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Chlorine in PDB 4gmd: The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate

Enzymatic activity of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate

All present enzymatic activity of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate:
2.7.4.9;

Protein crystallography data

The structure of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate, PDB code: 4gmd was solved by K.Tan, G.Joachimiak, R.Jedrzejczak, J.Sacchettini, A.Joachimiak, Midwestcenter For Structural Genomics (Mcsg), Structures Of Mtb Proteinsconferring Susceptibility To Known Mtb Inhibitors (Mtbi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.00 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.500, 123.404, 73.920, 90.00, 100.00, 90.00
R / Rfree (%) 17.7 / 22.6

Other elements in 4gmd:

The structure of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate (pdb code 4gmd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate, PDB code: 4gmd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4gmd

Go back to Chlorine Binding Sites List in 4gmd
Chlorine binding site 1 out of 6 in the The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:46.6
occ:1.00
 NH2 A:ARG20 3.2 45.7 1.0
C A:THR37 3.3 32.4 1.0
CA A:THR37 3.4 31.6 1.0
NH1 A:ARG20 3.5 37.3 1.0
O A:THR37 3.5 33.1 1.0
N A:THR37 3.7 29.4 1.0
CG A:ARG38 3.8 31.0 1.0
CZ A:ARG20 3.8 51.4 1.0
N A:ARG38 3.8 33.4 1.0
CB A:ARG38 3.8 28.7 1.0
C A:LEU36 4.1 40.2 1.0
O A:LEU36 4.3 40.6 1.0
CA A:ARG38 4.4 29.4 1.0
CB A:LEU36 4.6 36.2 1.0
CB A:THR37 4.9 33.3 1.0
CA A:LEU36 5.0 34.1 1.0

Chlorine binding site 2 out of 6 in 4gmd

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Chlorine binding site 2 out of 6 in the The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:50.5
occ:1.00
 NH1 B:ARG20 3.2 40.7 1.0
NH2 B:ARG20 3.2 46.7 1.0
O B:HOH436 3.4 45.2 1.0
CG B:ARG38 3.6 42.3 1.0
C B:THR37 3.6 38.4 1.0
CZ B:ARG20 3.7 48.7 1.0
O B:THR37 3.8 35.0 1.0
CB B:ARG38 3.8 41.6 1.0
CA B:THR37 3.8 39.2 1.0
N B:ARG38 3.9 42.1 1.0
N B:THR37 4.0 36.2 1.0
C B:LEU36 4.5 41.5 1.0
CA B:ARG38 4.5 36.8 1.0
O B:LEU36 4.7 37.6 1.0
CB B:LEU36 4.8 47.7 1.0

Chlorine binding site 3 out of 6 in 4gmd

Go back to Chlorine Binding Sites List in 4gmd
Chlorine binding site 3 out of 6 in the The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:51.0
occ:1.00
 NH1 C:ARG20 3.0 42.0 1.0
NH2 C:ARG20 3.2 46.1 1.0
C C:THR37 3.3 36.8 1.0
O C:THR37 3.4 29.6 1.0
CZ C:ARG20 3.6 48.5 1.0
CA C:THR37 3.6 32.3 1.0
CB C:ARG38 3.7 40.2 1.0
CG C:ARG38 3.8 38.4 1.0
N C:ARG38 3.8 36.9 1.0
N C:THR37 3.9 38.7 1.0
C C:LEU36 4.3 41.2 1.0
CA C:ARG38 4.4 32.7 1.0
O C:LEU36 4.5 40.9 1.0
CB C:LEU36 4.6 36.5 1.0
NE C:ARG20 4.9 35.1 1.0

Chlorine binding site 4 out of 6 in 4gmd

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Chlorine binding site 4 out of 6 in the The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:50.0
occ:1.00
 OH C:TYR104 2.8 41.9 1.0
C C:GLY10 3.3 47.0 1.0
N C:PRO11 3.4 48.2 1.0
O C:GLY10 3.6 45.3 1.0
OH C:TYR170 3.6 51.6 1.0
CZ C:TYR104 3.6 34.6 1.0
CE2 C:TYR104 3.6 38.7 1.0
CE2 C:TYR170 3.7 39.8 1.0
NH1 C:ARG96 3.7 57.9 1.0
CG1 C:VAL166 3.8 44.8 1.0
CA C:PRO11 3.8 52.9 1.0
O C:HOH456 3.8 44.6 1.0
CA C:GLY10 3.9 47.5 1.0
CB C:PRO11 4.1 50.7 1.0
CZ C:TYR170 4.2 45.7 1.0
CD C:PRO11 4.2 51.9 1.0
NE C:ARG96 4.2 55.0 1.0
N C:GLY10 4.3 48.0 1.0
CZ C:ARG96 4.4 55.5 1.0
CG C:PRO11 4.8 49.6 1.0
CD2 C:TYR170 4.9 46.5 1.0
CE1 C:TYR104 4.9 40.3 1.0
CD2 C:TYR104 4.9 41.6 1.0

Chlorine binding site 5 out of 6 in 4gmd

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Chlorine binding site 5 out of 6 in the The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:44.1
occ:1.00
 OH D:TYR104 3.1 45.8 1.0
C D:GLY10 3.2 43.7 1.0
N D:PRO11 3.3 41.8 1.0
NH1 D:ARG96 3.3 37.7 1.0
OH D:TYR170 3.4 44.7 1.0
O D:GLY10 3.4 44.0 1.0
CE2 D:TYR170 3.5 46.2 1.0
CA D:PRO11 3.6 39.0 1.0
CE2 D:TYR104 3.7 37.3 1.0
CA D:GLY10 3.8 43.7 1.0
CG1 D:VAL166 3.8 38.4 1.0
O D:HOH484 3.8 39.5 1.0
CZ D:TYR104 3.8 40.0 1.0
CD D:PRO11 3.8 43.1 1.0
CB D:PRO11 3.9 43.5 1.0
CZ D:TYR170 3.9 44.1 1.0
N D:GLY10 4.2 36.3 1.0
CZ D:ARG96 4.4 38.3 1.0
CG D:PRO11 4.4 47.6 1.0
NH2 D:ARG96 4.6 37.9 1.0
CD2 D:TYR170 4.6 43.6 1.0
CD2 D:TYR104 4.9 31.5 1.0
O D:HOH464 5.0 40.1 1.0

Chlorine binding site 6 out of 6 in 4gmd

Go back to Chlorine Binding Sites List in 4gmd
Chlorine binding site 6 out of 6 in the The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl304

b:49.8
occ:1.00
 NH2 D:ARG20 3.2 41.4 1.0
NH1 D:ARG20 3.4 33.2 1.0
O D:HOH467 3.4 50.6 1.0
C D:THR37 3.5 38.2 1.0
O D:THR37 3.6 38.0 1.0
CA D:THR37 3.7 34.0 1.0
CZ D:ARG20 3.8 39.4 1.0
CG D:ARG38 3.8 40.7 1.0
CB D:ARG38 3.8 29.1 1.0
N D:ARG38 3.9 32.2 1.0
N D:THR37 3.9 32.1 1.0
C D:LEU36 4.3 35.9 1.0
CA D:ARG38 4.5 31.9 1.0
O D:LEU36 4.6 36.2 1.0
CB D:LEU36 4.6 37.1 1.0

Reference:

K.Tan, G.Joachimiak, R.Jedrzejczak, J.Sacchettini, A.Joachimiak. The Crystal Structure of Thymidylate Kinase From Pseudomonas Aeruginosa PAO1 in Complex with Azt Monophosphate To Be Published.
Page generated: Fri Jul 11 15:45:36 2025

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