Sodium in PDB 4lz1: X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase

Enzymatic activity of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase

All present enzymatic activity of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase, PDB code: 4lz1 was solved by A.Pica, I.Russo Krauss, A.Merlino, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	25.20 / 1.65
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	42.892, 44.484, 52.643, 65.24, 82.53, 63.72
*R / R_free (%)*	15.5 / 19

Other elements in 4lz1:

The structure of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase also contains other interesting chemical elements:

Potassium

(K)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase (pdb code 4lz1). 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 X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase, PDB code: 4lz1:

Sodium binding site 1 out of 1 in 4lz1

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Sodium Binding Sites List in 4lz1

Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
H:Na302 b:26.2 occ:1.00	O	H:HOH431	2.2	26.5	1.0
	O	H:LYS224	2.2	22.4	1.0
	O	H:HOH449	2.3	16.5	1.0
	O	H:ARG221	2.3	18.8	1.0
	O	H:HOH432	2.4	21.4	1.0
	O	H:HOH434	2.8	22.6	1.0
	C	H:ARG221	3.4	19.5	1.0
	C	H:LYS224	3.4	18.1	1.0
	O	H:HOH451	3.8	22.5	1.0
	N	H:LYS224	3.8	21.8	1.0
	N	H:ARG221	3.9	17.6	1.0
	O	H:HOH450	4.0	26.4	1.0
	O	H:TYR184A	4.0	21.0	1.0
	C	H:ASP221A	4.1	19.0	1.0
	O	H:HOH429	4.2	31.8	1.0
	CA	H:LYS224	4.2	20.8	1.0
	O	H:HOH433	4.2	17.9	1.0
	N	H:GLY223	4.3	18.9	1.0
	CA	H:ARG221	4.3	21.0	1.0
	N	H:ASP222	4.3	21.1	1.0
	CA	H:ASP222	4.4	22.8	1.0
	N	H:TYR225	4.4	19.4	1.0
	CA	H:ASP221A	4.5	16.7	1.0
	CB	H:LYS224	4.5	20.9	1.0
	O	H:ASP221A	4.6	21.9	1.0
	C	H:ASP222	4.6	21.2	1.0
	CA	H:TYR225	4.7	17.6	1.0
	OD1	H:ASP221A	4.7	20.7	1.0
	C	H:GLY223	4.9	20.9	1.0
	CD1	H:TYR225	4.9	18.4	1.0

Reference:

A.Pica, I.Russo Krauss, A.Merlino, S.Nagatoishi, N.Sugimoto, F.Sica. Dissecting the Contribution of Thrombin Exosite I in the Recognition of Thrombin Binding Aptamer. Febs J. V. 280 6581 2013.
ISSN: ISSN 1742-464X
PubMed: 24128303
DOI: 10.1111/FEBS.12561

Page generated: Sun Aug 17 20:32:08 2025

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