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Chlorine in PDB 4nx5: Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate

Enzymatic activity of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate

All present enzymatic activity of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate:
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate, PDB code: 4nx5 was solved by A.A.Fedorov, E.V.Fedorov, K.K.Chan, 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) 32.41 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.737, 64.148, 61.527, 90.00, 115.36, 90.00
R / Rfree (%) 14.8 / 16.8

Other elements in 4nx5:

The structure of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate (pdb code 4nx5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate, PDB code: 4nx5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4nx5

Go back to Chlorine Binding Sites List in 4nx5
Chlorine binding site 1 out of 4 in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate


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 Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:26.2
occ:1.00
 N A:ASP104 3.3 8.8 1.0
NH2 A:ARG107 3.4 23.4 0.5
CA B:GLY130 3.6 9.2 1.0
CG A:ASP104 3.7 8.2 1.0
OD1 A:ASP104 3.8 7.1 1.0
CB A:ALA103 3.8 8.5 1.0
N A:ALA103 3.8 6.7 1.0
CB A:ASP104 3.8 8.4 1.0
CE B:MET133 3.8 15.5 0.4
SD B:MET133 4.0 13.1 0.6
N B:GLY130 4.0 8.1 1.0
CA A:ALA103 4.1 8.1 1.0
CA A:ASP104 4.1 10.2 1.0
C A:ALA103 4.1 9.9 1.0
OD2 A:ASP104 4.2 9.4 1.0
CZ A:ARG107 4.5 24.0 0.5
CG B:MET133 4.6 10.3 0.6
C B:PRO129 4.6 8.5 1.0
C A:GLY102 4.7 7.5 1.0
O B:PRO129 4.9 11.9 1.0
C B:GLY130 4.9 7.7 1.0

Chlorine binding site 2 out of 4 in 4nx5

Go back to Chlorine Binding Sites List in 4nx5
Chlorine binding site 2 out of 4 in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate


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 Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:23.2
occ:1.00
 O B:HOH482 2.6 23.3 1.0
O B:HOH571 2.7 27.3 1.0
N A:GLU78 3.1 7.8 1.0
CB A:GLU78 3.5 10.5 1.0
CD A:PRO77 3.7 7.1 1.0
CB A:PRO77 3.8 7.9 1.0
N A:PRO77 3.8 6.9 1.0
CD1 A:ILE76 3.8 8.6 1.0
CA A:GLU78 3.9 9.3 1.0
C A:PRO77 4.0 7.4 1.0
CG1 A:ILE76 4.1 7.4 1.0
CA A:PRO77 4.1 7.5 1.0
CG A:PRO77 4.1 8.5 1.0
CB A:ILE76 4.1 7.2 1.0
O A:HOH571 4.3 37.9 1.0
C A:ILE76 4.4 9.1 1.0
O B:HOH425 4.5 14.0 1.0
NH2 B:ARG203 4.7 12.1 1.0
OE1 A:GLU78 4.8 38.1 1.0
CG A:GLU78 4.8 20.9 1.0
CA A:ILE76 4.9 6.6 1.0
NH1 B:ARG203 5.0 14.2 1.0

Chlorine binding site 3 out of 4 in 4nx5

Go back to Chlorine Binding Sites List in 4nx5
Chlorine binding site 3 out of 4 in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate


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 Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:27.4
occ:1.00
 N B:ASP104 3.3 8.4 1.0
O2 B:GOL305 3.4 40.5 1.0
CG B:ASP104 3.6 10.8 1.0
CA A:GLY130 3.6 11.5 1.0
OD1 B:ASP104 3.7 9.8 1.0
CB B:ASP104 3.7 9.3 1.0
N B:ALA103 3.8 7.7 1.0
CB B:ALA103 3.9 8.6 1.0
SD A:MET133 4.0 13.3 0.7
N A:GLY130 4.0 9.5 1.0
CA B:ASP104 4.1 9.5 1.0
OD2 B:ASP104 4.1 10.7 1.0
CA B:ALA103 4.1 8.3 1.0
CE A:MET133 4.1 12.6 0.3
C B:ALA103 4.1 8.2 1.0
CG A:MET133 4.6 13.3 0.7
C A:PRO129 4.7 12.0 1.0
C B:GLY102 4.7 7.0 1.0
C2 B:GOL305 4.8 41.4 1.0
C A:GLY130 4.9 9.3 1.0
O A:PRO129 4.9 12.0 1.0

Chlorine binding site 4 out of 4 in 4nx5

Go back to Chlorine Binding Sites List in 4nx5
Chlorine binding site 4 out of 4 in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate


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 Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:26.2
occ:1.00
 O A:HOH486 2.7 27.9 1.0
N B:GLU78 3.0 9.7 1.0
O A:HOH538 3.3 25.1 1.0
CB B:GLU78 3.3 10.0 1.0
CD B:PRO77 3.6 9.4 1.0
CA B:GLU78 3.8 9.3 1.0
N B:PRO77 3.8 8.0 1.0
CB B:PRO77 3.8 8.8 1.0
CD1 B:ILE76 3.9 9.0 1.0
C B:PRO77 3.9 8.7 1.0
CA B:PRO77 4.0 8.3 1.0
CG1 B:ILE76 4.0 8.3 1.0
CG B:PRO77 4.1 8.7 1.0
O B:HOH568 4.1 28.8 1.0
CB B:ILE76 4.2 8.1 1.0
C B:ILE76 4.4 8.5 1.0
O A:HOH436 4.6 19.5 1.0
NH2 A:ARG203 4.7 11.1 1.0
CG B:GLU78 4.7 24.5 1.0
CA B:ILE76 4.9 7.5 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, K.K.Chan, J.A.Gerlt, S.C.Almo. Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 6-Azauridine 5'-Monophosphate To Be Published.
Page generated: Thu Jul 25 23:05:16 2024

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