Magnesium in PDB 4yes: Thrombin in Complex with (S)-(4-Chloro-2-((1-(5-Methyl-1H-Pyrrole-2- Carbonyl)Pyrrolidine-2-Carboxamido)Methyl)Phenyl)Methanaminium

Enzymatic activity of Thrombin in Complex with (S)-(4-Chloro-2-((1-(5-Methyl-1H-Pyrrole-2- Carbonyl)Pyrrolidine-2-Carboxamido)Methyl)Phenyl)Methanaminium

All present enzymatic activity of Thrombin in Complex with (S)-(4-Chloro-2-((1-(5-Methyl-1H-Pyrrole-2- Carbonyl)Pyrrolidine-2-Carboxamido)Methyl)Phenyl)Methanaminium:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with (S)-(4-Chloro-2-((1-(5-Methyl-1H-Pyrrole-2- Carbonyl)Pyrrolidine-2-Carboxamido)Methyl)Phenyl)Methanaminium, PDB code: 4yes was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	21.96 / 1.50
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	69.770, 71.190, 72.810, 90.00, 100.64, 90.00
*R / R_free (%)*	20.9 / 23.4

Other elements in 4yes:

The structure of Thrombin in Complex with (S)-(4-Chloro-2-((1-(5-Methyl-1H-Pyrrole-2- Carbonyl)Pyrrolidine-2-Carboxamido)Methyl)Phenyl)Methanaminium also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thrombin in Complex with (S)-(4-Chloro-2-((1-(5-Methyl-1H-Pyrrole-2- Carbonyl)Pyrrolidine-2-Carboxamido)Methyl)Phenyl)Methanaminium (pdb code 4yes). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Thrombin in Complex with (S)-(4-Chloro-2-((1-(5-Methyl-1H-Pyrrole-2- Carbonyl)Pyrrolidine-2-Carboxamido)Methyl)Phenyl)Methanaminium, PDB code: 4yes:

Magnesium binding site 1 out of 1 in 4yes

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Magnesium Binding Sites List in 4yes

Magnesium binding site 1 out of 1 in the Thrombin in Complex with (S)-(4-Chloro-2-((1-(5-Methyl-1H-Pyrrole-2- Carbonyl)Pyrrolidine-2-Carboxamido)Methyl)Phenyl)Methanaminium

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thrombin in Complex with (S)-(4-Chloro-2-((1-(5-Methyl-1H-Pyrrole-2- Carbonyl)Pyrrolidine-2-Carboxamido)Methyl)Phenyl)Methanaminium within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg701 b:26.6 occ:1.00	O	B:ARG596	2.3	27.0	1.0
	O	B:LYS599	2.4	22.6	1.0
	O	B:HOH952	2.4	27.4	1.0
	O	B:HOH874	2.4	28.3	1.0
	O	B:HOH889	2.5	24.1	1.0
	O	B:HOH865	2.7	26.9	1.0
	C	B:ARG596	3.4	29.9	1.0
	C	B:LYS599	3.4	23.3	1.0
	N	B:LYS599	3.8	23.4	1.0
	N	B:ARG596	3.8	25.7	1.0
	O	B:HOH935	3.9	26.1	1.0
	O	B:HOH864	4.0	30.4	1.0
	C	B:ASP595	4.0	28.2	1.0
	O	B:TYR553	4.1	26.2	1.0
	CA	B:LYS599	4.1	21.0	1.0
	O	B:HOH879	4.2	24.2	1.0
	N	B:ASP597	4.2	26.8	1.0
	CA	B:ARG596	4.2	25.9	1.0
	CA	B:ASP597	4.3	27.0	1.0
	N	B:GLY598	4.3	28.0	1.0
	CA	B:ASP595	4.4	23.0	1.0
	N	B:TYR600	4.4	20.8	1.0
	CB	B:LYS599	4.5	23.0	1.0
	C	B:ASP597	4.6	29.8	1.0
	O	B:ASP595	4.6	27.9	1.0
	CA	B:TYR600	4.6	20.9	1.0
	OD1	B:ASP595	4.6	29.6	1.0
	C	B:GLY598	4.8	27.6	1.0
	O	B:HOH853	5.0	27.9	1.0

Reference:

H.R.Chobanian, B.Pio, Y.Guo, H.Shen, M.A.Huffman, M.Madeira, G.Salituro, J.L.Terebetski, J.Ormes, N.Jochnowitz, L.Hoos, Y.Zhou, D.Lewis, B.Hawes, L.Mitnaul, K.O'neill, K.Ellsworth, L.Wang, T.Biftu, J.L.Duffy. Improved Stability of Proline-Derived Direct Thrombin Inhibitors Through Hydroxyl to Heterocycle Replacement. Acs Med.Chem.Lett. V. 6 553 2015.
ISSN: ISSN 1948-5875
PubMed: 26005532
DOI: 10.1021/ACSMEDCHEMLETT.5B00047

Page generated: Sat Sep 28 23:15:17 2024

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