Atomistry » Magnesium » PDB 5tff-5tv8 » 5tmc
Atomistry »
  Magnesium »
    PDB 5tff-5tv8 »
      5tmc »

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: Tue Aug 12 20:32:43 2025

Last articles

Mn in 5HWU
Mn in 5HRM
Mn in 5HUE
Mn in 5HUD
Mn in 5HUC
Mn in 5HRL
Mn in 5HRK
Mn in 5HRI
Mn in 5HRH
Mn in 5HRG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy