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Strontium in PDB 4jkr: Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp

Enzymatic activity of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp

All present enzymatic activity of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp, PDB code: 4jkr was solved by Y.Zuo, Y.Wang, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.97 / 4.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 187.575, 206.164, 311.062, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 31.8

Other elements in 4jkr:

The structure of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp (pdb code 4jkr). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 8 binding sites of Strontium where determined in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp, PDB code: 4jkr:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Strontium binding site 1 out of 8 in 4jkr

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Strontium binding site 1 out of 8 in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr401

b:0.8
occ:1.00
OD1 A:ASP15 3.0 0.2 1.0
O A:ILE16 3.2 0.8 1.0
CG A:ASP15 3.9 0.1 1.0
C A:ILE16 3.9 0.2 1.0
OD2 A:ASP15 4.0 0.3 1.0
CA A:GLU17 4.4 0.7 1.0
N A:GLU17 4.4 0.1 1.0
N A:ILE16 4.5 0.1 1.0
CA A:ILE16 4.8 0.7 1.0

Strontium binding site 2 out of 8 in 4jkr

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Strontium binding site 2 out of 8 in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr1401

b:0.8
occ:1.00
OE2 C:GLU813 3.1 0.2 1.0
O D:ALA459 3.5 0.4 1.0
CD C:GLU813 4.0 0.5 1.0
OD1 D:ASN458 4.1 0.5 1.0
OD2 D:ASP460 4.2 0.2 1.0
OE1 C:GLU813 4.2 0.5 1.0
C D:ALA459 4.3 0.9 1.0
CB D:ASP460 4.5 1.0 1.0
N D:ALA459 4.7 1.0 1.0
C D:ASN458 4.7 0.4 1.0
CG D:ASP460 4.8 0.8 1.0
N D:ASP460 4.9 0.3 1.0
O D:ASN458 5.0 0.2 1.0

Strontium binding site 3 out of 8 in 4jkr

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Strontium binding site 3 out of 8 in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr1402

b:0.0
occ:1.00
O C:VAL24 2.7 1.0 1.0
C C:VAL24 4.0 0.4 1.0
O C:PRO25 4.2 1.0 1.0
OD1 C:ASP711 4.5 0.4 1.0
C C:PRO25 4.5 0.6 1.0
OD2 C:ASP711 4.7 0.5 1.0
CA C:PRO25 4.8 0.6 1.0
N C:PRO25 4.8 0.1 1.0
CB C:VAL24 4.9 0.9 1.0
CA C:VAL24 4.9 0.6 1.0

Strontium binding site 4 out of 8 in 4jkr

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Strontium binding site 4 out of 8 in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr2004

b:0.0
occ:1.00
OD1 D:ASP460 3.1 0.7 1.0
OD1 D:ASP464 3.2 0.3 1.0
OD1 D:ASP462 3.9 0.3 1.0
CG D:ASP460 3.9 0.8 1.0
CG D:ASP464 4.0 0.4 1.0
OD2 D:ASP464 4.0 0.6 1.0
OD2 D:ASP460 4.0 0.2 1.0
OD2 D:ASP462 4.6 0.9 1.0
CG D:ASP462 4.7 0.6 1.0
NZ C:LYS1073 4.7 0.1 1.0
NH2 D:ARG425 4.9 0.0 1.0

Strontium binding site 5 out of 8 in 4jkr

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Strontium binding site 5 out of 8 in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Sr101

b:0.5
occ:1.00
OE1 E:GLU41 4.9 0.9 1.0

Strontium binding site 6 out of 8 in 4jkr

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Strontium binding site 6 out of 8 in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr701

b:0.4
occ:1.00
OD1 F:ASP581 3.1 0.4 1.0
CG F:ASP581 4.1 0.9 1.0
OD2 F:ASP581 4.5 0.7 1.0

Strontium binding site 7 out of 8 in 4jkr

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Strontium binding site 7 out of 8 in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Sr1401

b:0.6
occ:1.00
OE2 I:GLU813 3.0 0.1 1.0
O J:ALA459 3.9 0.9 1.0
CD I:GLU813 4.1 0.3 1.0
OD1 J:ASN458 4.2 0.1 1.0
C J:ALA459 4.5 0.4 1.0
OE1 I:GLU813 4.5 0.1 1.0
OD2 J:ASP460 4.6 0.0 1.0
CB J:ASP460 4.7 0.9 1.0
N J:ALA459 4.9 0.7 1.0
CG J:ASP460 5.0 0.1 1.0
N J:ASP460 5.0 0.6 1.0

Strontium binding site 8 out of 8 in 4jkr

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Strontium binding site 8 out of 8 in the Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structure of E. Coli Rna Polymerase in Complex with Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Sr1503

b:0.9
occ:1.00
OD1 J:ASP460 2.8 0.2 1.0
OD1 J:ASP464 3.3 0.7 1.0
OD2 J:ASP460 3.5 0.0 1.0
CG J:ASP460 3.5 0.1 1.0
OD2 J:ASP464 3.9 0.6 1.0
CG J:ASP464 4.0 0.5 1.0
OD1 J:ASP462 4.1 0.2 1.0
NH2 J:ARG425 4.5 0.4 1.0
OD2 J:ASP462 4.6 0.2 1.0
CG J:ASP462 4.8 0.4 1.0

Reference:

Y.Zuo, Y.Wang, T.A.Steitz. The Mechanism of E. Coli Rna Polymerase Regulation By Ppgpp Is Suggested By the Structure of Their Complex. Mol.Cell V. 50 430 2013.
ISSN: ISSN 1097-2765
PubMed: 23623685
DOI: 10.1016/J.MOLCEL.2013.03.020
Page generated: Wed Dec 16 02:24:11 2020

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