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
|