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Chlorine in PDB 4lc8: Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp

Enzymatic activity of Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp

All present enzymatic activity of Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp:
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp, PDB code: 4lc8 was solved by A.A.Fedorov, E.V.Fedorov, B.Desai, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.55 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.958, 63.703, 61.740, 90.00, 115.30, 90.00
R / Rfree (%) 16.1 / 17.8

Other elements in 4lc8:

The structure of Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp (pdb code 4lc8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp, PDB code: 4lc8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4lc8

Go back to Chlorine Binding Sites List in 4lc8
Chlorine binding site 1 out of 5 in the Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:16.8
occ:1.00
 O A:HOH509 3.1 31.1 1.0
N A:ASP104 3.4 7.8 1.0
O B:HOH546 3.4 31.1 1.0
CA B:GLY130 3.5 7.8 1.0
CB A:ASP104 3.7 7.8 1.0
CG A:ASP104 3.8 7.3 1.0
N B:GLY130 3.9 7.7 1.0
CB A:ALA103 3.9 8.1 1.0
N A:ALA103 4.0 6.4 1.0
OD1 A:ASP104 4.0 7.2 1.0
CA A:ASP104 4.1 8.3 1.0
OD2 A:ASP104 4.2 7.7 1.0
C A:ALA103 4.2 8.7 1.0
CA A:ALA103 4.2 7.5 1.0
SD B:MET133 4.2 12.8 1.0
C B:PRO129 4.5 9.0 1.0
O A:HOH587 4.7 28.9 1.0
O B:PRO129 4.7 9.2 1.0
CG B:MET133 4.8 11.1 1.0
C B:GLY130 4.8 6.9 1.0
C A:GLY102 4.9 6.7 1.0
CB B:PRO129 4.9 10.3 1.0

Chlorine binding site 2 out of 5 in 4lc8

Go back to Chlorine Binding Sites List in 4lc8
Chlorine binding site 2 out of 5 in the Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:24.2
occ:1.00
 N A:GLU162 3.4 12.0 1.0
CB A:ARG160 3.4 12.3 1.0
C A:ARG160 3.4 10.7 1.0
CA A:ARG160 3.4 10.6 1.0
CB A:GLU162 3.6 13.1 1.0
N A:PRO161 3.7 12.0 1.0
O A:ARG160 3.8 10.5 1.0
N A:ARG163 3.9 8.6 0.7
N A:ARG163 3.9 9.9 0.3
CA A:GLU162 3.9 9.8 1.0
CG A:ARG163 3.9 12.4 0.3
CG A:GLU162 4.0 17.9 1.0
CD A:PRO161 4.1 12.3 1.0
CG A:ARG160 4.1 16.4 1.0
CG A:ARG163 4.3 10.6 0.7
C A:PRO161 4.3 12.1 1.0
C A:GLU162 4.4 10.0 1.0
CA A:PRO161 4.5 11.6 1.0
CD A:ARG160 4.6 21.0 1.0
CB A:ARG163 4.7 8.3 0.3
CD A:ARG163 4.7 11.3 0.3
CB A:ARG163 4.7 8.3 0.7
N A:ARG160 4.8 9.9 1.0
CA A:ARG163 4.9 9.3 0.7
CA A:ARG163 4.9 9.5 0.3

Chlorine binding site 3 out of 5 in 4lc8

Go back to Chlorine Binding Sites List in 4lc8
Chlorine binding site 3 out of 5 in the Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:15.8
occ:1.00
 O B:HOH453 3.0 18.0 1.0
O A:HOH585 3.1 29.6 1.0
N A:GLU78 3.3 8.4 1.0
CD A:PRO77 3.6 7.4 1.0
CB A:GLU78 3.7 11.0 1.0
CB A:PRO77 3.7 7.9 1.0
N A:PRO77 3.7 7.3 1.0
CD1 A:ILE76 3.8 8.6 1.0
CG A:PRO77 3.9 8.0 1.0
CG1 A:ILE76 4.0 8.4 1.0
CB A:ILE76 4.0 7.5 1.0
CA A:PRO77 4.1 7.5 1.0
CA A:GLU78 4.1 8.9 1.0
C A:PRO77 4.1 7.9 1.0
C A:ILE76 4.4 7.0 1.0
O B:HOH651 4.4 24.9 1.0
O A:HOH577 4.5 25.4 1.0
O B:HOH622 4.5 33.5 1.0
O A:HOH630 4.8 49.1 1.0
CA A:ILE76 4.8 6.9 1.0
NH2 B:ARG203 4.9 9.9 1.0
OE1 A:GLU78 4.9 27.4 1.0

Chlorine binding site 4 out of 5 in 4lc8

Go back to Chlorine Binding Sites List in 4lc8
Chlorine binding site 4 out of 5 in the Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:20.4
occ:1.00
 NH2 B:ARG107 3.2 28.7 1.0
O A:HOH623 3.3 38.2 1.0
N B:ASP104 3.3 10.5 1.0
CA A:GLY130 3.5 11.3 1.0
CB B:ASP104 3.7 11.2 1.0
CG B:ASP104 3.7 9.8 1.0
N A:GLY130 3.9 10.8 1.0
CB B:ALA103 3.9 10.8 1.0
OD1 B:ASP104 3.9 9.6 1.0
N B:ALA103 4.0 9.7 1.0
CA B:ASP104 4.1 11.0 1.0
C B:ALA103 4.2 9.2 1.0
CA B:ALA103 4.2 9.5 1.0
OD2 B:ASP104 4.2 9.9 1.0
SD A:MET133 4.2 16.8 1.0
CZ B:ARG107 4.3 34.9 1.0
C A:PRO129 4.5 12.3 1.0
CG A:MET133 4.8 16.3 1.0
O A:PRO129 4.8 13.6 1.0
C A:GLY130 4.8 9.6 1.0
C B:GLY102 4.9 10.0 1.0
NH1 B:ARG107 4.9 36.4 1.0
O B:HOH584 5.0 30.0 1.0
CB A:PRO129 5.0 13.3 1.0

Chlorine binding site 5 out of 5 in 4lc8

Go back to Chlorine Binding Sites List in 4lc8
Chlorine binding site 5 out of 5 in the Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:20.1
occ:1.00
 O A:HOH472 2.5 23.5 1.0
O A:HOH651 3.0 19.7 1.0
O B:HOH664 3.1 31.7 1.0
N B:GLU78 3.2 10.1 1.0
CD B:PRO77 3.5 10.2 1.0
CB B:GLU78 3.6 11.2 1.0
CB B:PRO77 3.7 9.9 1.0
N B:PRO77 3.7 8.7 1.0
CD1 B:ILE76 3.8 10.8 1.0
CG B:PRO77 4.0 9.4 1.0
CA B:GLU78 4.0 10.7 1.0
CG1 B:ILE76 4.0 8.8 1.0
CA B:PRO77 4.0 9.2 1.0
C B:PRO77 4.1 9.7 1.0
O B:HOH592 4.1 28.7 1.0
CB B:ILE76 4.1 9.3 1.0
C B:ILE76 4.4 8.2 1.0
O A:HOH441 4.6 17.4 1.0
CA B:ILE76 4.8 7.8 1.0
CG B:GLU78 4.9 24.8 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, B.Desai, J.A.Gerlt, S.C.Almo. Crystal Structure of the Mutant H128N of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with the Inhibitor Bmp To Be Published.
Page generated: Fri Jul 11 18:30:51 2025

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