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

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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

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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

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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

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