Atomistry » Chlorine » PDB 6vch-6vkc » 6vcx
Atomistry »
  Chlorine »
    PDB 6vch-6vkc »
      6vcx »

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

Go back to Chlorine Binding Sites List in 6vcx
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

Go back to Chlorine Binding Sites List in 6vcx
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

Go back to Chlorine Binding Sites List in 6vcx
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

Go back to Chlorine Binding Sites List in 6vcx
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

Go back to Chlorine Binding Sites List in 6vcx
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

Go back to Chlorine Binding Sites List in 6vcx
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

Go back to Chlorine Binding Sites List in 6vcx
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

Go back to Chlorine Binding Sites List in 6vcx
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy