Calcium in PDB 5j48: Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp

Enzymatic activity of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp

All present enzymatic activity of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp:
2.7.11.12;

Protein crystallography data

The structure of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp, PDB code: 5j48 was solved by J.C.Campbell, B.Sankaran, C.W.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	34.95 / 1.49
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	35.510, 59.240, 67.320, 90.00, 100.17, 90.00
*R / R_free (%)*	16.3 / 18.9

Other elements in 5j48:

The structure of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp (pdb code 5j48). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp, PDB code: 5j48:

Calcium binding site 1 out of 1 in 5j48

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Calcium Binding Sites List in 5j48

Calcium binding site 1 out of 1 in the Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ca406 b:21.9 occ:1.00	H151	B:6FW405	2.6	16.9	1.0
	N12	B:6FW405	3.1	13.3	1.0
	HD3	B:ARG285	3.2	38.0	1.0
	HD2	B:ARG285	3.2	38.0	1.0
	N15	B:6FW405	3.4	14.1	1.0
	CD	B:ARG285	3.6	31.7	1.0
	C13	B:6FW405	3.7	13.2	1.0
	NE	B:ARG285	3.8	18.3	1.0
	HE	B:ARG285	4.0	21.9	1.0
	C10	B:6FW405	4.2	13.1	1.0
	H152	B:6FW405	4.2	16.9	1.0
	CZ	B:ARG285	4.2	20.7	1.0
	HH11	B:ARG285	4.3	36.0	1.0
	O11	B:6FW405	4.3	14.0	1.0
	HD13	B:LEU296	4.4	24.8	1.0
	NH1	B:ARG285	4.4	30.0	1.0
	HD11	B:LEU296	4.5	24.8	1.0
	HD22	B:LEU296	4.8	25.1	1.0
	HD21	B:LEU296	4.8	25.1	1.0
	CD1	B:LEU296	4.9	20.7	1.0
	NH2	B:ARG285	5.0	23.7	1.0

Reference:

J.C.Campbell, P.Henning, E.Franz, B.Sankaran, F.W.Herberg, C.Kim. Structural Basis of Analog Specificity in Pkg I and II. Acs Chem. Biol. V. 12 2388 2017.
ISSN: ESSN 1554-8937
PubMed: 28793191
DOI: 10.1021/ACSCHEMBIO.7B00369

Page generated: Wed Jul 9 07:01:41 2025

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