Bromine in PDB 3s2d: Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U

Enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U, PDB code: 3s2d was solved by X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	47.76 / 3.20
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	158.286, 220.768, 192.241, 90.00, 97.69, 90.00
*R / R_free (%)*	18.3 / 23.1

Other elements in 3s2d:

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	8 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U (pdb code 3s2d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total only one binding site of Bromine was determined in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U, PDB code: 3s2d:

Bromine binding site 1 out of 1 in 3s2d

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Bromine Binding Sites List in 3s2d

Bromine binding site 1 out of 1 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U

Mono view

Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rna Polymerase II Initiation Complex with A 5-Nt Rna Containing A 5BR- U within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
R:Br9 b:0.1 occ:0.60	BR	R:5BU9	0.0	0.1	0.6
	C5	R:5BU9	1.9	93.9	1.0
	C6	R:5BU9	2.8	89.3	1.0
	C4	R:5BU9	2.9	90.6	1.0
	O4	R:5BU9	3.1	89.9	1.0
	C5	R:G8	3.7	87.5	1.0
	C4	R:G8	3.7	87.7	1.0
	OP2	R:5BU9	3.8	81.2	1.0
	N9	R:G8	3.8	88.0	1.0
	N7	R:G8	3.8	87.7	1.0
	C8	R:G8	3.8	87.8	1.0
	C3'	R:G8	3.9	88.9	1.0
	N1	R:5BU9	4.1	85.8	1.0
	N3	R:5BU9	4.1	88.8	1.0
	C2'	R:G8	4.2	88.7	1.0
	C6	R:G8	4.3	87.0	1.0
	N3	R:G8	4.3	87.3	1.0
	NE2	B:GLN531	4.4	0.8	1.0
	C1'	R:G8	4.5	89.0	1.0
	O5'	R:5BU9	4.6	80.2	1.0
	P	R:5BU9	4.6	80.9	1.0
	O3'	R:G8	4.6	86.4	1.0
	N1	R:G8	4.7	87.1	1.0
	C2	R:G8	4.7	87.1	1.0
	C2	R:5BU9	4.7	87.8	1.0
	OE1	B:GLN531	4.8	0.4	1.0
	N7	R:G10	4.8	78.0	1.0
	O6	R:G8	4.9	86.5	1.0
	O4'	R:G8	4.9	90.4	1.0

Reference:

X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg. Initiation Complex Structure and Promoter Proofreading. Science V. 333 633 2011.
ISSN: ISSN 0036-8075
PubMed: 21798951
DOI: 10.1126/SCIENCE.1206629

Page generated: Mon Jul 7 05:54:04 2025

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