Calcium in PDB 3d8g: Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs I72R at Cryogenic Temperature

Enzymatic activity of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs I72R at Cryogenic Temperature

All present enzymatic activity of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs I72R at Cryogenic Temperature:
3.1.31.1;

Protein crystallography data

The structure of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs I72R at Cryogenic Temperature, PDB code: 3d8g was solved by M.J.Harms, J.L.Schlessman, E.B.Garcia-Moreno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	1.99 / 1.99
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	32.181, 60.425, 73.124, 90.00, 90.00, 90.00
*R / R_free (%)*	20 / 25.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs I72R at Cryogenic Temperature (pdb code 3d8g). 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 Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs I72R at Cryogenic Temperature, PDB code: 3d8g:

Calcium binding site 1 out of 1 in 3d8g

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Calcium Binding Sites List in 3d8g

Calcium binding site 1 out of 1 in the Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs I72R at Cryogenic Temperature

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs I72R at Cryogenic Temperature within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca150 b:11.3 occ:1.00	OD1	A:ASP40	2.6	10.5	1.0
	O	A:HOH204	2.8	10.6	1.0
	OD2	A:ASP21	2.8	5.7	1.0
	O	A:THR41	2.8	9.6	1.0
	O	A:HOH158	3.0	13.3	1.0
	O	A:HOH216	3.1	21.2	1.0
	O4P	A:THP151	3.2	12.8	1.0
	CG	A:ASP21	3.6	6.8	1.0
	OD1	A:ASP21	3.7	6.9	1.0
	CG	A:ASP40	3.8	8.6	1.0
	O	A:HOH201	3.9	8.0	1.0
	NH2	A:ARG35	3.9	3.0	1.0
	C	A:THR41	3.9	9.8	1.0
	O	A:HOH232	4.0	27.6	1.0
	N	A:THR41	4.0	8.0	1.0
	OG1	A:THR41	4.1	8.1	1.0
	P2	A:THP151	4.1	12.4	1.0
	OE2	A:GLU43	4.2	27.1	1.0
	O5P	A:THP151	4.3	12.9	1.0
	OD2	A:ASP40	4.5	8.9	1.0
	CA	A:THR41	4.5	8.9	1.0
	CZ	A:ARG35	4.6	4.7	1.0
	CA	A:ASP40	4.6	7.5	1.0
	C	A:ASP40	4.6	7.4	1.0
	O6P	A:THP151	4.7	13.6	1.0
	CB	A:ASP40	4.8	7.6	1.0
	NE	A:ARG35	4.8	5.3	1.0
	O	A:HOH170	4.8	13.0	1.0
	C	A:PRO42	4.8	13.2	1.0
	N	A:GLU43	4.9	14.5	1.0
	O	A:PRO42	4.9	12.6	1.0
	CB	A:THR41	5.0	8.5	1.0

Reference:

M.J.Harms, J.L.Schlessman, G.R.Sue, B.Garcia-Moreno E. Arginine Residues at Internal Positions in A Protein Are Always Charged. Proc.Natl.Acad.Sci.Usa V. 108 18954 2011.
ISSN: ISSN 0027-8424
PubMed: 22080604
DOI: 10.1073/PNAS.1104808108

Page generated: Tue Jul 8 11:33:24 2025

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