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Magnesium 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:

Chlorine (Cl) 7 atoms
Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III, PDB code: 7r97:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7r97

Go back to Magnesium Binding Sites List in 7r97
Magnesium binding site 1 out of 6 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg301

b:20.6
occ:1.00
 OP3 C:A1 2.1 22.4 1.0
OE2 A:GLU41 2.1 20.4 1.0
OE1 A:GLU117 2.1 19.3 1.0
O A:HOH469 2.1 21.0 1.0
OP2 C:A1 2.1 24.0 1.0
O A:HOH422 2.1 25.1 1.0
P C:A1 2.6 32.1 1.0
CD A:GLU41 3.1 23.5 1.0
CD A:GLU117 3.1 18.7 1.0
CG A:GLU41 3.5 16.4 1.0
OE2 A:GLU117 3.5 18.6 1.0
MG A:MG302 3.7 18.7 1.0
O A:HOH413 3.7 27.3 1.0
O5' C:A1 3.8 26.6 1.0
OP1 C:A1 3.8 27.5 1.0
MG C:MG101 3.9 28.8 1.0
C5' C:A1 4.0 23.5 1.0
OD1 A:ASP114 4.1 27.2 1.0
OE1 A:GLU41 4.3 22.9 1.0
O D:HOH234 4.3 22.3 1.0
CB A:ASP45 4.4 12.3 1.0
O C:HOH259 4.4 30.6 1.0
OD1 A:ASP45 4.4 20.2 1.0
OP2 C:A2 4.4 23.3 1.0
OP1 C:A2 4.4 23.2 1.0
CG A:GLU117 4.4 15.5 1.0
O3' D:U28 4.5 25.6 1.0
O A:GLU41 4.6 16.5 1.0
CG A:ASP45 4.7 20.7 1.0
CB A:GLU117 4.8 14.3 1.0
P C:A2 4.8 26.1 1.0
CB A:GLU41 4.9 16.7 1.0
CG A:ASP114 5.0 39.0 1.0

Magnesium binding site 2 out of 6 in 7r97

Go back to Magnesium Binding Sites List in 7r97
Magnesium binding site 2 out of 6 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg302

b:18.7
occ:1.00
 OP3 C:A1 2.0 22.4 1.0
OE2 A:GLU117 2.0 18.6 1.0
O3' D:U28 2.1 25.6 1.0
O A:HOH448 2.1 17.4 1.0
OD1 A:ASP45 2.1 20.2 1.0
O D:HOH234 2.1 22.3 1.0
CD A:GLU117 3.1 18.7 1.0
CG A:ASP45 3.2 20.7 1.0
C3' D:U28 3.4 22.8 1.0
P C:A1 3.4 32.1 1.0
OE1 A:GLU117 3.5 19.3 1.0
MG A:MG301 3.7 20.6 1.0
CB A:ASP45 3.8 12.3 1.0
OP1 C:A1 3.9 27.5 1.0
C4' D:U28 4.0 20.0 1.0
O2' D:U28 4.0 26.4 1.0
O5' C:A1 4.1 26.6 1.0
C5' C:A1 4.1 23.5 1.0
O A:HOH424 4.1 20.2 1.0
O D:HOH252 4.2 28.3 1.0
O A:HOH422 4.2 25.1 1.0
OD2 A:ASP45 4.2 21.6 1.0
O A:VAL76 4.3 17.0 1.0
C2' D:U28 4.3 23.0 1.0
CG A:GLU117 4.4 15.5 1.0
CD1 A:LEU81 4.4 18.2 1.0
C5' D:U28 4.5 20.1 1.0
OP2 C:A1 4.5 24.0 1.0
CA A:ASP45 4.6 14.4 1.0
O A:HOH469 4.6 21.0 1.0

Magnesium binding site 3 out of 6 in 7r97

Go back to Magnesium Binding Sites List in 7r97
Magnesium binding site 3 out of 6 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg301

b:23.0
occ:1.00
 O B:HOH432 2.1 26.5 1.0
OP3 D:A1 2.1 24.5 1.0
O D:HOH238 2.1 22.8 1.0
OE2 B:GLU41 2.1 22.9 1.0
OE1 B:GLU117 2.1 19.1 1.0
OP1 D:A1 2.1 25.2 1.0
P D:A1 2.7 33.7 1.0
CD B:GLU41 3.1 22.5 1.0
CD B:GLU117 3.1 20.6 1.0
CG B:GLU41 3.5 18.2 1.0
OE2 B:GLU117 3.5 20.4 1.0
MG B:MG302 3.7 20.9 1.0
O B:HOH420 3.8 27.1 1.0
O5' D:A1 3.8 27.9 1.0
OP2 D:A1 3.8 29.3 1.0
MG D:MG101 4.0 29.1 1.0
C5' D:A1 4.1 24.8 1.0
OD1 B:ASP114 4.2 28.6 1.0
OE1 B:GLU41 4.3 23.1 1.0
OP1 D:A2 4.4 21.9 1.0
CB B:ASP45 4.4 12.3 1.0
O C:HOH257 4.4 25.1 1.0
OD1 B:ASP45 4.4 22.6 1.0
OP2 D:A2 4.4 22.9 1.0
O D:HOH241 4.4 26.9 1.0
CG B:GLU117 4.5 18.1 1.0
O B:GLU41 4.6 15.7 1.0
O3' C:U28 4.6 27.2 1.0
CG B:ASP45 4.7 22.1 1.0
CB B:GLU117 4.8 15.0 1.0
P D:A2 4.8 23.2 1.0
CB B:GLU41 4.9 18.1 1.0
O D:HOH259 5.0 30.2 1.0

Magnesium binding site 4 out of 6 in 7r97

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Magnesium binding site 4 out of 6 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg302

b:20.9
occ:1.00
 OP3 D:A1 2.0 24.5 1.0
OE2 B:GLU117 2.1 20.4 1.0
O3' C:U28 2.1 27.2 1.0
O B:HOH458 2.1 22.4 1.0
OD1 B:ASP45 2.1 22.6 1.0
O C:HOH257 2.1 25.1 1.0
CD B:GLU117 3.1 20.6 1.0
CG B:ASP45 3.2 22.1 1.0
P D:A1 3.4 33.7 1.0
C3' C:U28 3.4 25.7 1.0
OE1 B:GLU117 3.5 19.1 1.0
MG B:MG301 3.7 23.0 1.0
CB B:ASP45 3.8 12.3 1.0
OP2 D:A1 3.8 29.3 1.0
C5' D:A1 4.0 24.8 1.0
C4' C:U28 4.0 20.1 1.0
O B:HOH408 4.1 22.6 1.0
O5' D:A1 4.1 27.9 1.0
O2' C:U28 4.1 27.6 1.0
O D:HOH259 4.1 30.2 1.0
O B:HOH432 4.2 26.5 1.0
OD2 B:ASP45 4.2 22.8 1.0
O B:VAL76 4.3 17.3 1.0
C2' C:U28 4.3 24.2 1.0
CG B:GLU117 4.4 18.1 1.0
CD1 B:LEU81 4.4 20.3 1.0
OP1 D:A1 4.5 25.2 1.0
C5' C:U28 4.5 22.3 1.0
O D:HOH238 4.6 22.8 1.0
CA B:ASP45 4.6 13.7 1.0

Magnesium binding site 5 out of 6 in 7r97

Go back to Magnesium Binding Sites List in 7r97
Magnesium binding site 5 out of 6 in the Crystal Structure of Postcleavge Complex of Escherichia Coli Rnase III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg101

b:28.8
occ:1.00
 OP2 C:A1 2.1 24.0 1.0
OP2 C:A2 2.1 23.3 1.0
O C:HOH287 2.1 27.6 1.0
O A:HOH413 2.1 27.3 1.0
O C:HOH275 2.1 28.6 1.0
O C:HOH259 2.1 30.6 1.0
P C:A1 3.2 32.1 1.0
P C:A2 3.5 26.1 1.0
OP1 C:A1 3.6 27.5 1.0
O5' C:A1 3.7 26.6 1.0
OE2 A:GLU41 3.8 20.4 1.0
O C:HOH286 3.9 39.2 1.0
MG A:MG301 3.9 20.6 1.0
OP1 C:A2 4.2 23.2 1.0
C5' C:A2 4.3 24.0 1.0
O C:HOH233 4.4 28.7 1.0
O A:HOH422 4.4 25.1 1.0
O C:HOH212 4.4 27.7 1.0
O5' C:A2 4.4 27.0 1.0
C3' C:A1 4.4 23.8 1.0
O A:HOH480 4.4 41.1 1.0
O A:HOH469 4.4 21.0 1.0
O3' C:A1 4.4 25.4 1.0
OP3 C:A1 4.5 22.4 1.0
C5' C:A1 4.6 23.5 1.0
O A:HOH412 4.8 32.9 1.0
CD A:GLU41 4.8 23.5 1.0

Magnesium binding site 6 out of 6 in 7r97

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg101

b:29.1
occ:1.00
 O D:HOH280 2.1 25.0 1.0
OP2 D:A2 2.1 22.9 1.0
O B:HOH420 2.1 27.1 1.0
OP1 D:A1 2.1 25.2 1.0
O D:HOH241 2.1 26.9 1.0
O D:HOH271 2.1 26.1 1.0
P D:A1 3.2 33.7 1.0
P D:A2 3.5 23.2 1.0
O5' D:A1 3.7 27.9 1.0
OP2 D:A1 3.7 29.3 1.0
OE2 B:GLU41 3.9 22.9 1.0
MG B:MG301 4.0 23.0 1.0
OP1 D:A2 4.2 21.9 1.0
O D:HOH216 4.3 26.8 1.0
C5' D:A2 4.3 23.2 1.0
C3' D:A1 4.3 24.2 1.0
O3' D:A1 4.4 25.5 1.0
O B:HOH432 4.4 26.5 1.0
O5' D:A2 4.4 24.2 1.0
O D:HOH238 4.5 22.8 1.0
OP3 D:A1 4.5 24.5 1.0
C5' D:A1 4.7 24.8 1.0
O B:HOH428 4.9 34.4 1.0
CD B:GLU41 4.9 22.5 1.0
O D:HOH277 5.0 52.2 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: Thu Oct 3 07:34:37 2024

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