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Sodium in PDB 3k4g: Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain

Enzymatic activity of Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain

All present enzymatic activity of Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain, PDB code: 3k4g was solved by S.Lara-Gonzalez, J.Birktoft, C.L.Lawson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.02 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.342, 67.612, 116.553, 90.00, 90.12, 90.00
R / Rfree (%) 19.3 / 23.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain (pdb code 3k4g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain, PDB code: 3k4g:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3k4g

Go back to Sodium Binding Sites List in 3k4g
Sodium binding site 1 out of 4 in the Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2

b:23.4
occ:1.00
O B:PRO322 2.6 23.0 1.0
O A:PRO322 2.7 23.7 1.0
O A:ASN320 2.7 23.2 1.0
O B:ASN320 2.8 23.0 1.0
O C:HOH107 3.0 19.3 1.0
C B:ASN320 3.5 24.1 1.0
C A:ASN320 3.5 24.3 1.0
C B:PRO322 3.6 24.3 1.0
C A:PRO322 3.6 24.0 1.0
CB B:ASN320 3.9 21.5 1.0
CB A:ASN320 4.0 23.1 1.0
C B:PRO323 4.0 23.8 1.0
CA B:PRO323 4.0 23.2 1.0
C A:PRO323 4.0 23.9 1.0
CA A:PRO323 4.0 23.6 1.0
N B:ALA324 4.0 23.1 1.0
N A:ALA324 4.1 23.2 1.0
N B:PRO323 4.1 23.4 1.0
CA B:ASN320 4.2 23.3 1.0
N A:PRO323 4.2 23.7 1.0
CA A:ASN320 4.2 23.6 1.0
N B:TRP321 4.4 22.8 1.0
N A:TRP321 4.4 22.8 1.0
N A:PRO322 4.5 24.1 1.0
CA A:TRP321 4.5 23.6 1.0
CA B:TRP321 4.5 22.9 1.0
O B:PRO323 4.5 23.8 1.0
O D:HOH132 4.5 22.9 1.0
O A:PRO323 4.5 23.4 1.0
C A:TRP321 4.5 23.1 1.0
N B:PRO322 4.6 24.4 1.0
CA A:PRO322 4.6 24.0 1.0
C B:TRP321 4.7 23.2 1.0
CA B:PRO322 4.7 24.2 1.0
CA B:ALA324 4.7 23.0 1.0
CA A:ALA324 4.7 23.3 1.0
CD A:PRO322 4.9 26.3 1.0
CB B:ALA324 5.0 22.8 1.0

Sodium binding site 2 out of 4 in 3k4g

Go back to Sodium Binding Sites List in 3k4g
Sodium binding site 2 out of 4 in the Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na4

b:25.1
occ:1.00
O D:PRO322 2.7 23.3 1.0
O C:PRO322 2.7 23.6 1.0
O C:ASN320 2.8 23.0 1.0
O D:ASN320 2.8 22.9 1.0
O B:HOH204 2.9 23.4 1.0
C C:ASN320 3.4 24.0 1.0
C D:ASN320 3.4 23.8 1.0
CB C:ASN320 3.6 22.8 1.0
CB D:ASN320 3.7 20.2 1.0
C C:PRO322 3.7 23.9 1.0
C D:PRO322 3.8 24.0 1.0
CA C:ASN320 3.9 23.2 1.0
CA D:ASN320 4.0 23.7 1.0
O D:HOH132 4.2 22.9 1.0
N C:TRP321 4.2 22.1 1.0
C C:PRO323 4.3 23.9 1.0
N D:TRP321 4.3 23.1 1.0
N C:ALA324 4.4 23.7 1.0
CA C:PRO323 4.4 23.8 1.0
N C:PRO323 4.4 24.1 1.0
C D:PRO323 4.4 24.0 1.0
N D:ALA324 4.5 23.0 1.0
C D:TRP321 4.5 23.6 1.0
CA C:TRP321 4.5 23.6 1.0
CA D:PRO323 4.5 23.6 1.0
CA D:TRP321 4.5 23.6 1.0
C C:TRP321 4.5 23.2 1.0
N C:PRO322 4.5 24.4 1.0
N D:PRO322 4.5 23.7 1.0
N D:PRO323 4.6 23.8 1.0
O C:PRO323 4.7 23.9 1.0
CA C:PRO322 4.7 23.6 1.0
OD1 B:ASN320 4.7 22.1 1.0
CG C:ASN320 4.8 24.3 1.0
CA D:PRO322 4.8 24.2 1.0
O C:HOH107 4.9 19.3 1.0
O D:PRO323 4.9 23.8 1.0
O D:TRP321 4.9 23.3 1.0
CA C:ALA324 4.9 23.6 1.0
CG D:ASN320 5.0 22.7 1.0
CD C:PRO322 5.0 25.1 1.0
CA D:ALA324 5.0 22.7 1.0

Sodium binding site 3 out of 4 in 3k4g

Go back to Sodium Binding Sites List in 3k4g
Sodium binding site 3 out of 4 in the Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na3

b:24.1
occ:1.00
O G:HOH331 2.4 29.4 1.0
O E:PRO322 2.8 23.3 1.0
O F:PRO322 2.8 22.9 1.0
O F:ASN320 2.8 22.9 1.0
O E:ASN320 2.8 23.3 1.0
C E:ASN320 3.3 24.4 1.0
C F:ASN320 3.3 24.0 1.0
CB F:ASN320 3.6 23.2 1.0
CB E:ASN320 3.7 20.7 1.0
CA E:ASN320 3.7 23.1 1.0
O F:HOH113 3.8 22.5 1.0
CA F:ASN320 3.8 23.1 1.0
C E:PRO322 3.9 24.3 1.0
C F:PRO322 4.0 23.9 1.0
N E:TRP321 4.1 22.8 1.0
N F:TRP321 4.1 23.2 1.0
C F:TRP321 4.3 23.4 1.0
C E:TRP321 4.4 22.9 1.0
CA F:TRP321 4.4 23.3 1.0
N F:PRO322 4.4 24.4 1.0
CA E:TRP321 4.5 23.3 1.0
N E:PRO322 4.5 23.9 1.0
C E:PRO323 4.5 23.7 1.0
OD1 G:ASN320 4.6 20.8 1.0
C F:PRO323 4.7 24.0 1.0
CA E:PRO323 4.7 23.4 1.0
N E:PRO323 4.7 23.5 1.0
N E:ALA324 4.7 22.8 1.0
CG E:ASN320 4.7 22.1 1.0
CD F:PRO322 4.8 24.5 1.0
O E:PRO323 4.8 23.9 1.0
O F:TRP321 4.8 23.4 1.0
N F:ALA324 4.8 23.6 1.0
CA F:PRO323 4.8 24.2 1.0
CA E:PRO322 4.8 23.8 1.0
ND2 E:ASN320 4.8 20.4 1.0
N F:PRO323 4.8 23.2 1.0
CA F:PRO322 4.8 24.1 1.0
O E:TRP321 4.9 22.6 1.0
O E:HOH76 4.9 16.3 1.0
CD E:PRO322 4.9 20.6 1.0
CG F:ASN320 5.0 24.7 1.0

Sodium binding site 4 out of 4 in 3k4g

Go back to Sodium Binding Sites List in 3k4g
Sodium binding site 4 out of 4 in the Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1

b:27.1
occ:1.00
O H:PRO322 2.6 24.4 1.0
O G:PRO322 2.7 23.4 1.0
O H:ASN320 2.8 23.3 1.0
O G:ASN320 2.8 23.3 1.0
O E:HOH76 3.1 16.3 1.0
C H:PRO322 3.5 24.5 1.0
C G:PRO322 3.6 24.0 1.0
C G:ASN320 3.6 24.2 1.0
C H:ASN320 3.7 24.1 1.0
CA G:PRO323 3.8 23.6 1.0
C G:PRO323 3.8 23.4 1.0
CA H:PRO323 3.8 23.6 1.0
N G:ALA324 3.9 23.0 1.0
C H:PRO323 3.9 24.0 1.0
N H:ALA324 3.9 23.2 1.0
CB H:ASN320 4.0 22.0 1.0
N G:PRO323 4.0 22.9 1.0
CB G:ASN320 4.0 24.0 1.0
N H:PRO323 4.1 23.6 1.0
CA G:ASN320 4.3 23.6 1.0
O G:PRO323 4.3 24.1 1.0
CA H:ASN320 4.4 23.4 1.0
O H:PRO323 4.5 23.6 1.0
N G:TRP321 4.5 22.7 1.0
CA H:ALA324 4.5 23.1 1.0
CA G:ALA324 4.6 23.1 1.0
N H:TRP321 4.6 23.0 1.0
CA G:TRP321 4.6 23.4 1.0
N H:PRO322 4.6 24.0 1.0
CA H:TRP321 4.6 23.5 1.0
CA H:PRO322 4.7 24.2 1.0
C H:TRP321 4.7 24.0 1.0
O F:HOH113 4.7 22.5 1.0
CA G:PRO322 4.8 24.3 1.0
CB H:ALA324 4.8 21.6 1.0
O G:HOH138 4.8 24.5 1.0
N G:PRO322 4.8 24.9 1.0
CB G:ALA324 4.8 20.9 1.0
C G:TRP321 4.9 23.7 1.0

Reference:

S.Lara-Gonzalez, J.J.Birktoft, C.L.Lawson. Structure of the Escherichia Coli Rna Polymerase Alpha Subunit C-Terminal Domain. Acta Crystallogr.,Sect.D V. 66 806 2010.
ISSN: ISSN 0907-4449
PubMed: 20606261
DOI: 10.1107/S0907444910018470
Page generated: Mon Oct 7 11:10:08 2024

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