Manganese in PDB 8u9x: Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser

Enzymatic activity of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser

All present enzymatic activity of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser:
2.7.7.6;

Protein crystallography data

The structure of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser, PDB code: 8u9x was solved by P.Arjunan, G.Calero, C.D.Kaplan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	18.00 / 3.05
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	220.167, 392.604, 280.921, 90, 90, 90
*R / R_free (%)*	28.3 / 30.7

Other elements in 8u9x:

The structure of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser (pdb code 8u9x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser, PDB code: 8u9x:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 8u9x

Go back to

Manganese Binding Sites List in 8u9x

Manganese binding site 1 out of 3 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn1803 b:69.6 occ:0.96	O2A	B:ATP2501	2.1	117.3	1.0
	OD1	A:ASP485	2.5	93.0	1.0
	OD1	A:ASP481	2.6	89.2	1.0
	OD2	A:ASP481	3.0	103.7	1.0
	OD2	A:ASP485	3.1	67.7	1.0
	CG	A:ASP481	3.1	98.7	1.0
	CG	A:ASP485	3.2	85.7	1.0
	C3'	R:G10	3.3	108.4	1.0
	OD1	A:ASP483	3.3	102.2	1.0
	PA	B:ATP2501	3.5	172.7	1.0
	C4'	R:G10	3.5	90.1	1.0
	OD2	A:ASP483	3.6	121.4	1.0
	MN	A:MN1804	3.8	78.7	0.9
	CG	A:ASP483	3.8	109.3	1.0
	C5'	R:G10	3.8	98.5	1.0
	O2B	B:ATP2501	3.8	118.4	1.0
	O5'	B:ATP2501	4.1	170.7	1.0
	O2'	R:G10	4.2	74.4	1.0
	O3A	B:ATP2501	4.2	169.3	1.0
	C5'	B:ATP2501	4.3	156.6	1.0
	C2'	R:G10	4.3	101.8	1.0
	NH2	A:ARG446	4.4	107.9	1.0
	C4'	B:ATP2501	4.5	151.4	1.0
	CB	A:ASP481	4.6	94.3	1.0
	O1A	B:ATP2501	4.6	162.4	1.0
	PB	B:ATP2501	4.7	151.6	1.0
	O5'	R:G10	4.7	115.9	1.0
	CB	A:ASP485	4.7	87.0	1.0
	O4'	B:ATP2501	4.7	151.4	1.0
	O4'	R:G10	4.9	100.1	1.0
	N	A:ASP481	5.0	78.4	1.0

Manganese binding site 2 out of 3 in 8u9x

Go back to

Manganese Binding Sites List in 8u9x

Manganese binding site 2 out of 3 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn1804 b:78.7 occ:0.90	O2B	B:ATP2501	2.0	118.4	1.0
	OD2	A:ASP483	2.1	121.4	1.0
	OD2	A:ASP481	2.2	103.7	1.0
	CG	A:ASP481	3.3	98.7	1.0
	CG	A:ASP483	3.3	109.3	1.0
	OD2	B:ASP837	3.4	125.7	1.0
	PB	B:ATP2501	3.4	151.6	1.0
	MN	A:MN1803	3.8	69.6	1.0
	O3G	B:ATP2501	3.9	138.0	1.0
	O3B	B:ATP2501	4.0	160.6	1.0
	O2A	B:ATP2501	4.0	117.3	1.0
	OD1	A:ASP483	4.0	102.2	1.0
	CB	A:ASP481	4.1	94.3	1.0
	O1B	B:ATP2501	4.2	139.7	1.0
	NH2	B:ARG1020	4.2	132.7	1.0
	OD1	A:ASP481	4.2	89.2	1.0
	CG	B:ASP837	4.3	121.2	1.0
	O3A	B:ATP2501	4.3	169.3	1.0
	CB	A:ASP483	4.4	92.1	1.0
	CB	B:ASP837	4.4	114.4	1.0
	PG	B:ATP2501	4.5	163.5	1.0
	NH1	B:ARG1020	4.7	130.8	1.0
	PA	B:ATP2501	4.8	172.7	1.0
	CZ	B:ARG1020	4.9	116.7	1.0

Manganese binding site 3 out of 3 in 8u9x

Go back to

Manganese Binding Sites List in 8u9x

Manganese binding site 3 out of 3 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn2503 b:138.7 occ:0.64	O1A	B:ATP2501	2.3	162.4	1.0
	OH	B:TYR769	3.5	94.6	1.0
	O3B	B:ATP2501	3.5	160.6	1.0
	CE2	B:TYR769	3.7	103.7	1.0
	PA	B:ATP2501	3.7	172.7	1.0
	CZ	B:TYR769	3.7	109.2	1.0
	OE2	B:GLU529	3.9	88.2	1.0
	CE1	A:PHE1084	4.1	167.8	1.0
	O3A	B:ATP2501	4.2	169.3	1.0
	O2G	B:ATP2501	4.2	171.1	1.0
	CZ	A:PHE1084	4.2	173.9	1.0
	O1G	B:ATP2501	4.4	152.0	1.0
	PG	B:ATP2501	4.4	163.5	1.0
	CD	B:GLU529	4.5	118.1	1.0
	O5'	B:ATP2501	4.5	170.7	1.0
	PB	B:ATP2501	4.5	151.6	1.0
	CD2	B:TYR769	4.6	97.9	1.0
	OE1	B:GLU529	4.6	116.9	1.0
	CE1	B:TYR769	4.6	115.6	1.0
	O2A	B:ATP2501	4.7	117.3	1.0
	NZ	B:LYS987	4.9	82.0	1.0

Reference:

G.Lin, C.O.Barnes, S.Weiss, B.Dutagaci, C.Qiu, M.Feig, J.Song, A.Lyubimov, A.E.Cohen, C.D.Kaplan, G.Calero. Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser. Proc.Natl.Acad.Sci.Usa V. 121 27121 2024.
ISSN: ESSN 1091-6490
PubMed: 39190355
DOI: 10.1073/PNAS.2318527121

Page generated: Sun Oct 6 13:59:14 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy