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Manganese in PDB 1twf: Rna Polymerase II Complexed with Utp at 2.3 A Resolution

Enzymatic activity of Rna Polymerase II Complexed with Utp at 2.3 A Resolution

All present enzymatic activity of Rna Polymerase II Complexed with Utp at 2.3 A Resolution:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Complexed with Utp at 2.3 A Resolution, PDB code: 1twf was solved by K.D.Westover, D.A.Bushnell, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 123.000, 223.000, 374.000, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 29.4

Other elements in 1twf:

The structure of Rna Polymerase II Complexed with Utp at 2.3 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution (pdb code 1twf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution, PDB code: 1twf:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 1twf

Go back to Manganese Binding Sites List in 1twf
Manganese binding site 1 out of 2 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rna Polymerase II Complexed with Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3009

b:44.8
occ:1.00
OD1 A:ASP481 2.2 22.5 1.0
OD2 A:ASP483 2.3 32.4 1.0
OD2 A:ASP485 2.3 28.7 1.0
O2G B:UTP3571 2.5 53.3 1.0
O1B B:UTP3571 2.7 60.0 1.0
O2B B:UTP3571 2.8 54.8 1.0
CG A:ASP481 3.0 22.3 1.0
OD2 A:ASP481 3.0 24.7 1.0
CG A:ASP483 3.1 34.4 1.0
PB B:UTP3571 3.1 62.8 1.0
CG A:ASP485 3.2 29.5 1.0
OD1 A:ASP483 3.2 32.9 1.0
OD1 A:ASP485 3.4 25.7 1.0
O3B B:UTP3571 3.7 59.9 1.0
PG B:UTP3571 3.7 64.9 1.0
MN A:MN3010 3.8 41.0 1.0
CB A:ASP481 4.4 25.4 1.0
N A:ASP483 4.4 30.2 1.0
O A:ASP481 4.4 24.3 1.0
CB A:ASP483 4.5 33.3 1.0
CB A:ASP485 4.6 28.1 1.0
O3A B:UTP3571 4.6 61.3 1.0
N A:ASP481 4.6 27.1 1.0
C A:ASP481 4.6 27.7 1.0
N A:ASP485 4.7 29.8 1.0
O3G B:UTP3571 4.7 60.6 1.0
O1G B:UTP3571 4.8 57.6 1.0
CA A:ASP481 4.8 26.5 1.0
CA A:ASP483 4.8 29.5 1.0
C A:ASP483 4.9 30.5 1.0

Manganese binding site 2 out of 2 in 1twf

Go back to Manganese Binding Sites List in 1twf
Manganese binding site 2 out of 2 in the Rna Polymerase II Complexed with Utp at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rna Polymerase II Complexed with Utp at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3010

b:41.0
occ:1.00
OD1 A:ASP483 2.1 32.9 1.0
OD2 A:ASP481 2.3 24.7 1.0
O1B B:UTP3571 2.6 60.0 1.0
OD2 B:ASP837 2.7 30.4 1.0
O1A B:UTP3571 2.9 57.6 1.0
PB B:UTP3571 2.9 62.8 1.0
O2B B:UTP3571 3.0 54.8 1.0
O3A B:UTP3571 3.2 61.3 1.0
CG B:ASP837 3.2 34.3 1.0
CG A:ASP481 3.3 22.3 1.0
CG A:ASP483 3.3 34.4 1.0
PA B:UTP3571 3.6 62.4 1.0
MN A:MN3009 3.8 44.8 1.0
OD1 B:ASP837 3.9 36.5 1.0
OD1 A:ASP481 3.9 22.5 1.0
CB B:ASP837 3.9 32.4 1.0
NH2 B:ARG1020 3.9 65.6 1.0
OD2 A:ASP483 3.9 32.4 1.0
O5' B:UTP3571 4.0 61.0 1.0
CB A:ASP481 4.4 25.4 1.0
O3B B:UTP3571 4.5 59.9 1.0
CB A:ASP483 4.5 33.3 1.0
NE2 B:GLN986 4.6 54.5 1.0
C6 B:UTP3571 4.7 64.0 1.0
CZ B:ARG1020 4.8 65.6 1.0
O4' B:UTP3571 4.8 63.0 1.0
OE1 B:GLN986 4.8 54.2 1.0
NH1 B:ARG1020 5.0 68.2 1.0
O2A B:UTP3571 5.0 63.9 1.0

Reference:

K.D.Westover, D.A.Bushnell, R.D.Kornberg. Structural Basis of Transcription: Nucleotide Selection By Rotation in the Rna Polymerase II Active Center. Cell(Cambridge,Mass.) V. 119 481 2004.
ISSN: ISSN 0092-8674
PubMed: 15537538
DOI: 10.1016/J.CELL.2004.10.016
Page generated: Tue Dec 15 03:56:08 2020

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