Sodium in PDB 5to3: Crystal Structure of Thrombin Mutant W215A/E217A Fused to EGF456 of Thrombomodulin Via A 31-Residue Linker and Bound to Ppack

Enzymatic activity of Crystal Structure of Thrombin Mutant W215A/E217A Fused to EGF456 of Thrombomodulin Via A 31-Residue Linker and Bound to Ppack

All present enzymatic activity of Crystal Structure of Thrombin Mutant W215A/E217A Fused to EGF456 of Thrombomodulin Via A 31-Residue Linker and Bound to Ppack:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Thrombin Mutant W215A/E217A Fused to EGF456 of Thrombomodulin Via A 31-Residue Linker and Bound to Ppack, PDB code: 5to3 was solved by S.Barranco-Medina, M.Murphy, L.Pelc, Z.Chen, E.Di Cera, N.Pozzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	40.00 / 2.34
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	62.939, 162.174, 128.859, 90.00, 90.00, 90.00
*R / R_free (%)*	21.4 / 25.5

Other elements in 5to3:

The structure of Crystal Structure of Thrombin Mutant W215A/E217A Fused to EGF456 of Thrombomodulin Via A 31-Residue Linker and Bound to Ppack also contains other interesting chemical elements:

Potassium

(K)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Thrombin Mutant W215A/E217A Fused to EGF456 of Thrombomodulin Via A 31-Residue Linker and Bound to Ppack (pdb code 5to3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Thrombin Mutant W215A/E217A Fused to EGF456 of Thrombomodulin Via A 31-Residue Linker and Bound to Ppack, PDB code: 5to3:

Sodium binding site 1 out of 1 in 5to3

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Sodium Binding Sites List in 5to3

Sodium binding site 1 out of 1 in the Crystal Structure of Thrombin Mutant W215A/E217A Fused to EGF456 of Thrombomodulin Via A 31-Residue Linker and Bound to Ppack

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Thrombin Mutant W215A/E217A Fused to EGF456 of Thrombomodulin Via A 31-Residue Linker and Bound to Ppack within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na503 b:52.9 occ:1.00	O	B:HOH605	2.2	30.6	1.0
	O	B:HOH658	2.4	52.1	1.0
	O	B:HOH619	2.5	35.2	1.0
	O	B:ARG248	2.5	45.5	1.0
	O	B:LYS251	2.6	44.5	1.0
	O	B:HOH607	2.9	32.7	1.0
	C	B:ARG248	3.6	48.0	1.0
	O	B:HOH666	3.6	38.2	1.0
	C	B:LYS251	3.8	43.4	1.0
	O	B:TYR205	4.0	46.8	1.0
	N	B:ARG248	4.0	46.2	1.0
	C	B:ASP247	4.1	45.0	1.0
	N	B:LYS251	4.2	45.6	1.0
	CA	B:ASP247	4.3	44.9	1.0
	N	B:ASP249	4.4	50.3	1.0
	CA	B:ARG248	4.4	47.2	1.0
	N	B:GLY250	4.5	50.2	1.0
	CA	B:ASP249	4.5	50.9	1.0
	CA	B:LYS251	4.5	43.5	1.0
	O	B:ASP247	4.6	44.4	1.0
	OD1	B:ASP247	4.6	50.3	1.0
	N	B:TYR252	4.7	41.2	1.0
	O	B:GLY213	4.8	42.9	1.0
	C	B:ASP249	4.8	50.0	1.0
	CB	B:LYS251	4.8	43.3	1.0
	O	B:HOH651	4.9	30.7	1.0
	CA	B:TYR252	5.0	37.8	1.0

Reference:

S.Barranco-Medina, M.Murphy, L.Pelc, Z.Chen, E.Di Cera, N.Pozzi. Rational Design of Protein C Activators. Sci Rep V. 7 44596 2017.
ISSN: ESSN 2045-2322
PubMed: 28294177
DOI: 10.1038/SREP44596

Page generated: Tue Oct 8 00:11:56 2024

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