 25.3 1.0
CB A:ASP122 3.9 24.9 1.0
CG2 A:VAL278 3.9 26.8 1.0
C A:LYS277 3.9 24.9 1.0
CG A:LYS277 4.0 26.5 1.0
O A:GLY121 4.1 27.0 1.0
O A:HOH736 4.2 43.4 1.0
CA A:ASP122 4.2 24.7 1.0
CA A:VAL278 4.5 28.5 1.0
O A:THR276 4.6 38.7 1.0
N A:LYS277 4.6 26.0 1.0
CB A:VAL278 4.6 27.8 1.0
C A:ALA120 4.6 29.4 1.0
CG1 A:VAL278 4.7 29.2 1.0
O A:HOH791 4.8 35.8 1.0
O A:ASP122 4.9 23.5 1.0
O A:HOH555 4.9 30.7 1.0
C A:THR276 5.0 31.6 1.0

Chlorine binding site 5 out of 7 in 6vcy

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Chlorine binding site 5 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:49.1
occ:1.00
 O A:HOH716 2.8 49.1 1.0
N A:VAL92 3.2 25.5 1.0
NH2 A:ARG70 3.3 26.5 1.0
CA A:LYS91 3.7 29.8 1.0
O A:VAL92 3.8 27.2 1.0
C A:LYS91 3.9 28.4 1.0
O A:CYS90 3.9 26.5 1.0
CA A:VAL92 4.2 26.1 1.0
C A:VAL92 4.4 26.7 1.0
CG A:LYS91 4.5 38.3 1.0
OE1 A:GLU66 4.5 35.2 1.0
CB A:VAL92 4.5 24.5 1.0
CB A:LYS91 4.6 32.6 1.0
N A:LYS91 4.6 28.4 1.0
CZ A:ARG70 4.6 26.9 1.0
C A:CYS90 4.7 27.1 1.0
O A:HOH622 4.9 54.0 1.0

Chlorine binding site 6 out of 7 in 6vcy

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Chlorine binding site 6 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:64.4
occ:1.00
 N A:GLU199 3.2 42.5 1.0
CB A:ASP198 3.5 35.8 1.0
CB A:GLU199 3.8 53.1 1.0
CA A:GLU199 3.9 48.6 1.0
NH2 A:ARG165 4.0 39.1 1.0
CG A:ASP198 4.0 37.0 1.0
CG2 A:THR200 4.0 56.8 1.0
N A:THR200 4.1 50.0 1.0
C A:ASP198 4.1 39.1 1.0
CA A:ASP198 4.2 35.2 1.0
C A:GLU199 4.3 48.8 1.0
OD1 A:ASP198 4.4 39.9 1.0
OD2 A:ASP198 4.4 39.5 1.0
CG A:GLU199 4.6 55.3 1.0
O A:HOH734 4.6 55.7 1.0

Chlorine binding site 7 out of 7 in 6vcy

Go back to Chlorine Binding Sites List in 6vcy
Chlorine binding site 7 out of 7 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) in Complex with 5'-Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:55.9
occ:1.00
 N A:ASP102 3.2 29.2 1.0
CA A:PRO101 3.7 26.7 1.0
O A:HOH560 3.7 43.6 1.0
O A:HOH626 3.8 43.9 1.0
CB A:ASP102 3.9 35.7 1.0
O A:HOH533 3.9 48.6 1.0
C A:PRO101 4.0 27.1 1.0
CG2 A:THR58 4.0 27.0 1.0
CA A:ASP102 4.1 29.7 1.0
CB A:PRO101 4.1 27.9 1.0
N A:PRO101 5.0 25.2 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: Sat Jul 12 20:50:20 2025

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