Sodium in PDB 6px5: Crystal Structure of Human Meizothrombin DESF1 Mutant S195A Bound with Ppack

Enzymatic activity of Crystal Structure of Human Meizothrombin DESF1 Mutant S195A Bound with Ppack

All present enzymatic activity of Crystal Structure of Human Meizothrombin DESF1 Mutant S195A Bound with Ppack:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Human Meizothrombin DESF1 Mutant S195A Bound with Ppack, PDB code: 6px5 was solved by L.A.Pelc, S.K.Koester, Z.Chen, N.Gistover, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	36.02 / 2.40
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	100.134, 100.134, 118.679, 90.00, 90.00, 120.00
*R / R_free (%)*	22.3 / 28.2

Other elements in 6px5:

The structure of Crystal Structure of Human Meizothrombin DESF1 Mutant S195A Bound with Ppack also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Meizothrombin DESF1 Mutant S195A Bound with Ppack (pdb code 6px5). 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 Human Meizothrombin DESF1 Mutant S195A Bound with Ppack, PDB code: 6px5:

Sodium binding site 1 out of 1 in 6px5

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Sodium Binding Sites List in 6px5

Sodium binding site 1 out of 1 in the Crystal Structure of Human Meizothrombin DESF1 Mutant S195A Bound with 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 Human Meizothrombin DESF1 Mutant S195A Bound with Ppack within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na802 b:79.8 occ:1.00	O	B:LYS224	2.3	85.6	1.0
	O	B:ARG221A	2.4	82.8	1.0
	O	B:TYR184A	2.4	72.2	1.0
	O	B:HOH905	2.4	58.7	1.0
	O	B:HOH907	2.4	69.6	1.0
	O	B:HOH904	2.6	65.6	1.0
	C	B:ARG221A	3.6	83.5	1.0
	C	B:LYS224	3.6	76.4	1.0
	C	B:TYR184A	3.7	70.1	1.0
	O	B:HOH917	4.0	61.9	1.0
	N	B:LYS224	4.1	78.5	1.0
	N	B:GLY223	4.3	80.1	1.0
	CA	B:ASP222	4.3	87.6	1.0
	N	B:TYR184A	4.3	77.2	1.0
	N	B:ASP222	4.4	78.0	1.0
	CD2	B:TYR225	4.4	78.9	1.0
	CE2	B:TYR225	4.4	74.3	1.0
	CA	B:LYS224	4.4	75.5	1.0
	N	B:ARG221A	4.5	87.8	1.0
	CA	B:TYR184A	4.6	70.5	1.0
	N	B:TYR225	4.6	71.9	1.0
	C	B:ASP222	4.6	85.6	1.0
	CA	B:ARG221A	4.7	84.3	1.0
	N	B:LYS185	4.7	74.7	1.0
	CG	B:TYR225	4.8	79.7	1.0
	CZ	B:TYR225	4.8	83.2	1.0
	CA	B:TYR225	4.8	66.7	1.0

Reference:

L.A.Pelc, S.K.Koester, Z.Chen, N.E.Gistover, E.Di Cera. Residues W215, E217 and E192 Control the Allosteric E*-E Equilibrium of Thrombin. Sci Rep V. 9 12304 2019.
ISSN: ESSN 2045-2322
PubMed: 31444378
DOI: 10.1038/S41598-019-48839-1

Page generated: Tue Oct 8 12:47:21 2024

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