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Caesium in PDB 3wrx: Crystal Structure of Heliase Complex 1

Enzymatic activity of Crystal Structure of Heliase Complex 1

All present enzymatic activity of Crystal Structure of Heliase Complex 1:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Heliase Complex 1, PDB code: 3wrx was solved by H.Matsumura, E.Katoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.31 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.215, 133.710, 195.220, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24

Other elements in 3wrx:

The structure of Crystal Structure of Heliase Complex 1 also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Caesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Caesium atom in the Crystal Structure of Heliase Complex 1 (pdb code 3wrx). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 18 binding sites of Caesium where determined in the Crystal Structure of Heliase Complex 1, PDB code: 3wrx:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Caesium binding site 1 out of 18 in 3wrx

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Caesium binding site 1 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs503

b:56.5
occ:1.00
 OG1 A:THR271 3.0 21.7 1.0
O A:MET308 3.0 37.6 1.0
OD2 A:ASP275 3.1 36.7 1.0
OD1 A:ASN310 3.2 37.8 1.0
O A:HOH617 3.3 20.8 1.0
O A:THR271 3.4 24.4 1.0
CG A:ASP275 3.4 35.6 1.0
OD1 A:ASP275 3.6 37.7 1.0
N A:ASN310 3.8 38.5 1.0
C A:MET308 4.0 36.1 1.0
CG2 A:THR271 4.0 18.8 1.0
CB A:THR271 4.0 22.0 1.0
C A:THR271 4.0 24.9 1.0
CA A:VAL309 4.0 36.4 1.0
CG A:ASN310 4.1 37.5 1.0
CZ A:PHE219 4.1 26.8 1.0
CE1 A:PHE219 4.2 26.6 1.0
C A:VAL309 4.3 38.1 1.0
CB A:ASN310 4.3 37.6 1.0
CB A:ASP275 4.4 33.8 1.0
N A:VAL309 4.4 36.5 1.0
CA A:THR271 4.6 23.0 1.0
CA A:ASN310 4.6 38.5 1.0
N A:ASP275 4.7 30.0 1.0
CB A:ALA274 4.8 29.2 1.0
CG A:MET308 4.8 33.1 1.0
N A:GLU272 4.8 25.4 1.0
O A:MET282 4.8 32.4 1.0
O A:ALA305 5.0 32.9 1.0

Caesium binding site 2 out of 18 in 3wrx

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Caesium binding site 2 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs504

b:52.1
occ:1.00
 O A:CYS403 3.0 32.7 1.0
O A:ASN400 3.2 29.6 1.0
O A:LEU397 3.2 30.4 1.0
O A:HOH658 3.6 35.1 1.0
O A:GLU398 3.8 32.1 1.0
C A:GLU398 4.1 31.9 1.0
C A:ASN400 4.1 30.0 1.0
C A:CYS403 4.2 32.5 1.0
N A:ASN400 4.2 29.1 1.0
C A:LEU397 4.3 30.6 1.0
CA A:GLU398 4.3 33.0 1.0
O A:HOH792 4.5 33.1 1.0
CA A:ASN400 4.6 29.6 1.0
CB A:ASN400 4.6 29.9 1.0
N A:GLU398 4.8 31.5 1.0
N A:ASN399 4.8 30.7 1.0
CA A:GLN404 5.0 31.8 1.0

Caesium binding site 3 out of 18 in 3wrx

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Caesium binding site 3 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs505

b:66.6
occ:1.00
 O A:HOH686 3.0 29.6 1.0
O A:SER76 3.2 29.1 1.0
O A:HIS78 3.2 29.2 1.0
O A:HOH696 3.5 25.9 1.0
O A:HOH736 3.6 28.6 1.0
CG2 A:THR79 3.7 35.0 1.0
C A:SER76 4.0 30.1 1.0
C A:HIS78 4.1 29.2 1.0
N A:HIS78 4.5 29.3 1.0
CA A:SER76 4.5 29.6 1.0
O A:LEU75 4.8 24.8 1.0
N A:THR79 4.8 30.0 1.0
C A:CYS77 4.8 30.3 1.0
CA A:THR79 4.8 31.5 1.0
CB A:THR79 4.9 34.2 1.0
N A:CYS77 4.9 31.3 1.0
CA A:HIS78 4.9 28.1 1.0

Caesium binding site 4 out of 18 in 3wrx

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Caesium binding site 4 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs506

b:32.4
occ:1.00
 O B:SER39 2.9 37.4 1.0
O A:SER39 3.0 41.6 1.0
OD1 A:ASN40 3.1 61.2 1.0
O A:PHE38 3.2 32.5 1.0
O B:PHE38 3.3 31.9 1.0
O B:SER37 3.3 27.9 1.0
O A:SER37 3.3 25.0 1.0
C B:PHE38 3.6 33.1 1.0
C A:PHE38 3.7 33.0 1.0
C B:SER39 4.0 38.9 1.0
C A:SER39 4.0 43.2 1.0
CG A:ASN40 4.0 59.9 1.0
CA B:PHE38 4.1 31.9 1.0
CS A:CS507 4.2 92.0 1.0
CA A:PHE38 4.2 29.7 1.0
CS B:CS505 4.2 0.3 1.0
C B:SER37 4.3 30.9 1.0
N B:SER39 4.4 35.2 1.0
N A:SER39 4.4 36.0 1.0
C A:SER37 4.4 28.1 1.0
ND2 A:ASN40 4.4 60.2 1.0
CA A:SER39 4.7 40.8 1.0
O A:HOH784 4.7 34.9 1.0
N B:PHE38 4.7 32.2 1.0
CA B:SER39 4.8 36.9 1.0
N A:PHE38 4.8 29.1 1.0
N B:ASN40 4.8 42.9 1.0
N A:ASN40 4.9 49.2 1.0
CA B:ASN40 4.9 47.5 1.0

Caesium binding site 5 out of 18 in 3wrx

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Caesium binding site 5 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs507

b:92.0
occ:1.00
 O A:SER39 3.1 41.6 1.0
O A:SER37 3.1 25.0 1.0
O A:ASN36 3.2 29.9 1.0
NZ A:LYS41 3.2 57.8 1.0
C A:SER37 4.0 28.1 1.0
C A:SER39 4.0 43.2 1.0
CS A:CS506 4.2 32.4 1.0
C A:ASN36 4.3 29.1 1.0
CA A:SER37 4.3 27.8 1.0
CE A:LYS41 4.5 59.6 1.0
N A:SER39 4.7 36.0 1.0
N A:SER37 4.8 27.4 1.0
OG A:SER39 4.8 47.2 1.0
N A:ASN40 4.8 49.2 1.0
CA A:ASN40 4.8 54.4 1.0
CA A:SER39 4.9 40.8 1.0
OD1 A:ASN40 4.9 61.2 1.0

Caesium binding site 6 out of 18 in 3wrx

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Caesium binding site 6 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs502

b:55.0
occ:1.00
 OG1 B:THR271 2.9 19.4 1.0
OD1 B:ASN310 3.0 32.8 1.0
OD2 B:ASP275 3.2 31.8 1.0
O B:MET308 3.2 32.0 1.0
O B:HOH608 3.2 24.2 1.0
O B:THR271 3.4 27.9 1.0
CG B:ASP275 3.4 32.5 1.0
OD1 B:ASP275 3.5 34.0 1.0
N B:ASN310 3.7 31.1 1.0
CA B:VAL309 3.9 29.9 1.0
CB B:THR271 3.9 21.6 1.0
CG2 B:THR271 4.0 18.0 1.0
CG B:ASN310 4.0 33.3 1.0
C B:THR271 4.0 26.6 1.0
C B:MET308 4.0 31.6 1.0
C B:VAL309 4.1 30.8 1.0
CZ B:PHE219 4.2 33.2 1.0
CE1 B:PHE219 4.2 32.9 1.0
CB B:ASN310 4.3 32.9 1.0
N B:VAL309 4.3 31.5 1.0
CB B:ASP275 4.4 30.7 1.0
CA B:THR271 4.5 24.5 1.0
CA B:ASN310 4.6 32.9 1.0
N B:ASP275 4.6 30.2 1.0
CG B:MET308 4.7 38.1 1.0
N B:GLU272 4.8 26.8 1.0
CB B:ALA274 4.9 28.4 1.0
O B:MET282 4.9 30.7 1.0
CA B:GLU272 5.0 27.7 1.0

Caesium binding site 7 out of 18 in 3wrx

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Caesium binding site 7 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs503

b:59.5
occ:1.00
 O B:LEU397 3.0 42.6 1.0
O B:ASN400 3.0 56.3 1.0
O B:HOH733 3.2 41.1 1.0
O B:CYS403 3.2 44.5 1.0
O B:GLU398 3.5 49.3 1.0
C B:ASN400 4.0 56.4 1.0
C B:LEU397 4.1 44.0 1.0
OE2 B:GLU401 4.1 67.3 1.0
C B:GLU398 4.1 50.5 1.0
C B:CYS403 4.3 44.2 1.0
N B:ASN400 4.4 54.8 1.0
CA B:GLU398 4.5 49.6 1.0
CA B:GLN404 4.7 40.4 1.0
N B:GLU398 4.7 46.6 1.0
CA B:ASN400 4.7 55.7 1.0
CG2 B:VAL405 4.8 31.0 1.0
CD B:GLU401 4.9 66.2 1.0
N B:GLN404 4.9 42.5 1.0
N B:VAL405 4.9 37.7 1.0
N B:GLU401 5.0 57.0 1.0

Caesium binding site 8 out of 18 in 3wrx

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Caesium binding site 8 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 8 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs504

b:83.5
occ:1.00
 O B:SER76 3.0 36.3 1.0
O B:HIS78 3.4 44.0 1.0
CG2 B:THR79 3.6 46.0 1.0
C B:SER76 4.0 37.6 1.0
C B:HIS78 4.1 44.7 1.0
N B:HIS78 4.3 42.1 1.0
CA B:SER76 4.6 36.6 1.0
N B:THR79 4.7 46.7 1.0
CA B:HIS78 4.7 43.5 1.0
C B:CYS77 4.8 41.6 1.0
O B:LEU75 4.9 31.7 1.0
CB B:THR79 4.9 48.3 1.0
CA B:THR79 4.9 49.4 1.0
N B:CYS77 4.9 39.9 1.0

Caesium binding site 9 out of 18 in 3wrx

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Caesium binding site 9 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 9 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs505

b:0.3
occ:1.00
 O B:ASN36 3.2 36.2 1.0
O B:SER39 3.3 37.4 1.0
O B:SER37 3.3 27.9 1.0
C B:SER37 4.1 30.9 1.0
C B:SER39 4.2 38.9 1.0
CS A:CS506 4.2 32.4 1.0
OD1 A:ASN40 4.3 61.2 1.0
CA B:SER37 4.3 31.8 1.0
C B:ASN36 4.3 35.0 1.0
N B:SER39 4.7 35.2 1.0
N B:LYS41 4.8 54.1 1.0
N B:SER37 4.8 33.4 1.0
ND2 A:ASN40 4.8 60.2 1.0
CA B:SER39 4.9 36.9 1.0
CG A:ASN40 5.0 59.9 1.0
CB B:SER39 5.0 36.8 1.0

Caesium binding site 10 out of 18 in 3wrx

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Caesium binding site 10 out of 18 in the Crystal Structure of Heliase Complex 1


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 10 of Crystal Structure of Heliase Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs506

b:73.2
occ:1.00
 O D:ASN978 2.9 31.0 1.0
O D:GLY983 2.9 32.0 1.0
O B:GLY86 3.0 46.5 1.0
O D:TYR981 3.0 31.6 1.0
O B:MET85 3.2 55.2 1.0
C B:MET85 3.3 55.1 1.0
CA B:MET85 3.6 57.8 1.0
C D:GLY983 3.7 32.0 1.0
C B:GLY86 3.8 45.5 1.0
N B:GLY86 3.8 52.1 1.0
C D:ASN978 3.9 29.6 1.0
N D:GLY983 4.0 33.6 1.0
O B:THR84 4.1 63.5 1.0
ND2 D:ASN978 4.1 37.0 1.0
C D:TYR981 4.2 31.6 1.0
CA B:GLY86 4.3 48.8 1.0
N D:HIS984 4.4 33.6 1.0
CA D:ASN978 4.4 29.8 1.0
CA D:GLY983 4.4 32.5 1.0
CA D:HIS984 4.5 34.3 1.0
C D:GLU982 4.5 34.4 1.0
CG D:ASN978 4.5 34.6 1.0
CB B:MET85 4.6 59.3 1.0
N B:MET85 4.7 61.1 1.0
N B:THR87 4.7 41.9 1.0
C B:THR84 4.8 63.7 1.0
CA D:GLU982 4.8 34.7 1.0
CB D:ASN978 4.8 32.7 1.0
ND1 D:HIS984 4.9 43.3 1.0
N D:GLU982 4.9 33.1 1.0
CA B:THR87 4.9 38.6 1.0
CE2 B:PHE88 4.9 21.4 1.0
N D:GLN979 5.0 31.0 1.0

Reference:

K.Ishibashi, Y.Kezuka, C.Kobayashi, M.Kato, T.Inoue, T.Nonaka, M.Ishikawa, H.Matsumura, E.Katoh. Structural Basis For the Recognition-Evasion Arms Race Between Tomato Mosaic Virus and the Resistance Gene Tm-1 Proc.Natl.Acad.Sci.Usa 2014.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1407888111
Page generated: Tue Jul 30 20:26:12 2024

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