Chlorine in PDB 5yw3: X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant

Protein crystallography data

The structure of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant, PDB code: 5yw3 was solved by C.Sakai, T.Yamaguchi, T.Kohzuma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.72 / 1.19
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 34.699, 51.227, 57.723, 88.88, 77.16, 86.58
R / Rfree (%) 12.7 / 17.3

Other elements in 5yw3:

The structure of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant (pdb code 5yw3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant, PDB code: 5yw3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5yw3

Go back to Chlorine Binding Sites List in 5yw3
Chlorine binding site 1 out of 4 in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:30.6
occ:0.50
CL B:CL202 0.0 30.6 0.5
CL B:CL202 2.3 37.0 0.5
O B:HOH462 2.6 19.0 1.0
O B:HOH323 3.1 24.9 1.0
CA B:GLY14 3.7 12.5 1.0
O B:ASP13 4.0 13.8 1.0
N B:GLY14 4.2 10.9 1.0
C B:ASP13 4.3 11.5 1.0
O B:HOH396 4.5 12.2 1.0
O B:HOH454 4.6 24.9 1.0
O B:HOH321 4.8 24.6 1.0
C B:GLY14 4.9 8.1 1.0

Chlorine binding site 2 out of 4 in 5yw3

Go back to Chlorine Binding Sites List in 5yw3
Chlorine binding site 2 out of 4 in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:37.0
occ:0.50
CL B:CL202 0.0 37.0 0.5
CL B:CL202 2.3 30.6 0.5
O B:HOH396 3.1 12.2 1.0
O B:ASP13 3.3 13.8 1.0
CA B:GLY14 3.7 12.5 1.0
C B:ASP13 4.1 11.5 1.0
O B:HOH462 4.3 19.0 1.0
N B:GLY14 4.4 10.9 1.0
O B:HOH323 4.6 24.9 1.0
O B:HOH349 4.7 28.0 1.0
C B:GLY14 4.9 8.1 1.0
O B:HOH466 4.9 17.1 0.6
N B:ALA15 4.9 8.6 1.0

Chlorine binding site 3 out of 4 in 5yw3

Go back to Chlorine Binding Sites List in 5yw3
Chlorine binding site 3 out of 4 in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:13.7
occ:1.00
O D:HOH385 3.1 14.5 1.0
N D:LYS24 3.2 6.0 1.0
NZ C:LYS57 3.3 12.9 1.0
O D:HOH343 3.3 15.0 1.0
O D:HOH490 3.5 7.8 0.2
O C:HOH435 3.6 15.4 1.0
CE C:LYS57 3.6 10.7 1.0
CA D:LEU23 3.7 5.9 1.0
O D:HOH484 3.9 24.0 1.0
C D:LEU23 4.0 5.8 1.0
CG2 C:THR79 4.0 9.1 1.0
O D:SER22 4.1 7.9 1.0
CD1 D:LEU23 4.2 10.2 1.0
CB D:LYS24 4.2 8.2 1.0
CA D:LYS24 4.3 7.0 1.0
N D:LEU23 4.4 5.7 1.0
CD2 D:LEU122 4.5 9.4 1.0
CB C:THR79 4.5 7.8 1.0
O D:LYS24 4.6 8.6 1.0
C D:SER22 4.6 6.2 1.0
O D:HOH490 4.7 17.2 0.5
CB D:LEU23 4.8 7.3 1.0
O D:HOH381 4.8 9.6 1.0
CG D:LEU23 4.9 8.1 1.0
OG1 C:THR79 4.9 8.3 1.0
C D:LYS24 4.9 7.2 1.0
O C:HOH358 5.0 12.1 1.0

Chlorine binding site 4 out of 4 in 5yw3

Go back to Chlorine Binding Sites List in 5yw3
Chlorine binding site 4 out of 4 in the X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl202

b:15.2
occ:1.00
O C:HOH453 3.1 28.4 1.0
O D:HOH348 3.2 21.8 1.0
O D:HOH319 3.3 16.5 1.0
O C:HOH382 3.3 9.2 1.0
N D:GLU4 3.3 6.5 1.0
O D:HOH492 3.4 17.4 1.0
CA D:PHE3 3.6 6.3 1.0
CB D:PHE3 4.0 6.7 1.0
CD2 D:PHE3 4.0 7.2 1.0
C D:PHE3 4.0 6.3 1.0
CD2 C:TYR82 4.2 6.3 1.0
NZ C:LYS77 4.2 9.4 1.0
O D:HOH420 4.2 22.8 1.0
O D:GLU4 4.3 7.8 1.0
O D:HOH422 4.4 19.2 1.0
CG D:PHE3 4.4 6.5 1.0
CA D:GLU4 4.4 6.6 1.0
O C:HOH405 4.4 10.6 0.5
O D:ASP2 4.4 10.4 1.0
CE2 C:TYR82 4.5 7.1 1.0
CB D:GLU4 4.5 6.9 1.0
O D:HOH465 4.5 13.4 1.0
N D:PHE3 4.8 6.3 1.0
CG D:GLU4 4.8 7.3 1.0
C D:GLU4 4.8 6.7 1.0
O C:HOH405 4.9 14.6 0.5
CE2 D:PHE3 4.9 9.5 1.0

Reference:

T.Yamaguchi, C.Sakai, T.Kohzuma. X-Ray Crystal Structure of Pseudoazurin THR36LYS Variant To Be Published.
Page generated: Sat Dec 12 12:41:34 2020

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