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Magnesium in PDB 2o5j: Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog

Enzymatic activity of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog

All present enzymatic activity of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog, PDB code: 2o5j was solved by D.G.Vassylyev, M.N.Vassylyeva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.00
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 152.340, 152.340, 524.567, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 25.7

Other elements in 2o5j:

The structure of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog (pdb code 2o5j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog, PDB code: 2o5j:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2o5j

Go back to Magnesium Binding Sites List in 2o5j
Magnesium binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg8001

b:23.4
occ:1.00
O3' H:G16 2.1 34.6 1.0
OD1 D:ASP739 2.2 61.0 1.0
OD1 D:ASP741 2.3 60.9 1.0
OD1 D:ASP743 2.3 63.9 1.0
O1A D:APC3999 2.3 48.2 1.0
CG D:ASP739 3.1 61.0 1.0
C3' H:G16 3.2 35.3 1.0
CG D:ASP741 3.3 62.4 1.0
OD2 D:ASP739 3.3 61.6 1.0
O2' H:G16 3.4 39.6 1.0
CG D:ASP743 3.4 63.4 1.0
C5' D:APC3999 3.4 51.5 1.0
O D:HOH8354 3.5 34.5 1.0
OD2 D:ASP741 3.6 64.2 1.0
PA D:APC3999 3.7 49.7 1.0
C2' H:G16 3.9 36.6 1.0
MG D:MG8002 3.9 25.2 1.0
OD2 D:ASP743 3.9 63.6 1.0
C4' D:APC3999 4.0 52.7 1.0
O5' D:APC3999 4.0 50.4 1.0
O D:ASP739 4.1 60.0 1.0
C4' H:G16 4.2 33.7 1.0
OD1 C:ASP686 4.3 71.6 1.0
O D:ASP741 4.4 62.8 1.0
CB D:ASP739 4.5 61.7 1.0
CB D:ASP741 4.5 61.5 1.0
C3A D:APC3999 4.6 46.2 1.0
CB D:ASP743 4.7 62.5 1.0
NH2 D:ARG704 4.7 60.5 1.0
O4' D:APC3999 4.7 53.0 1.0
O2A D:APC3999 4.7 48.2 1.0
N D:ASP739 4.7 62.2 1.0
C D:ASP739 5.0 60.7 1.0
NH1 D:ARG704 5.0 60.4 1.0

Magnesium binding site 2 out of 4 in 2o5j

Go back to Magnesium Binding Sites List in 2o5j
Magnesium binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg8002

b:25.2
occ:1.00
OD2 D:ASP739 2.1 61.6 1.0
O3G D:APC3999 2.1 42.8 1.0
O2B D:APC3999 2.3 43.6 1.0
O D:HOH8003 2.3 21.9 1.0
O1A D:APC3999 2.3 48.2 1.0
C3A D:APC3999 2.7 46.2 1.0
PB D:APC3999 2.9 42.9 1.0
PA D:APC3999 2.9 49.7 1.0
CG D:ASP739 3.0 61.0 1.0
PG D:APC3999 3.2 44.7 1.0
O3B D:APC3999 3.2 41.3 1.0
O2A D:APC3999 3.5 48.2 1.0
OD1 D:ASP739 3.5 61.0 1.0
MG D:MG8001 3.9 23.4 1.0
O1G D:APC3999 4.0 43.8 1.0
CB D:ASP739 4.0 61.7 1.0
OD1 C:ASP686 4.1 71.6 1.0
O1B D:APC3999 4.3 43.4 1.0
O5' D:APC3999 4.3 50.4 1.0
O2G D:APC3999 4.4 43.1 1.0
NH2 C:ARG879 4.5 76.5 1.0
O D:HOH8354 4.6 34.5 1.0
NH2 D:ARG1029 4.7 59.0 1.0
OD1 D:ASN737 4.7 65.0 1.0
OE2 C:GLU685 4.8 64.4 1.0
OE1 C:GLU685 4.8 65.0 1.0
NH2 D:ARG783 4.9 53.7 1.0

Magnesium binding site 3 out of 4 in 2o5j

Go back to Magnesium Binding Sites List in 2o5j
Magnesium binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg9001

b:21.8
occ:1.00
OD1 N:ASP739 2.0 61.4 1.0
O3' Y:G16 2.0 45.9 1.0
OD1 N:ASP741 2.3 51.8 1.0
O1A N:APC4999 2.4 47.9 1.0
OD1 N:ASP743 2.4 54.7 1.0
CG N:ASP739 2.6 61.3 1.0
OD2 N:ASP739 2.7 61.4 1.0
C3' Y:G16 3.2 45.7 1.0
O2' Y:G16 3.3 48.3 1.0
CG N:ASP741 3.5 51.9 1.0
C5' N:APC4999 3.7 48.5 1.0
CG N:ASP743 3.7 55.5 1.0
O N:ASP739 3.7 58.4 1.0
PA N:APC4999 3.8 49.5 1.0
C2' Y:G16 3.8 47.0 1.0
MG N:MG9002 4.0 23.6 1.0
CB N:ASP739 4.0 60.8 1.0
OD2 N:ASP741 4.1 51.5 1.0
C4' Y:G16 4.1 45.7 1.0
C4' N:APC4999 4.1 49.4 1.0
O5' N:APC4999 4.2 46.7 1.0
N N:ASP739 4.2 62.5 1.0
OD1 M:ASP686 4.2 65.1 1.0
OD2 N:ASP743 4.3 56.2 1.0
O N:ASP741 4.4 56.0 1.0
CA N:ASP739 4.5 60.0 1.0
C N:ASP739 4.5 58.3 1.0
C3A N:APC4999 4.5 48.3 1.0
O Y:HOH968 4.6 21.5 1.0
CB N:ASP741 4.7 52.0 1.0
O4' N:APC4999 4.7 49.3 1.0
CB N:ASP743 4.8 53.2 1.0
O2A N:APC4999 4.9 45.9 1.0
NH1 N:ARG704 4.9 66.0 1.0
NH2 N:ARG704 5.0 65.7 1.0
C5' Y:G16 5.0 44.4 1.0

Magnesium binding site 4 out of 4 in 2o5j

Go back to Magnesium Binding Sites List in 2o5j
Magnesium binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg9002

b:23.6
occ:1.00
O3G N:APC4999 2.0 47.9 1.0
O2B N:APC4999 2.1 49.4 1.0
OD2 N:ASP739 2.3 61.4 1.0
O M:HOH1120 2.3 24.3 1.0
O1A N:APC4999 2.4 47.9 1.0
C3A N:APC4999 2.5 48.3 1.0
PB N:APC4999 2.7 50.6 1.0
PA N:APC4999 2.9 49.5 1.0
CG N:ASP739 3.0 61.3 1.0
PG N:APC4999 3.1 49.3 1.0
O3B N:APC4999 3.1 48.4 1.0
O2A N:APC4999 3.5 45.9 1.0
OD1 N:ASP739 3.5 61.4 1.0
OE2 M:GLU685 3.5 54.5 1.0
O1G N:APC4999 3.9 47.9 1.0
CB N:ASP739 3.9 60.8 1.0
MG N:MG9001 4.0 21.8 1.0
O1B N:APC4999 4.2 49.1 1.0
O2G N:APC4999 4.3 50.8 1.0
OD1 M:ASP686 4.3 65.1 1.0
O5' N:APC4999 4.4 46.7 1.0
NH2 M:ARG879 4.5 59.1 1.0
NH2 N:ARG783 4.6 36.3 1.0
CD M:GLU685 4.6 55.3 1.0
OE1 M:GLU685 5.0 54.0 1.0

Reference:

D.G.Vassylyev, M.N.Vassylyeva, J.Zhang, M.Palangat, I.Artsimovitch, R.Landick. Structural Basis For Substrate Loading in Bacterial Rna Polymerase. Nature V. 448 163 2007.
ISSN: ISSN 0028-0836
PubMed: 17581591
DOI: 10.1038/NATURE05931
Page generated: Mon Dec 14 07:31:49 2020

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