Sodium in PDB 5m4l: Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand

Enzymatic activity of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand

All present enzymatic activity of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand:
3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand, PDB code: 5m4l was solved by P.Wilk, M.S.Weiss, U.Mueller, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	46.75 / 1.49
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	103.605, 106.839, 216.990, 90.00, 90.00, 90.00
*R / R_free (%)*	14.6 / 17.1

Other elements in 5m4l:

The structure of Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand (pdb code 5m4l). 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 Wild-Type Human Prolidase with Mg Ions and Leupro Ligand, PDB code: 5m4l:

Sodium binding site 1 out of 1 in 5m4l

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Sodium Binding Sites List in 5m4l

Sodium binding site 1 out of 1 in the Crystal Structure of Wild-Type Human Prolidase with Mg Ions and Leupro Ligand

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 Wild-Type Human Prolidase with Mg Ions and Leupro Ligand within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na509 b:37.0 occ:1.00	O	B:HOH729	2.3	46.3	1.0
	O	B:HOH1023	2.4	40.8	1.0
	O	B:HOH1032	2.5	54.8	1.0
	O	B:MET479	2.5	34.0	1.0
	O	B:HOH786	2.5	22.1	1.0
	O	B:LYS211	2.6	23.1	1.0
	O	B:HOH1019	3.5	58.9	1.0
	C	B:LYS211	3.6	22.5	1.0
	O	B:HOH1068	3.7	36.0	1.0
	C	B:MET479	3.7	30.4	1.0
	CA	B:LYS211	4.1	22.2	1.0
	O	B:VAL213	4.4	23.4	1.0
	CA	B:MET479	4.4	25.9	1.0
	O	B:MET210	4.4	21.5	1.0
	O	B:GLY481	4.5	58.4	1.0
	N	B:ALA212	4.7	21.8	1.0
	N	B:ALA480	4.7	30.4	1.0
	CA	B:ALA480	4.9	32.7	1.0
	CB	B:LYS211	4.9	25.2	1.0
	CB	B:MET479	5.0	22.3	1.0

Reference:

P.Wilk, M.Uehlein, J.Kalms, H.Dobbek, U.Mueller, M.S.Weiss. Substrate Specificity and Reaction Mechanism of Human Prolidase. Febs J. V. 284 2870 2017.
ISSN: ISSN 1742-4658
PubMed: 28677335
DOI: 10.1111/FEBS.14158

Page generated: Mon Oct 7 22:28:54 2024

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