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Chlorine in PDB 4zu4: X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans

Protein crystallography data

The structure of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans, PDB code: 4zu4 was solved by J.B.Thoden, E.Vinogradov, M.Gilbert, A.J.Salinger, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.28 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.405, 64.579, 112.968, 90.00, 111.39, 90.00
R / Rfree (%) 17.1 / 20.7

Other elements in 4zu4:

The structure of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans (pdb code 4zu4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans, PDB code: 4zu4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4zu4

Go back to Chlorine Binding Sites List in 4zu4
Chlorine binding site 1 out of 6 in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:29.6
occ:1.00
 O A:HOH526 3.0 27.0 1.0
O A:HOH610 3.2 45.5 1.0
N A:VAL251 3.2 21.1 1.0
ND2 A:ASN162 3.4 35.9 1.0
CA A:TYR250 3.8 21.0 1.0
CE2 A:PHE163 3.8 30.3 1.0
C A:TYR250 4.0 20.0 1.0
CD1 A:TYR250 4.0 23.2 1.0
O A:VAL251 4.1 26.3 1.0
CB A:ASN162 4.2 38.3 1.0
CA A:VAL251 4.2 20.6 1.0
CB A:TYR250 4.2 21.4 1.0
CB A:VAL251 4.2 22.6 1.0
CG A:ASN162 4.3 34.9 1.0
CD2 A:PHE163 4.4 26.5 1.0
CG2 A:VAL251 4.6 27.0 1.0
O A:GLU249 4.6 22.4 1.0
C A:VAL251 4.6 24.2 1.0
CG A:TYR250 4.6 22.0 1.0
O A:HOH643 4.7 53.0 1.0
O A:HOH599 4.7 38.3 1.0
CZ A:PHE163 4.9 25.8 1.0
N A:TYR250 5.0 19.4 1.0

Chlorine binding site 2 out of 6 in 4zu4

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Chlorine binding site 2 out of 6 in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:38.9
occ:1.00
 O B:HOH531 3.1 36.2 1.0
ND2 B:ASN162 3.2 46.4 1.0
N B:VAL251 3.3 27.1 1.0
CA B:TYR250 3.7 25.7 1.0
CB B:ASN162 3.8 53.5 1.0
CE2 B:PHE163 4.0 32.4 1.0
C B:TYR250 4.0 26.2 1.0
CG B:ASN162 4.0 47.5 1.0
CB B:VAL251 4.2 32.9 1.0
CD1 B:TYR250 4.2 29.0 1.0
CB B:TYR250 4.2 25.0 1.0
CA B:VAL251 4.3 28.3 1.0
O B:VAL251 4.3 27.1 1.0
CG2 B:VAL251 4.4 37.1 1.0
CD2 B:PHE163 4.4 39.6 1.0
O B:GLU249 4.6 25.6 1.0
CG B:TYR250 4.7 26.2 1.0
C B:VAL251 4.7 27.0 1.0
N B:TYR250 4.9 26.4 1.0

Chlorine binding site 3 out of 6 in 4zu4

Go back to Chlorine Binding Sites List in 4zu4
Chlorine binding site 3 out of 6 in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:34.5
occ:1.00
 OD1 D:ASN162 3.1 40.5 1.0
O D:HOH520 3.1 32.1 1.0
N D:VAL251 3.3 23.3 1.0
CB D:ASN162 3.7 43.2 1.0
CE1 D:PHE163 3.8 29.8 1.0
CG D:ASN162 3.8 41.1 1.0
CA D:TYR250 3.8 26.8 1.0
C D:TYR250 4.1 25.7 1.0
CD1 D:TYR250 4.1 28.4 1.0
CA D:VAL251 4.3 24.2 1.0
CB D:TYR250 4.3 23.4 1.0
O D:VAL251 4.3 22.7 1.0
CD1 D:PHE163 4.3 31.3 1.0
CB D:VAL251 4.4 25.4 1.0
O D:GLU249 4.7 27.6 1.0
CG D:TYR250 4.7 26.4 1.0
C D:VAL251 4.7 21.6 1.0
CG2 D:VAL251 4.8 29.1 1.0
N D:ASN162 4.8 42.9 1.0
CA D:ASN162 4.9 41.5 1.0
CZ D:PHE163 4.9 30.0 1.0
O D:HOH511 5.0 38.1 1.0

Chlorine binding site 4 out of 6 in 4zu4

Go back to Chlorine Binding Sites List in 4zu4
Chlorine binding site 4 out of 6 in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:46.1
occ:1.00
 N D:ARG293 3.3 21.6 1.0
N D:ASP294 3.5 26.0 1.0
CB D:ASP294 3.9 31.0 1.0
CA D:ILE292 4.0 24.7 1.0
CG2 D:ILE292 4.0 29.3 1.0
C D:ILE292 4.1 21.9 1.0
CA D:ARG293 4.2 30.4 1.0
C D:ARG293 4.2 25.7 1.0
CA D:ASP294 4.3 28.3 1.0
CB D:THR297 4.5 27.7 1.0
CG2 D:THR297 4.6 33.2 1.0
CB D:ILE292 4.6 26.5 1.0
OG1 D:THR297 4.6 26.2 1.0
CB D:ARG293 4.6 35.9 1.0
O D:TYR291 4.8 23.9 1.0
O D:ASP294 4.8 25.3 1.0

Chlorine binding site 5 out of 6 in 4zu4

Go back to Chlorine Binding Sites List in 4zu4
Chlorine binding site 5 out of 6 in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:27.9
occ:1.00
 O E:HOH599 3.1 36.3 1.0
ND2 E:ASN162 3.1 36.2 1.0
O E:HOH532 3.2 24.5 1.0
N E:VAL251 3.4 18.5 1.0
CA E:TYR250 3.8 20.6 1.0
CE2 E:PHE163 3.8 23.4 1.0
CB E:ASN162 4.0 30.0 1.0
CG E:ASN162 4.0 33.5 1.0
CD1 E:TYR250 4.0 24.5 1.0
C E:TYR250 4.1 21.4 1.0
CB E:TYR250 4.2 20.3 1.0
CD2 E:PHE163 4.2 23.1 1.0
O E:VAL251 4.2 21.3 1.0
CA E:VAL251 4.4 20.5 1.0
CB E:VAL251 4.5 23.9 1.0
O E:GLU249 4.6 21.6 1.0
CG E:TYR250 4.6 23.8 1.0
CG2 E:VAL251 4.6 28.5 1.0
C E:VAL251 4.8 19.4 1.0
O E:HOH585 4.9 40.2 1.0
N E:TYR250 4.9 22.0 1.0
CZ E:PHE163 5.0 21.9 1.0

Chlorine binding site 6 out of 6 in 4zu4

Go back to Chlorine Binding Sites List in 4zu4
Chlorine binding site 6 out of 6 in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl401

b:22.8
occ:1.00
 OD1 F:ASN162 3.1 27.1 1.0
O F:HOH596 3.2 29.2 1.0
O F:HOH515 3.2 23.3 1.0
N F:VAL251 3.3 17.7 1.0
O F:HOH585 3.3 39.2 1.0
CB F:ASN162 3.6 31.2 1.0
CA F:TYR250 3.7 18.6 1.0
CG F:ASN162 3.8 28.5 1.0
CE1 F:PHE163 3.9 15.1 1.0
C F:TYR250 4.0 17.6 1.0
CD1 F:TYR250 4.2 19.9 1.0
CB F:TYR250 4.2 16.6 1.0
O F:VAL251 4.2 16.8 1.0
CD1 F:PHE163 4.2 16.6 1.0
CA F:VAL251 4.3 18.4 1.0
CB F:VAL251 4.4 20.0 1.0
O F:GLU249 4.5 20.0 1.0
O F:HOH653 4.7 49.4 1.0
CG F:TYR250 4.7 18.0 1.0
C F:VAL251 4.7 14.7 1.0
CG2 F:VAL251 4.7 20.6 1.0
O F:HOH568 4.8 37.7 1.0
CA F:ASN162 4.9 33.7 1.0
N F:TYR250 4.9 15.6 1.0
O D:HOH600 4.9 39.9 1.0

Reference:

J.B.Thoden, E.Vinogradov, M.Gilbert, A.J.Salinger, H.M.Holden. Bacterial Sugar 3,4-Ketoisomerases: Structural Insight Into Product Stereochemistry. Biochemistry V. 54 4495 2015.
ISSN: ISSN 0006-2960
PubMed: 26125548
DOI: 10.1021/ACS.BIOCHEM.5B00541
Page generated: Fri Jul 26 04:51:28 2024

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