Sodium in PDB 6wox: Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 2'Dctp

Enzymatic activity of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 2'Dctp

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 2'Dctp:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 2'Dctp, PDB code: 6wox was solved by Y.Shin, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 3.14
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.435, 102.654, 295.382, 90.00, 98.91, 90.00
R / Rfree (%) 19.6 / 26.1

Other elements in 6wox:

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 2'Dctp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 2'Dctp (pdb code 6wox). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 2'Dctp, PDB code: 6wox:

Sodium binding site 1 out of 1 in 6wox

Go back to Sodium Binding Sites List in 6wox
Sodium binding site 1 out of 1 in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 2'Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 2'Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1201

b:70.1
occ:1.00
 O2B D:DCP1601 2.3 88.3 1.0
OD2 D:ASP739 2.5 78.1 1.0
O2G D:DCP1601 2.6 84.0 1.0
O1G D:DCP1601 2.7 85.9 1.0
NH1 C:ARG879 2.7 75.6 1.0
NH2 C:ARG879 2.9 81.9 1.0
PG D:DCP1601 3.1 93.4 1.0
CZ C:ARG879 3.2 67.8 1.0
PB D:DCP1601 3.3 0.7 1.0
CG D:ASP739 3.6 71.2 1.0
O3A D:DCP1601 3.6 96.7 1.0
O3B D:DCP1601 3.7 95.7 1.0
OD2 C:ASP686 3.7 64.3 1.0
NH2 D:ARG1029 4.0 72.8 1.0
CB D:ASP739 4.1 64.0 1.0
O3G D:DCP1601 4.4 89.1 1.0
NE C:ARG879 4.5 61.8 1.0
OE1 C:GLU685 4.5 67.8 1.0
NH2 C:ARG557 4.6 64.2 1.0
OD1 D:ASP739 4.7 63.0 1.0
O1B D:DCP1601 4.7 90.3 1.0
NH1 D:ARG1029 4.7 69.0 1.0
CZ D:ARG1029 4.8 71.1 1.0
CG C:ASP686 4.9 66.2 1.0

Reference:

Y.Shin, K.S.Murakami. The Mechanism of Discrimination Against 2DNTPS By the Multisubunit Rna Polymerases To Be Published.
Page generated: Tue Dec 15 15:43:26 2020

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