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Magnesium in PDB 5tmc: Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure

Enzymatic activity of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure

All present enzymatic activity of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure:
2.7.7.6;

Protein crystallography data

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

Resolution Low / High (Å) 48.51 / 2.71
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 236.350, 236.350, 249.040, 90.00, 90.00, 120.00
R / Rfree (%) 26.5 / 28.6

Other elements in 5tmc:

The structure of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure 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 Thermopiles Dna-Directed Rna Polymerase Structure (pdb code 5tmc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure, PDB code: 5tmc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5tmc

Go back to Magnesium Binding Sites List in 5tmc
Magnesium binding site 1 out of 4 in the Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure


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 Thermopiles Dna-Directed Rna Polymerase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1201

b:0.9
occ:1.00
 O C:GLU796 2.6 70.1 1.0
O C:PRO793 2.6 66.3 1.0
O C:GLY795 2.9 52.7 1.0
O C:PRO794 2.9 52.7 1.0
C C:GLY795 3.2 62.0 1.0
NZ C:LYS1004 3.3 74.2 1.0
C C:PRO793 3.3 61.6 1.0
C C:PRO794 3.4 61.8 1.0
CB C:PRO793 3.6 50.7 1.0
C C:GLU796 3.6 75.8 1.0
N C:GLU796 3.8 72.1 1.0
N C:GLY795 3.9 63.2 1.0
CA C:GLY795 4.0 67.7 1.0
CA C:PRO793 4.0 58.0 1.0
N C:PRO794 4.0 62.7 1.0
CA C:GLU796 4.2 79.7 1.0
CA C:PRO794 4.3 64.3 1.0
CG C:PRO793 4.4 60.2 1.0
CE C:LYS1004 4.4 83.0 1.0
N C:PRO793 4.5 56.2 1.0
CD C:PRO793 4.6 57.6 1.0
N C:GLY797 4.7 72.3 1.0
CD C:PRO794 4.9 63.2 1.0
OH C:TYR708 5.0 59.2 1.0
CG1 C:VAL792 5.0 69.5 1.0

Magnesium binding site 2 out of 4 in 5tmc

Go back to Magnesium Binding Sites List in 5tmc
Magnesium binding site 2 out of 4 in the Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure


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 Thermopiles Dna-Directed Rna Polymerase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1601

b:0.4
occ:1.00
 O1A D:G4P1605 1.9 0.2 1.0
O2B D:G4P1605 3.1 0.5 1.0
O D:HOH1729 3.2 54.9 1.0
PA D:G4P1605 3.3 0.6 1.0
OE2 C:GLU685 3.5 79.8 1.0
OD2 D:ASP739 3.8 55.9 1.0
O3A D:G4P1605 3.9 0.4 1.0
PB D:G4P1605 4.0 0.0 1.0
O3B D:G4P1605 4.1 0.7 1.0
O5' D:G4P1605 4.1 0.5 1.0
CD C:GLU685 4.4 71.8 1.0
O2A D:G4P1605 4.4 0.8 1.0
OE1 C:GLU685 4.5 68.3 1.0
CB D:ASP739 4.5 55.0 1.0
NH2 C:ARG879 4.6 89.4 1.0
CG D:ASP739 4.7 55.5 1.0
NH2 D:ARG1029 4.7 54.1 1.0
OD2 C:ASP686 4.9 65.0 1.0
NH1 D:ARG1029 4.9 54.0 1.0
O D:HOH1758 5.0 61.4 1.0

Magnesium binding site 3 out of 4 in 5tmc

Go back to Magnesium Binding Sites List in 5tmc
Magnesium binding site 3 out of 4 in the Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:86.4
occ:1.00
 O D:HOH1745 1.9 56.9 1.0
OD1 D:ASP741 2.3 57.0 1.0
OD1 D:ASP743 2.6 55.8 1.0
OD2 D:ASP741 3.0 57.4 1.0
CG D:ASP741 3.0 57.3 1.0
OD1 D:ASP739 3.0 55.6 1.0
CG D:ASP743 3.4 62.0 1.0
OD2 D:ASP739 3.4 55.9 1.0
CG D:ASP739 3.6 55.5 1.0
OD2 D:ASP743 3.6 69.3 1.0
O C:HOH1321 3.7 77.3 1.0
CB D:ASP741 4.5 57.6 1.0
O D:HOH1758 4.5 61.4 1.0
N D:ASP743 4.7 59.8 1.0
CB D:ASP743 4.7 56.8 1.0
NZ C:LYS846 4.8 86.2 1.0
N D:ASP741 4.9 56.4 1.0
C D:ASP741 4.9 57.1 1.0
O D:ASP741 5.0 57.7 1.0

Magnesium binding site 4 out of 4 in 5tmc

Go back to Magnesium Binding Sites List in 5tmc
Magnesium binding site 4 out of 4 in the Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Re-Refinement of Thermus Thermopiles Dna-Directed Rna Polymerase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1606

b:0.3
occ:1.00
 O3D D:G4P1605 1.5 0.2 1.0
O2C D:G4P1605 1.8 0.8 1.0
O D:HOH1707 2.0 64.5 1.0
PD D:G4P1605 2.5 0.4 1.0
O3C D:G4P1605 2.5 0.4 1.0
PC D:G4P1605 2.5 0.2 1.0
O D:HOH1730 2.8 71.6 1.0
NZ D:LYS908 3.0 79.6 1.0
O1C D:G4P1605 3.3 0.9 1.0
O1D D:G4P1605 3.5 0.3 1.0
O2D D:G4P1605 3.6 0.5 1.0
O3' D:G4P1605 3.9 0.6 1.0
CE D:LYS908 4.4 74.0 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 Sep 30 04:54:56 2024

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