Bromine in PDB 5jvn: C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism

Enzymatic activity of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism

All present enzymatic activity of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism:
2.7.9.1;

Protein crystallography data

The structure of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism, PDB code: 5jvn was solved by A.Minges, A.Hoeppner, G.Groth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.54 / 2.90
*Space group*	P 6 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	249.430, 249.430, 84.060, 90.00, 90.00, 120.00
*R / R_free (%)*	19.8 / 23.5

Other elements in 5jvn:

The structure of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism (pdb code 5jvn). 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 C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism, PDB code: 5jvn:

Bromine binding site 1 out of 1 in 5jvn

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Bromine Binding Sites List in 5jvn

Bromine binding site 1 out of 1 in the C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism

Mono view

Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Br901 b:0.2 occ:0.87	BR	A:6NQ901	0.0	0.2	0.9
	C2'	A:6NQ901	2.0	0.9	0.9
	C1'	A:6NQ901	2.9	0.4	0.9
	C3'	A:6NQ901	3.0	1.0	0.9
	O3'	A:6NQ901	3.2	0.5	0.9
	N9	A:6NQ901	3.4	0.6	0.9
	CG	A:GLN336	3.8	89.7	1.0
	C4	A:6NQ901	3.9	0.4	0.9
	OE2	A:GLU324	3.9	88.8	1.0
	N3	A:6NQ901	4.0	0.1	0.9
	CD	A:GLN336	4.0	98.8	1.0
	O4'	A:6NQ901	4.1	0.1	0.9
	C8	A:6NQ901	4.2	0.1	0.9
	C4'	A:6NQ901	4.2	0.1	0.9
	NE2	A:GLN336	4.2	0.8	1.0
	CB	A:LEU335	4.3	68.0	1.0
	CD1	A:LEU335	4.5	75.0	1.0
	OE1	A:GLN336	4.6	0.8	1.0
	CD	A:GLU324	4.8	79.5	1.0
	C5	A:6NQ901	4.8	0.2	0.9
	CG	A:LEU335	4.9	70.2	1.0
	N7	A:6NQ901	5.0	0.9	0.9

Reference:

A.Minges, D.Ciupka, C.Winkler, A.Hoppner, H.Gohlke, G.Groth. Structural Intermediates and Directionality of the Swiveling Motion of Pyruvate Phosphate Dikinase. Sci Rep V. 7 45389 2017.
ISSN: ESSN 2045-2322
PubMed: 28358005
DOI: 10.1038/SREP45389

Page generated: Thu Jul 11 00:07:52 2024

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