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Chlorine in PDB 8up3: Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)

Enzymatic activity of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)

All present enzymatic activity of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F):
3.5.1.1;

Protein crystallography data

The structure of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F), PDB code: 8up3 was solved by J.Lubkowski, A.Wlodawer, D.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.40 / 1.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 245.644, 63.185, 92.968, 90, 103.42, 90
R / Rfree (%) 16.4 / 21.6

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) (pdb code 8up3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F), PDB code: 8up3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 8up3

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Chlorine binding site 1 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:21.9
occ:1.00
 O A:HOH411 3.2 17.6 1.0
N A:SER58 3.2 20.9 1.0
ND2 D:ASN26 3.3 14.8 1.0
N A:THR16 3.3 11.7 1.0
OG1 A:THR16 3.4 14.0 1.0
CA A:GLY15 3.4 11.4 1.0
O1 A:EDO201 3.6 22.5 0.7
CB A:SER58 3.6 26.4 1.0
OG A:SER58 3.8 29.7 1.0
C A:GLY15 3.8 10.4 1.0
CA A:GLY86 3.9 12.6 1.0
CA A:ASP57 3.9 20.9 1.0
CA A:SER58 4.0 21.6 1.0
CB A:ASP57 4.0 24.2 1.0
C A:ASP57 4.0 19.5 1.0
O1 A:EDO201 4.1 14.4 0.3
CA A:THR16 4.2 11.3 1.0
CG D:ASN26 4.3 19.5 1.0
CE A:LYS19 4.3 18.1 1.0
OD1 D:ASN26 4.4 17.6 1.0
CB A:THR16 4.4 12.2 1.0
C1 A:EDO201 4.5 16.7 0.3
O A:HOH423 4.5 32.7 1.0
N A:GLY15 4.6 11.4 1.0
NZ A:LYS19 4.7 17.6 1.0
C A:GLY86 4.8 13.6 1.0
N A:GLY86 4.9 13.0 1.0
O A:GLY15 4.9 10.9 1.0
C1 A:EDO201 4.9 26.7 0.7
O A:HOH348 4.9 19.4 1.0

Chlorine binding site 2 out of 12 in 8up3

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Chlorine binding site 2 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:25.3
occ:0.50
 CL A:CL210 0.0 25.3 0.5
CL A:CL210 2.0 26.5 0.5
N A:LEU28 3.1 16.0 1.0
O D:HOH407 3.1 30.0 1.0
CA A:GLY27 3.5 15.7 1.0
C A:GLY27 3.8 15.1 1.0
CB A:LEU28 3.9 14.4 1.0
CG A:LEU28 4.0 14.4 1.0
CA A:LEU28 4.0 14.8 1.0
CD1 D:LEU28 4.1 17.4 1.0
CG D:LEU28 4.3 16.2 1.0
CB D:LEU28 4.3 16.5 1.0
O A:HOH376 4.3 28.4 1.0
O A:LEU28 4.5 16.6 1.0
CD1 A:LEU28 4.5 15.8 1.0
N D:LEU28 4.6 15.6 1.0
C A:LEU28 4.8 17.0 1.0
N A:GLY27 5.0 15.4 1.0

Chlorine binding site 3 out of 12 in 8up3

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Chlorine binding site 3 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:26.5
occ:0.50
 CL A:CL210 0.0 26.5 0.5
CL A:CL210 2.0 25.3 0.5
O A:HOH376 3.2 28.4 1.0
N D:LEU28 3.4 15.6 1.0
CA D:GLY27 3.7 14.8 1.0
C D:GLY27 4.0 13.9 1.0
CB D:LEU28 4.2 16.5 1.0
CD1 A:LEU28 4.3 15.8 1.0
O D:HOH407 4.3 30.0 1.0
CA D:LEU28 4.4 15.4 1.0
CB A:LEU28 4.4 14.4 1.0
CG D:LEU28 4.4 16.2 1.0
CG A:LEU28 4.4 14.4 1.0
O D:HOH310 4.6 33.7 1.0
N A:LEU28 4.6 16.0 1.0
O D:LEU28 4.6 17.4 1.0
CD1 D:LEU28 4.9 17.4 1.0

Chlorine binding site 4 out of 12 in 8up3

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Chlorine binding site 4 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:24.6
occ:1.00
 N B:SER58 3.0 29.4 1.0
OG B:SER58 3.2 34.5 1.0
O B:HOH386 3.2 27.4 1.0
ND2 C:ASN26 3.2 24.9 1.0
CB B:SER58 3.6 32.4 1.0
N B:THR16 3.6 13.6 1.0
CA B:GLY15 3.6 13.4 1.0
OG1 B:THR16 3.7 16.4 1.0
CA B:ASP57 3.7 23.1 1.0
CB B:ASP57 3.8 27.0 1.0
CA B:GLY86 3.9 16.3 1.0
C B:ASP57 3.9 23.9 1.0
CA B:SER58 3.9 27.0 1.0
C B:GLY15 4.0 12.9 1.0
O2 B:EDO201 4.1 38.4 1.0
O B:HOH323 4.3 12.7 0.3
CG C:ASN26 4.4 24.6 1.0
CA B:THR16 4.5 13.9 1.0
O B:HOH359 4.5 45.6 1.0
CE B:LYS19 4.6 19.9 1.0
OD1 C:ASN26 4.6 22.6 1.0
CB B:THR16 4.7 13.2 1.0
C2 B:EDO201 4.7 32.9 1.0
N B:GLY15 4.7 15.8 1.0
C B:GLY86 4.8 16.9 1.0
NZ B:LYS19 4.8 23.5 1.0
N B:GLY86 4.8 15.9 1.0
N B:THR87 4.9 14.3 1.0

Chlorine binding site 5 out of 12 in 8up3

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Chlorine binding site 5 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl206

b:51.3
occ:1.00
 N B:LEU28 3.1 15.3 1.0
CB B:LEU28 3.6 18.3 1.0
N C:LEU28 3.8 15.9 1.0
O C:HOH370 3.8 27.6 1.0
CG B:LEU28 3.8 18.5 1.0
O B:HOH333 3.8 27.4 1.0
CA B:LEU28 3.9 16.4 1.0
CB C:LEU28 4.0 16.6 1.0
CG C:LEU28 4.0 16.9 1.0
CA B:GLY27 4.0 16.0 1.0
C B:GLY27 4.1 15.1 1.0
CD1 C:LEU28 4.2 17.0 1.0
CD1 B:LEU28 4.2 19.5 1.0
O B:LEU28 4.3 17.5 1.0
CA C:LEU28 4.5 17.0 1.0
O B:HOH393 4.5 48.0 1.0
C B:LEU28 4.6 18.0 1.0
CA C:GLY27 4.6 17.1 1.0
O C:HOH355 4.7 43.5 1.0
C C:GLY27 4.7 14.9 1.0
O C:LEU28 4.9 19.7 1.0

Chlorine binding site 6 out of 12 in 8up3

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Chlorine binding site 6 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:19.7
occ:1.00
 N C:SER58 3.2 21.5 1.0
O C:HOH384 3.2 18.3 1.0
O2 C:EDO201 3.2 23.3 1.0
ND2 B:ASN26 3.3 20.2 1.0
CA C:GLY15 3.4 13.7 1.0
N C:THR16 3.5 13.7 1.0
OG1 C:THR16 3.6 14.2 1.0
CA C:ASP57 3.7 22.6 1.0
C C:GLY15 3.8 13.3 1.0
CB C:SER58 3.9 28.5 1.0
C C:ASP57 3.9 21.9 1.0
CB C:ASP57 3.9 24.8 1.0
CA C:GLY86 4.0 14.4 1.0
CA C:SER58 4.1 28.1 1.0
C2 C:EDO201 4.2 23.5 1.0
OG C:SER58 4.3 28.3 1.0
CG B:ASN26 4.3 21.1 1.0
CA C:THR16 4.4 13.4 1.0
O C:HOH314 4.4 41.5 1.0
CE C:LYS19 4.4 19.5 1.0
OD1 B:ASN26 4.6 20.9 1.0
N C:GLY15 4.6 13.7 1.0
CB C:THR16 4.6 14.1 1.0
O C:HOH376 4.7 29.5 1.0
NZ C:LYS19 4.7 21.9 1.0
O C:GLY15 4.9 14.7 1.0
N C:GLY86 5.0 14.8 1.0
O C:HOH310 5.0 25.4 1.0

Chlorine binding site 7 out of 12 in 8up3

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Chlorine binding site 7 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl206

b:25.6
occ:1.00
 O D:HOH409 3.0 20.0 1.0
ND2 A:ASN26 3.2 17.8 1.0
O1 D:EDO201 3.3 26.8 1.0
N D:SER58 3.3 28.9 1.0
N D:THR16 3.5 12.8 1.0
OG1 D:THR16 3.5 11.9 1.0
CA D:GLY15 3.5 15.3 1.0
CB D:SER58 3.8 36.9 1.0
CA D:ASP57 3.9 30.5 1.0
C D:GLY15 3.9 13.8 1.0
CA D:GLY86 4.0 13.1 1.0
C D:ASP57 4.0 27.8 1.0
CB D:ASP57 4.1 31.8 1.0
CA D:SER58 4.1 33.8 1.0
OG D:SER58 4.2 37.6 1.0
CE D:LYS19 4.2 18.4 1.0
CG A:ASN26 4.2 19.4 1.0
C1 D:EDO201 4.3 26.1 1.0
CA D:THR16 4.4 12.6 1.0
O D:HOH341 4.4 27.1 1.0
OD1 A:ASN26 4.4 19.1 1.0
NZ D:LYS19 4.5 19.1 1.0
CB D:THR16 4.6 12.7 1.0
N D:GLY15 4.7 14.8 1.0
O D:HOH301 4.8 35.5 1.0
O D:GLY15 4.9 13.3 1.0
C D:GLY86 5.0 14.1 1.0

Chlorine binding site 8 out of 12 in 8up3

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Chlorine binding site 8 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl204

b:31.6
occ:1.00
 N E:LEU28 3.4 16.4 1.0
N H:LEU28 3.4 16.4 1.0
O H:HOH386 3.7 45.0 1.0
CB E:LEU28 3.8 17.1 1.0
CG E:LEU28 3.8 17.8 1.0
CB H:LEU28 3.9 17.6 1.0
CG H:LEU28 4.0 17.2 1.0
O H:HOH367 4.0 35.9 1.0
CA H:GLY27 4.0 16.9 1.0
CD1 E:LEU28 4.1 19.3 1.0
CA E:GLY27 4.1 19.2 1.0
O H:HOH373 4.1 40.8 1.0
CA E:LEU28 4.2 17.4 1.0
C H:GLY27 4.2 15.4 1.0
C E:GLY27 4.3 15.7 1.0
CA H:LEU28 4.3 16.8 1.0
CD1 H:LEU28 4.4 17.5 1.0
O E:LEU28 4.6 16.6 1.0
O H:LEU28 4.7 17.9 1.0
C E:LEU28 4.9 17.6 1.0

Chlorine binding site 9 out of 12 in 8up3

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Chlorine binding site 9 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl203

b:33.3
occ:1.00
 N F:LEU28 3.4 16.7 1.0
N G:LEU28 3.6 16.8 1.0
CB F:LEU28 3.7 18.3 1.0
CG F:LEU28 3.9 16.6 1.0
O G:HOH370 3.9 31.9 1.0
CG G:LEU28 4.1 15.8 1.0
CB G:LEU28 4.1 15.5 1.0
CA F:LEU28 4.1 17.8 1.0
CA G:GLY27 4.2 18.2 1.0
O F:HOH403 4.2 38.8 1.0
O F:HOH362 4.2 31.9 1.0
CA F:GLY27 4.2 20.0 1.0
CD1 G:LEU28 4.3 17.3 1.0
C F:GLY27 4.3 17.2 1.0
CD1 F:LEU28 4.3 17.0 1.0
C G:GLY27 4.4 16.5 1.0
CA G:LEU28 4.5 16.0 1.0
O F:LEU28 4.5 21.6 1.0
O G:HOH321 4.8 41.5 1.0
C F:LEU28 4.8 19.4 1.0
O G:LEU28 4.9 18.8 1.0

Chlorine binding site 10 out of 12 in 8up3

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Chlorine binding site 10 out of 12 in the Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of Atypical Asparaginase From Rhodospirillum Rubrum (Mutant Y21F) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl203

b:27.6
occ:1.00
 O G:HOH387 3.2 27.0 1.0
ND2 F:ASN26 3.3 26.7 1.0
N G:THR16 3.4 12.7 1.0
O2 G:EDO201 3.4 39.6 1.0
CA G:GLY15 3.5 14.4 1.0
OG1 G:THR16 3.6 14.8 1.0
N G:SER58 3.8 32.4 1.0
C G:GLY15 3.8 13.3 1.0
CB G:ASP57 3.8 33.1 1.0
CA G:ASP57 3.9 28.8 1.0
CA G:GLY86 3.9 15.5 1.0
C G:ASP57 4.3 30.3 1.0
CG F:ASN26 4.3 29.0 1.0
CA G:THR16 4.3 12.1 1.0
CE G:LYS19 4.4 18.9 1.0
OD1 F:ASN26 4.5 25.0 1.0
N G:GLY15 4.5 14.6 1.0
NZ G:LYS19 4.6 22.3 1.0
CB G:THR16 4.6 13.1 1.0
CB G:SER58 4.6 44.5 1.0
CA G:SER58 4.8 36.3 1.0
C2 G:EDO201 4.9 34.9 1.0
C G:GLY86 4.9 15.6 1.0
N G:GLY86 4.9 14.7 1.0
O G:GLY15 4.9 13.2 1.0
O G:HOH326 4.9 25.4 1.0
OG G:SER58 4.9 44.9 1.0
N G:THR87 5.0 13.8 1.0

Reference:

D.Zhang, H.Czapinska, M.Bochtler, A.Wlodawer, J.Lubkowski. Rra, An Enzyme From Rhodospirillum Rubrum, Is A Prototype of A New Family of Short-Chain L-Asparaginases. Protein Sci. V. 33 E4920 2024.
ISSN: ESSN 1469-896X
PubMed: 38501449
DOI: 10.1002/PRO.4920
Page generated: Tue Jul 30 13:16:36 2024

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