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Chlorine in PDB 6vcx: Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1):
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1), PDB code: 6vcx 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) 48.78 / 1.10
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.722, 68.096, 209.697, 90.00, 90.00, 90.00
R / Rfree (%) 11.1 / 13.5

Other elements in 6vcx:

The structure of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) (pdb code 6vcx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1), PDB code: 6vcx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6vcx

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Chlorine binding site 1 out of 8 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:22.8
occ:0.80
 O A:HOH761 3.1 35.7 1.0
N A:VAL239 3.2 13.9 1.0
N A:ILE240 3.4 17.4 1.0
O A:ARG237 3.7 19.0 1.0
CG A:ARG237 3.7 25.3 0.5
CA A:PHE238 3.9 13.3 1.0
CB A:ILE240 4.0 21.7 1.0
CG1 A:ILE240 4.0 26.3 1.0
C A:PHE238 4.0 12.3 1.0
C A:ARG237 4.0 16.3 1.0
CA A:VAL239 4.1 14.6 1.0
N A:PHE238 4.2 14.7 1.0
CA A:ILE240 4.2 17.6 1.0
CB A:VAL239 4.2 17.2 1.0
C A:VAL239 4.2 16.4 1.0
CD1 A:ILE240 4.3 30.5 1.0
CD A:ARG237 4.3 27.7 0.5
NE A:ARG237 4.4 33.2 0.5
O A:ILE240 4.5 20.5 1.0
C A:ILE240 4.9 15.7 1.0
CG2 A:VAL239 4.9 17.3 1.0
CB A:ARG237 5.0 20.9 0.5

Chlorine binding site 2 out of 8 in 6vcx

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Chlorine binding site 2 out of 8 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:13.8
occ:0.90
 O A:HOH908 3.0 46.7 1.0
O A:HOH596 3.1 13.3 1.0
O A:HOH670 3.2 17.6 1.0
NZ A:LYS384 3.3 22.4 0.6
O A:HOH858 3.3 44.8 1.0
N A:ASP342 3.3 9.5 1.0
NZ A:LYS384 3.5 20.9 0.5
CA A:PHE341 3.7 10.5 1.0
CE A:LYS384 3.7 17.4 0.5
ND2 A:ASN351 4.0 13.4 1.0
C A:PHE341 4.0 10.9 1.0
CD1 A:ILE285 4.0 14.4 0.5
CD2 A:PHE341 4.1 10.9 1.0
O A:SER340 4.2 21.1 1.0
CE A:LYS384 4.2 21.7 0.6
CD A:LYS384 4.2 20.3 0.6
CB A:ASP342 4.2 10.6 1.0
CA A:ASP342 4.3 9.6 1.0
CB A:PHE341 4.3 11.2 1.0
CB A:ASN351 4.4 11.4 1.0
O A:ASP342 4.4 10.7 1.0
CD1 A:ILE285 4.5 9.4 0.5
CG A:ASN351 4.5 12.7 1.0
CG A:PHE341 4.5 10.4 1.0
C A:ASP342 4.8 9.4 1.0
N A:PHE341 4.8 11.4 1.0
CE2 A:PHE341 4.8 12.4 1.0
O A:HOH886 4.9 36.5 1.0
C A:SER340 4.9 14.0 1.0
CG1 A:ILE285 4.9 11.1 0.5
OE1 A:GLN288 5.0 10.2 1.0

Chlorine binding site 3 out of 8 in 6vcx

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Chlorine binding site 3 out of 8 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:14.1
occ:0.90
 O A:HOH940 3.1 26.0 1.0
O A:HOH825 3.1 11.1 1.0
N A:VAL278 3.3 8.5 1.0
CA A:GLY121 3.4 9.8 1.0
N A:ASP122 3.4 9.5 1.0
O A:HOH817 3.4 17.5 1.0
CA A:LYS277 3.4 8.3 1.0
C A:GLY121 3.4 9.4 1.0
N A:GLY121 3.5 10.3 1.0
O A:HOH577 3.6 15.4 1.0
C A:LYS277 3.9 8.0 1.0
CB A:ASP122 3.9 10.3 1.0
CB A:LYS277 3.9 9.5 1.0
CG2 A:VAL278 3.9 9.9 1.0
CG A:LYS277 4.0 11.3 1.0
O A:GLY121 4.1 11.1 1.0
O A:HOH810 4.1 26.0 1.0
O A:THR276 4.2 8.7 0.5
CA A:ASP122 4.2 8.8 1.0
CA A:VAL278 4.5 8.5 1.0
N A:LYS277 4.5 8.6 1.0
CB A:VAL278 4.5 9.8 1.0
O A:THR276 4.6 16.0 0.5
O A:HOH926 4.6 17.0 1.0
C A:ALA120 4.7 9.9 1.0
CG1 A:VAL278 4.7 11.3 1.0
C A:THR276 4.8 8.0 0.5
O A:ASP122 4.9 9.8 1.0
C A:THR276 5.0 12.3 0.5
O A:HOH567 5.0 18.6 1.0
C A:ASP122 5.0 8.7 1.0

Chlorine binding site 4 out of 8 in 6vcx

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Chlorine binding site 4 out of 8 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:22.5
occ:0.76
 O A:HOH784 2.7 30.5 1.0
O A:HOH833 2.7 31.7 1.0
O A:HOH882 3.2 35.8 1.0
N A:VAL92 3.2 9.1 1.0
NH2 A:ARG70 3.5 12.0 1.0
CA A:LYS91 3.6 9.9 0.6
CA A:LYS91 3.6 10.1 0.4
O A:VAL92 3.7 11.4 1.0
C A:LYS91 3.9 9.1 1.0
O A:CYS90 4.0 11.7 1.0
O A:HOH598 4.2 26.0 1.0
CA A:VAL92 4.2 9.0 1.0
CG A:LYS91 4.3 12.8 0.6
C A:VAL92 4.3 8.9 1.0
OE1 A:GLU66 4.4 20.4 1.0
CB A:LYS91 4.4 11.8 0.4
CB A:LYS91 4.4 11.6 0.6
CB A:VAL92 4.6 9.6 1.0
N A:LYS91 4.6 9.8 1.0
O A:HOH991 4.7 39.5 1.0
C A:CYS90 4.7 10.4 1.0
CZ A:ARG70 4.8 10.8 1.0
CG A:LYS91 4.9 13.2 0.4
O A:HOH970 4.9 38.5 1.0

Chlorine binding site 5 out of 8 in 6vcx

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Chlorine binding site 5 out of 8 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:40.9
occ:1.00
 N A:GLU199 3.1 19.1 1.0
CB A:ASP198 3.5 15.7 1.0
O A:HOH556 3.7 35.8 1.0
CB A:GLU199 3.7 28.9 1.0
NH2 A:ARG165 3.8 23.2 1.0
CA A:GLU199 3.8 23.8 1.0
CG2 A:THR200 3.9 35.5 1.0
C A:ASP198 4.0 14.8 1.0
CA A:ASP198 4.1 13.3 1.0
CG A:ASP198 4.1 22.7 1.0
N A:THR200 4.2 23.6 1.0
O A:HOH519 4.2 42.7 1.0
C A:GLU199 4.3 32.1 1.0
CG A:GLU199 4.3 32.8 1.0
OD1 A:ASP198 4.5 22.6 1.0
OD2 A:ASP198 4.7 30.8 1.0
CZ A:ARG165 4.8 18.6 1.0
CD A:GLU199 4.9 40.4 1.0

Chlorine binding site 6 out of 8 in 6vcx

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Chlorine binding site 6 out of 8 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:39.6
occ:1.00
 N A:GLY119 3.2 15.3 1.0
CE A:LYS113 3.5 58.6 1.0
O A:HOH508 3.6 27.6 0.6
O A:HOH680 3.9 39.8 1.0
CA A:GLY119 3.9 13.5 1.0
CG1 A:ILE118 4.0 16.8 1.0
CD A:LYS113 4.0 54.4 1.0
CA A:ILE118 4.1 14.5 1.0
C A:ILE118 4.1 14.9 1.0
NZ A:LYS113 4.4 62.4 1.0
O A:GLY311 4.6 18.2 1.0
CB A:ILE118 4.7 15.1 1.0
CB A:LYS113 4.7 44.4 1.0
O A:GLU117 4.8 18.2 1.0
O A:HOH746 4.8 33.9 1.0
O A:GLY119 4.8 13.5 1.0
C A:GLY119 4.9 12.1 1.0
CG A:LYS113 5.0 47.8 1.0
CA A:GLY311 5.0 13.3 1.0

Chlorine binding site 7 out of 8 in 6vcx

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Chlorine binding site 7 out of 8 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:29.5
occ:0.69
 O A:HOH832 2.8 24.7 1.0
O A:HOH996 3.0 18.0 1.0
N A:VAL318 3.1 8.5 1.0
NZ A:LYS338 3.3 34.2 1.0
O A:VAL318 3.6 8.8 1.0
CA A:SER317 3.8 8.6 1.0
C A:SER317 3.8 8.0 1.0
CA A:VAL318 4.0 8.8 1.0
CB A:VAL318 4.0 9.6 1.0
O A:HOH931 4.2 38.2 1.0
C A:VAL318 4.3 8.4 1.0
CG2 A:VAL318 4.3 11.1 1.0
CE A:LYS338 4.4 28.0 1.0
CD A:LYS338 4.6 22.3 1.0
CB A:SER317 4.6 8.8 1.0
N A:SER317 4.7 8.7 1.0
O A:LEU316 4.9 10.9 1.0
O A:SER317 4.9 8.5 1.0

Chlorine binding site 8 out of 8 in 6vcx

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Chlorine binding site 8 out of 8 in the Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Arabidopsis Thaliana S-Adenosylmethionine Synthase 1 (ATMAT1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:38.0
occ:0.85
 N A:ASP102 3.0 12.9 1.0
CB A:ASP102 3.5 19.3 1.0
CA A:PRO101 3.6 10.8 1.0
O A:HOH624 3.7 34.8 1.0
C A:PRO101 3.8 10.5 1.0
CA A:ASP102 3.9 14.5 1.0
O A:HOH682 3.9 28.0 1.0
CG2 A:THR58 3.9 10.8 1.0
CB A:PRO101 4.1 11.9 1.0
O A:SER100 4.9 11.5 1.0
CG A:ASP102 4.9 23.9 1.0
N A:PRO101 4.9 9.9 1.0
CD A:LYS39 5.0 20.1 0.5

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: Mon Jul 29 16:14:58 2024

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