Magnesium in PDB 5tmf: Re-Refinement of Thermus Thermophilus Rna Polymerase

Enzymatic activity of Re-Refinement of Thermus Thermophilus Rna Polymerase

All present enzymatic activity of Re-Refinement of Thermus Thermophilus Rna Polymerase:
2.7.7.6;

Protein crystallography data

The structure of Re-Refinement of Thermus Thermophilus Rna Polymerase, PDB code: 5tmf was solved by J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.80 / 3.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 235.090, 235.090, 250.880, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 23.4

Other elements in 5tmf:

The structure of Re-Refinement of Thermus Thermophilus Rna Polymerase also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Re-Refinement of Thermus Thermophilus Rna Polymerase (pdb code 5tmf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Re-Refinement of Thermus Thermophilus Rna Polymerase, PDB code: 5tmf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5tmf

Go back to Magnesium Binding Sites List in 5tmf
Magnesium binding site 1 out of 2 in the Re-Refinement of Thermus Thermophilus Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Re-Refinement of Thermus Thermophilus Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:0.2
occ:1.00
O D:LYS840 2.2 0.6 1.0
OD2 B:ASP168 3.1 0.4 1.0
C D:LYS840 3.4 0.6 1.0
OE2 B:GLU154 3.8 0.9 1.0
CG B:ASP168 4.0 0.9 1.0
OD1 B:ASP168 4.0 0.0 1.0
CG2 D:VAL842 4.2 0.0 1.0
N D:VAL842 4.2 0.7 1.0
N D:TYR841 4.3 0.4 1.0
CA D:TYR841 4.4 98.3 1.0
CA D:LYS840 4.4 0.6 1.0
O D:LEU839 4.5 0.9 1.0
CD B:GLU154 4.6 0.4 1.0
OE1 B:GLU154 4.6 0.0 1.0
CB D:VAL842 4.7 1.0 1.0
C D:TYR841 4.8 98.6 1.0

Magnesium binding site 2 out of 2 in 5tmf

Go back to Magnesium Binding Sites List in 5tmf
Magnesium binding site 2 out of 2 in the Re-Refinement of Thermus Thermophilus Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Re-Refinement of Thermus Thermophilus Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1605

b:98.0
occ:1.00
OD1 D:ASP741 2.6 82.5 1.0
OD1 D:ASP743 2.6 97.2 1.0
OD1 D:ASP739 2.7 90.4 1.0
OD2 D:ASP741 3.0 95.3 1.0
CG D:ASP741 3.1 90.0 1.0
CG D:ASP743 3.4 86.7 1.0
OD2 D:ASP743 3.5 92.4 1.0
CG D:ASP739 3.8 79.5 1.0
OD2 D:ASP739 4.2 80.9 1.0
NH2 D:ARG704 4.6 93.5 1.0
CB D:ASP741 4.7 79.9 1.0
O D:ASP739 4.8 65.6 1.0
CB D:ASP743 4.9 71.3 1.0

Reference:

J.Wang, J.Wang. N/A N/A.
ISSN: ESSN 1469-896X
PubMed: 25352397
DOI: 10.1002/PRO.2595
Page generated: Mon Dec 14 21:12:48 2020

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