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Magnesium in PDB 2wb1: The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase

Protein crystallography data

The structure of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase, PDB code: 2wb1 was solved by Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, N.G.A.Abrescia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.20 / 3.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 196.095, 211.871, 238.905, 90.00, 90.00, 90.00
R / Rfree (%) 33.3 / 38.4

Other elements in 2wb1:

The structure of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase also contains other interesting chemical elements:

Iron (Fe) 6 atoms
Zinc (Zn) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase (pdb code 2wb1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase, PDB code: 2wb1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2wb1

Go back to Magnesium Binding Sites List in 2wb1
Magnesium binding site 1 out of 2 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1882

b:79.3
occ:1.00
OD1 A:ASP456 2.1 65.8 1.0
OD1 A:ASP458 2.4 66.5 1.0
OD1 A:ASP460 2.8 66.0 1.0
CG A:ASP456 3.0 65.9 1.0
OD2 A:ASP456 3.2 66.1 1.0
CG A:ASP458 3.2 66.9 1.0
OD2 A:ASP458 3.3 67.1 1.0
CG A:ASP460 3.6 65.7 1.0
OD2 A:ASP460 3.7 65.5 1.0
CB A:ASP456 4.4 65.9 1.0
CB A:ASP458 4.7 67.4 1.0
O A:ASP456 4.7 65.8 1.0
N A:ASP456 4.8 65.4 1.0
C A:ASP456 4.9 65.9 1.0
CA A:ASP456 4.9 65.7 1.0
N A:ASP458 5.0 67.0 1.0

Magnesium binding site 2 out of 2 in 2wb1

Go back to Magnesium Binding Sites List in 2wb1
Magnesium binding site 2 out of 2 in the The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg1882

b:81.1
occ:1.00
OD1 W:ASP458 1.9 64.7 1.0
OD1 W:ASP456 2.0 63.7 1.0
OD1 W:ASP460 2.4 63.8 1.0
CG W:ASP458 2.8 65.2 1.0
OD2 W:ASP458 3.0 65.5 1.0
CG W:ASP456 3.0 63.7 1.0
CG W:ASP460 3.3 63.4 1.0
OD2 W:ASP456 3.5 64.0 1.0
OD2 W:ASP460 3.6 63.1 1.0
CB W:ASP458 4.2 65.7 1.0
O W:ASP456 4.3 63.5 1.0
N W:ASP458 4.3 65.0 1.0
CB W:ASP456 4.3 63.6 1.0
C W:ASP456 4.5 63.6 1.0
CA W:ASP458 4.6 65.7 1.0
C W:ASP458 4.7 65.8 1.0
CB W:ASP460 4.7 63.5 1.0
O W:GLY459 4.7 65.0 1.0
CA W:ASP456 4.8 63.3 1.0
N W:ASP456 4.8 62.8 1.0
C W:GLY459 4.9 65.0 1.0
N W:GLY459 4.9 65.5 1.0

Reference:

Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, N.G.A.Abrescia. Evolution of Complex Rna Polymerase: the Complete Archaeal Rna Polymerase Structure Plos Biol. V. 7 E102 2009.
ISSN: ISSN 1544-9173
PubMed: 19419240
DOI: 10.1371/JOURNAL.PBIO.1000102
Page generated: Mon Dec 14 07:43:57 2020

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