Bromine in PDB 8ke4: Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp

Enzymatic activity of Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp

All present enzymatic activity of Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp:
6.1.1.26;

Protein crystallography data

The structure of Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp, PDB code: 8ke4 was solved by J.H.Weng, M.D.Tsai, Y.S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	28.17 / 1.75
*Space group*	P 6₄
*Cell size a, b, c (Å), α, β, γ (°)*	105.198, 105.198, 71.694, 90, 90, 120
*R / R_free (%)*	17.2 / 18.4

Other elements in 8ke4:

The structure of Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp (pdb code 8ke4). 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 Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp, PDB code: 8ke4:

Bromine binding site 1 out of 1 in 8ke4

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Bromine Binding Sites List in 8ke4

Bromine binding site 1 out of 1 in the Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp

Mono view

Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Br504 b:73.6 occ:0.52	BR1	A:FXF504	0.0	73.6	0.5
	CE1	A:FXF504	1.9	34.8	0.5
	CD1	A:FXF504	2.9	32.1	0.5
	CZ	A:FXF504	2.9	28.3	0.5
	N	A:GLY401	3.2	24.7	1.0
	O	A:GLY419	3.4	20.4	1.0
	C	A:ALA400	3.6	27.0	1.0
	CA	A:GLY401	3.7	28.8	1.0
	C	A:GLY419	3.8	21.1	1.0
	CA	A:ALA400	3.8	24.2	1.0
	O	A:SER399	4.1	21.1	1.0
	CZ3	A:TRP417	4.1	24.8	1.0
	N	A:ALA420	4.1	18.4	1.0
	CA	A:ALA420	4.2	18.8	1.0
	CG	A:FXF504	4.2	32.0	0.5
	CE2	A:FXF504	4.2	28.8	0.5
	O	A:ALA400	4.3	28.0	1.0
	CH2	A:TRP417	4.3	27.9	1.0
	N	A:ALA400	4.5	21.3	1.0
	OXT	A:FXF504	4.5	38.3	0.5
	CA	A:GLY419	4.6	19.1	1.0
	C	A:SER399	4.6	24.3	1.0
	C	A:GLY401	4.6	27.2	1.0
	O	A:HOH838	4.7	40.2	1.0
	O	A:GLY401	4.7	20.9	1.0
	CD2	A:FXF504	4.7	31.1	0.5
	C	A:ALA420	4.8	21.1	1.0
	N	A:GLY419	4.9	21.1	1.0

Reference:

H.K.Jiang, J.H.Weng, Y.H.Wang, J.C.Tsou, P.J.Chen, A.L.A.Ko, D.Soll, M.D.Tsai, Y.S.Wang. Rational Design of the Genetic Code Expansion Toolkit For in Vivo Encoding of D-Amino Acids Front Genet 2023.
DOI: 10.3389/FGENE.2023.1277489

Page generated: Mon Jul 7 12:27:27 2025

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