Chlorine in PDB 7r97: Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III

Enzymatic activity of Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III

All present enzymatic activity of Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III:
3.1.26.3;

Protein crystallography data

The structure of Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III, PDB code: 7r97 was solved by S.Dharavath, G.X.Shaw, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.31 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.929, 65.753, 84.519, 90, 102.09, 90
R / Rfree (%) 17.1 / 20.2

Other elements in 7r97:

The structure of Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Potassium (K) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III (pdb code 7r97). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III, PDB code: 7r97:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 7r97

Go back to Chlorine Binding Sites List in 7r97
Chlorine binding site 1 out of 7 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


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 Postcleavge Complex of Escherichia Coli Rnase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:55.5
occ:1.00
 NH1 A:ARG11 3.5 42.4 1.0
NE A:ARG8 3.6 45.2 1.0
CG A:ARG8 3.9 35.2 1.0
CD A:ARG8 4.0 37.3 1.0
CZ A:ARG11 4.6 42.5 1.0
CZ A:ARG8 4.7 39.9 1.0
NH2 A:ARG11 4.9 44.9 1.0
NH2 A:ARG8 4.9 42.9 1.0

Chlorine binding site 2 out of 7 in 7r97

Go back to Chlorine Binding Sites List in 7r97
Chlorine binding site 2 out of 7 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


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 Postcleavge Complex of Escherichia Coli Rnase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:32.9
occ:1.00
 N A:ARG62 3.2 22.4 1.0
CB A:ARG62 3.4 30.8 1.0
C A:PHE60 3.5 21.1 1.0
CA A:PHE60 3.5 19.6 1.0
N A:PRO61 3.5 20.7 1.0
CD A:PRO61 3.7 22.4 1.0
CA A:ARG62 3.7 27.3 1.0
CG A:ARG62 4.0 39.7 1.0
CB A:PHE60 4.0 18.7 1.0
CG1 A:VAL63 4.1 25.2 1.0
O A:PHE60 4.1 19.3 1.0
C A:PRO61 4.2 25.9 1.0
N A:VAL63 4.2 24.5 1.0
CG A:PRO61 4.2 27.1 1.0
CD1 A:PHE60 4.2 21.8 1.0
C A:ARG62 4.3 29.4 1.0
CA A:PRO61 4.4 23.6 1.0
CG A:PHE60 4.6 18.6 1.0
O A:ARG59 4.6 19.8 1.0
N A:PHE60 4.8 16.5 1.0
CD A:ARG62 4.9 51.0 1.0
CB A:PRO61 5.0 25.1 1.0

Chlorine binding site 3 out of 7 in 7r97

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Chlorine binding site 3 out of 7 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


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 Postcleavge Complex of Escherichia Coli Rnase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:31.2
occ:1.00
 O C:HOH260 3.1 38.1 1.0
NH1 A:ARG208 3.4 27.7 1.0
CD A:ARG208 3.7 28.9 1.0
C4' C:C22 4.0 19.9 1.0
C5' C:C22 4.0 20.1 1.0
CE2 A:PHE188 4.1 23.8 1.0
CG2 A:VAL176 4.2 24.4 1.0
O3' C:C22 4.2 21.1 1.0
CG A:ARG208 4.4 30.1 1.0
CZ A:ARG208 4.5 29.9 1.0
CB A:ARG208 4.5 24.4 1.0
NE A:ARG208 4.6 27.9 1.0
C3' C:C22 4.7 21.6 1.0
CD2 A:PHE188 4.8 23.0 1.0
O C:HOH249 4.8 30.9 1.0
CB A:VAL176 4.9 24.7 1.0
CZ A:PHE188 4.9 23.1 1.0
O2' C:C22 5.0 22.1 1.0

Chlorine binding site 4 out of 7 in 7r97

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Chlorine binding site 4 out of 7 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


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 Postcleavge Complex of Escherichia Coli Rnase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:30.0
occ:0.64
 OG1 A:THR142 2.7 26.2 1.0
O A:TRP139 2.8 18.4 1.0
NH1 A:ARG143 3.0 25.7 1.0
CG A:ARG143 3.1 21.8 1.0
N A:ARG143 3.2 21.0 1.0
C A:TYR140 3.4 18.9 1.0
CA A:TYR140 3.4 16.7 1.0
CD A:ARG143 3.5 21.7 1.0
N A:THR142 3.6 19.9 1.0
O A:HOH501 3.6 21.0 1.0
O A:TYR140 3.6 17.0 1.0
CB A:ARG143 3.6 21.0 1.0
C A:TRP139 3.8 18.9 1.0
H22 A:EDO310 3.9 50.3 1.0
CB A:THR142 3.9 24.4 1.0
N A:GLN141 3.9 16.2 1.0
O A:HOH514 4.0 38.2 1.0
CA A:THR142 4.0 21.8 1.0
CA A:ARG143 4.0 21.1 1.0
C A:THR142 4.0 25.4 1.0
CZ A:ARG143 4.0 27.4 1.0
N A:TYR140 4.1 15.1 1.0
NE A:ARG143 4.2 24.5 1.0
H12 A:EDO310 4.2 40.2 1.0
O A:HOH493 4.3 47.4 1.0
C A:GLN141 4.4 22.2 1.0
CB A:TYR140 4.6 16.1 1.0
CA A:GLN141 4.8 21.3 1.0
CG2 A:THR142 4.8 26.2 1.0
C2 A:EDO310 4.8 41.9 1.0
CD2 A:LEU84 4.8 25.1 1.0
C1 A:EDO310 4.9 33.5 1.0

Chlorine binding site 5 out of 7 in 7r97

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Chlorine binding site 5 out of 7 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


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 Postcleavge Complex of Escherichia Coli Rnase III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:28.7
occ:1.00
 NH1 B:ARG208 3.4 26.2 1.0
CD B:ARG208 3.6 32.2 1.0
CE2 B:PHE188 4.0 23.8 1.0
C4' D:C22 4.1 20.6 1.0
C5' D:C22 4.1 21.4 1.0
CG B:ARG208 4.3 28.1 1.0
CG2 B:VAL176 4.3 32.1 1.0
O3' D:C22 4.4 22.7 1.0
CZ B:ARG208 4.4 27.8 1.0
NE B:ARG208 4.5 27.6 1.0
CB B:ARG208 4.5 25.3 1.0
O D:HOH227 4.7 36.4 1.0
CD2 B:PHE188 4.7 23.7 1.0
C3' D:C22 4.9 21.4 1.0
CZ B:PHE188 4.9 21.5 1.0

Chlorine binding site 6 out of 7 in 7r97

Go back to Chlorine Binding Sites List in 7r97
Chlorine binding site 6 out of 7 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:39.2
occ:1.00
 N B:GLY91 3.1 26.0 1.0
CA B:GLY91 3.7 28.4 1.0
N B:LEU90 3.7 27.0 1.0
C B:GLU89 3.8 29.1 1.0
CA B:GLU89 3.9 31.3 1.0
CA B:ARG86 4.0 32.4 1.0
O B:ALA85 4.0 25.6 1.0
C B:LEU90 4.2 27.3 1.0
CD2 B:LEU112 4.4 24.3 1.0
O B:ARG86 4.5 27.2 1.0
O B:GLU89 4.5 29.6 1.0
CA B:LEU90 4.5 27.7 1.0
N B:ARG86 4.6 25.0 1.0
C B:ALA85 4.6 25.9 1.0
CG B:ARG86 4.6 50.6 1.0
N B:GLU89 4.7 28.9 1.0
C B:ARG86 4.7 33.9 1.0
CB B:ARG86 4.7 36.1 1.0
CD1 B:LEU112 4.8 24.5 1.0
O B:PHE106 4.8 30.8 1.0
C B:GLY91 4.8 29.1 1.0
N B:GLU92 4.9 26.5 1.0
CB B:GLU89 4.9 35.8 1.0

Chlorine binding site 7 out of 7 in 7r97

Go back to Chlorine Binding Sites List in 7r97
Chlorine binding site 7 out of 7 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:35.6
occ:1.00
 N B:ARG62 3.1 22.5 1.0
CB B:ARG62 3.5 32.1 1.0
C B:PHE60 3.5 22.2 1.0
N B:PRO61 3.5 24.2 1.0
CA B:PHE60 3.5 23.1 1.0
CD B:PRO61 3.6 23.8 1.0
CA B:ARG62 3.7 28.1 1.0
CG B:ARG62 4.0 38.0 1.0
O B:PHE60 4.1 21.1 1.0
CG1 B:VAL63 4.1 25.5 1.0
CB B:PHE60 4.1 22.2 1.0
CG B:PRO61 4.1 27.2 1.0
C B:PRO61 4.1 26.2 1.0
N B:VAL63 4.2 23.9 1.0
C B:ARG62 4.3 27.0 1.0
CD1 B:PHE60 4.3 26.3 1.0
CA B:PRO61 4.3 22.8 1.0
O B:ARG59 4.6 23.1 1.0
CG B:PHE60 4.7 22.1 1.0
N B:PHE60 4.7 19.2 1.0
CB B:PRO61 4.9 28.4 1.0

Reference:

S.Dharavath, G.X.Shaw, X.Ji. Structural Basis For Dicer-Like Function of An Engineered Rnase III Variant and Insights Into the Reaction Trajectory of Two-Mg 2+ -Ion Catalysis. Rna Biol. V. 19 908 2022.
ISSN: ESSN 1555-8584
PubMed: 35829618
DOI: 10.1080/15476286.2022.2099650
Page generated: Tue Apr 4 21:34:00 2023

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