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Chlorine in PDB 3q80: Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me

Enzymatic activity of Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me

All present enzymatic activity of Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me:
2.7.7.60;

Protein crystallography data

The structure of Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me, PDB code: 3q80 was solved by M.C.M.Reddy, J.B.Bruning, C.Thurman, T.R.Ioerger, J.C.Sacchettini, Tbstructural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.80 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.581, 92.668, 146.421, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.2

Other elements in 3q80:

The structure of Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me (pdb code 3q80). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me, PDB code: 3q80:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3q80

Go back to Chlorine Binding Sites List in 3q80
Chlorine binding site 1 out of 4 in the Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl233

b:39.2
occ:1.00
 O A:HOH386 2.8 34.2 1.0
O A:HOH404 2.9 28.4 1.0
O A:HOH403 3.1 22.9 1.0
N A:GLY18 3.1 26.4 1.0
C A:GLY16 3.5 31.1 1.0
CA A:GLY16 3.6 27.4 1.0
CA A:GLY18 3.6 28.5 1.0
N A:SER17 3.6 29.4 1.0
CE A:LYS27 3.8 26.1 1.0
CL A:CL234 3.8 59.6 1.0
CB A:LYS27 3.8 29.4 1.0
O A:GLY16 4.1 28.7 1.0
C A:SER17 4.2 32.2 1.0
O A:HOH387 4.2 39.4 1.0
N A:LYS27 4.4 29.3 1.0
NZ A:LYS27 4.5 25.2 1.0
O2A A:CDM500 4.5 28.9 1.0
CA A:SER17 4.5 33.1 1.0
O2' A:CDM500 4.5 27.1 1.0
C2' A:CDM500 4.5 26.0 1.0
N A:GLY16 4.6 26.4 1.0
O A:HOH328 4.6 52.1 1.0
C A:GLY18 4.6 28.2 1.0
CD A:LYS27 4.7 26.8 1.0
CA A:LYS27 4.8 28.7 1.0
CG A:LYS27 4.9 32.2 1.0
N A:GLU19 4.9 22.1 1.0
OG A:SER17 4.9 28.9 1.0
O A:HOH298 5.0 25.5 1.0

Chlorine binding site 2 out of 4 in 3q80

Go back to Chlorine Binding Sites List in 3q80
Chlorine binding site 2 out of 4 in the Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl234

b:59.6
occ:1.00
 O A:HOH328 2.7 52.1 1.0
N A:ARG20 3.2 29.5 1.0
N A:GLU19 3.4 22.1 1.0
O A:HOH403 3.4 22.9 1.0
OG A:SER17 3.5 28.9 1.0
O A:HOH387 3.6 39.4 1.0
CB A:ARG20 3.7 36.3 1.0
O A:HOH386 3.8 34.2 1.0
CL A:CL233 3.8 39.2 1.0
CB A:GLU19 3.9 25.4 1.0
CA A:GLU19 3.9 25.3 1.0
N A:GLY18 4.0 26.4 1.0
MG A:MG232 4.0 74.6 1.0
CA A:ARG20 4.0 29.8 1.0
C A:GLU19 4.0 31.3 1.0
C A:GLY18 4.1 28.2 1.0
O A:HOH335 4.3 45.9 1.0
CA A:GLY18 4.4 28.5 1.0
O A:HOH399 4.5 42.4 1.0
N A:SER17 4.7 29.4 1.0
O2A A:CDM500 4.8 28.9 1.0
CB A:SER17 4.8 29.5 1.0
C A:SER17 4.9 32.2 1.0
CG A:GLU19 4.9 33.0 1.0

Chlorine binding site 3 out of 4 in 3q80

Go back to Chlorine Binding Sites List in 3q80
Chlorine binding site 3 out of 4 in the Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl233

b:34.5
occ:1.00
 O B:HOH390 3.0 27.7 1.0
O B:HOH380 3.2 34.2 1.0
N B:GLY18 3.2 28.3 1.0
CA B:GLY16 3.5 29.4 1.0
C B:GLY16 3.6 33.3 1.0
O2' B:CDM501 3.6 25.3 1.0
CE B:LYS27 3.6 26.6 1.0
CA B:GLY18 3.6 31.3 1.0
N B:SER17 3.7 31.3 1.0
C2' B:CDM501 3.8 26.0 1.0
CB B:LYS27 3.8 37.0 1.0
CL B:CL234 4.1 30.5 1.0
O B:GLY16 4.1 34.2 1.0
O B:HOH379 4.2 28.5 1.0
N B:GLY16 4.2 28.2 1.0
C B:SER17 4.3 34.9 1.0
O B:HOH343 4.3 39.6 1.0
CD B:LYS27 4.4 33.0 1.0
N B:LYS27 4.4 28.0 1.0
C3' B:CDM501 4.4 23.5 1.0
NZ B:LYS27 4.4 24.2 1.0
CA B:SER17 4.6 33.8 1.0
C6 B:CDM501 4.6 26.7 1.0
CG B:LYS27 4.7 45.8 1.0
O2A B:CDM501 4.7 30.2 1.0
CA B:LYS27 4.7 35.2 1.0
O5' B:CDM501 4.8 26.1 1.0
O B:HOH312 4.9 26.9 1.0
C B:GLY18 4.9 34.8 1.0
O B:HOH394 4.9 34.8 1.0
MG B:MG232 5.0 33.2 1.0

Chlorine binding site 4 out of 4 in 3q80

Go back to Chlorine Binding Sites List in 3q80
Chlorine binding site 4 out of 4 in the Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Mtb 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd) Complexed with Cdp-Me within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl234

b:30.5
occ:1.00
 O B:HOH381 2.7 33.5 1.0
O B:HOH394 3.2 34.8 1.0
N B:ARG20 3.3 28.5 1.0
N B:LEU21 3.4 29.3 1.0
CA B:GLY18 3.4 31.3 1.0
C B:GLY18 3.4 34.8 1.0
N B:GLU19 3.6 31.5 1.0
CB B:ARG20 3.7 34.2 1.0
NZ B:LYS27 3.7 24.2 1.0
CE B:LYS27 3.8 26.6 1.0
CD B:LYS27 3.8 33.0 1.0
CA B:ARG20 3.9 31.8 1.0
O B:GLY18 3.9 29.1 1.0
CL B:CL233 4.1 34.5 1.0
C B:ARG20 4.1 30.6 1.0
CB B:LEU21 4.1 29.1 1.0
N B:GLY18 4.2 28.3 1.0
O B:HOH253 4.2 31.8 1.0
C B:GLU19 4.3 29.0 1.0
CA B:LEU21 4.4 32.2 1.0
O B:HOH390 4.5 27.7 1.0
CA B:GLU19 4.5 28.4 1.0
O2A B:CDM501 4.6 30.2 1.0
OE1 B:GLU19 4.6 29.4 1.0
CG B:ARG20 4.7 40.6 1.0
CD B:GLU19 4.8 33.9 1.0
MG B:MG232 5.0 33.2 1.0
O B:THR217 5.0 29.6 1.0
CG B:LYS27 5.0 45.8 1.0

Reference:

M.C.M.Reddy, J.B.Bruning, C.Thurman, T.R.Ioerger, J.C.Sacchettini. Crystal Structure of Mycobacterium Tuberculosis 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd): A Candidate Antitubercular Drug Target Proteins 2011.
ISSN: ESSN 1097-0134
Page generated: Sun Jul 21 02:46:47 2024

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