Magnesium in PDB 7y1h: Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

Enzymatic activity of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

All present enzymatic activity of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1:
6.1.1.15; 6.1.1.17;

Protein crystallography data

The structure of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y1h was solved by S.Kim, I.Yoon, J.Son, S.Park, K.Y.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	37.90 / 1.99
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	71.698, 92.364, 87.504, 90, 108.2, 90
*R / R_free (%)*	20.7 / 24.3

Other elements in 7y1h:

The structure of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 (pdb code 7y1h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y1h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7y1h

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Magnesium Binding Sites List in 7y1h

Magnesium binding site 1 out of 4 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg2604 b:22.5 occ:1.00	O	A:HOH2773	2.2	31.2	1.0
	O2B	A:ATP2602	2.2	31.0	1.0
	O3G	A:ATP2602	2.3	34.6	1.0
	O	A:HOH2710	2.3	30.3	1.0
	O	A:HOH2786	2.4	33.3	1.0
	PB	A:ATP2602	3.4	35.1	1.0
	O3B	A:ATP2602	3.5	38.3	1.0
	PG	A:ATP2602	3.5	42.8	1.0
	NH1	A:ARG1163	3.9	28.3	1.0
	NH1	A:ARG1152	4.0	27.1	1.0
	O1G	A:ATP2602	4.4	46.7	1.0
	O1B	A:ATP2602	4.4	39.5	1.0
	OE2	A:GLU1154	4.5	34.9	1.0
	N	A:F992601	4.5	40.7	1.0
	N7	A:ATP2602	4.5	29.8	1.0
	O3A	A:ATP2602	4.5	32.8	1.0
	OE1	A:GLU1100	4.5	44.5	1.0
	O2G	A:ATP2602	4.7	39.1	1.0
	OE1	A:GLU1154	4.7	37.6	1.0
	C7	A:F992601	4.7	36.0	1.0
	OE2	A:GLU1100	4.7	54.7	1.0
	C8	A:ATP2602	4.9	32.6	1.0
	CE1	A:PHE1097	4.9	50.4	1.0

Magnesium binding site 2 out of 4 in 7y1h

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Magnesium Binding Sites List in 7y1h

Magnesium binding site 2 out of 4 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg2605 b:29.0 occ:1.00	O1B	A:ATP2602	2.3	39.5	1.0
	O1G	A:ATP2602	2.4	46.7	1.0
	NE2	A:GLN1237	2.7	37.6	1.0
	PB	A:ATP2602	3.4	35.1	1.0
	PG	A:ATP2602	3.5	42.8	1.0
	O3B	A:ATP2602	3.5	38.3	1.0
	CD	A:GLN1237	3.7	30.6	1.0
	OE1	A:GLN1237	3.8	45.3	1.0
	O2B	A:ATP2602	4.2	31.0	1.0
	O3G	A:ATP2602	4.3	34.6	1.0
	OE1	A:GLU1214	4.4	45.9	1.0
	O	A:GLU1214	4.5	41.6	1.0
	O3A	A:ATP2602	4.7	32.8	1.0
	O2G	A:ATP2602	4.7	39.1	1.0
	CE	A:LYS1210	4.8	41.3	1.0
	NZ	A:LYS1210	4.8	39.0	1.0

Magnesium binding site 3 out of 4 in 7y1h

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Magnesium Binding Sites List in 7y1h

Magnesium binding site 3 out of 4 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg2604 b:41.9 occ:1.00	O	B:HOH2713	2.3	52.3	1.0
	O2B	B:ATP2602	2.3	61.3	1.0
	O	B:HOH2722	2.6	46.0	1.0
	O3G	B:ATP2602	3.6	77.0	1.0
	PB	B:ATP2602	3.8	71.8	1.0
	N	B:F992601	4.0	39.2	1.0
	NH1	B:ARG1152	4.0	32.9	1.0
	O3B	B:ATP2602	4.2	72.7	1.0
	PG	B:ATP2602	4.3	76.4	1.0
	C7	B:F992601	4.4	35.4	1.0
	OE1	B:GLU1100	4.4	69.7	1.0
	CE1	B:PHE1097	4.4	61.5	1.0
	OE1	B:GLU1154	4.5	54.3	1.0
	NH1	B:ARG1163	4.5	58.6	1.0
	O1G	B:ATP2602	4.6	77.1	1.0
	OE2	B:GLU1100	4.6	69.5	1.0
	O3A	B:ATP2602	4.6	67.0	1.0
	OE2	B:GLU1154	4.6	56.8	1.0
	N7	B:ATP2602	4.7	49.6	1.0
	O1B	B:ATP2602	4.7	64.5	1.0
	CZ	B:PHE1097	4.7	56.5	1.0
	CD	B:ARG1152	4.8	35.7	1.0
	CD	B:GLU1100	4.9	71.7	1.0

Magnesium binding site 4 out of 4 in 7y1h

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Magnesium Binding Sites List in 7y1h

Magnesium binding site 4 out of 4 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg2605 b:80.9 occ:1.00	O1B	B:ATP2602	2.9	64.5	1.0
	OE1	B:GLU1214	3.2	59.7	1.0
	O1G	B:ATP2602	3.3	77.1	1.0
	NE2	B:GLN1237	3.5	49.2	1.0
	O	B:GLU1214	3.9	46.0	1.0
	PB	B:ATP2602	4.0	71.8	1.0
	O3B	B:ATP2602	4.2	72.7	1.0
	PG	B:ATP2602	4.3	76.4	1.0
	CD	B:GLU1214	4.4	59.0	1.0
	NZ	B:LYS1210	4.5	51.6	1.0
	CD	B:GLN1237	4.6	49.8	1.0
	CE	B:LYS1210	4.6	46.2	1.0
	O2B	B:ATP2602	4.6	61.3	1.0
	OE1	B:GLN1237	4.8	59.4	1.0
	O	B:HOH2775	4.8	38.7	1.0

Reference:

S.Kim, K.Hwang, I.Yoon. Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl-Trna Synthetase 1 To Be Published.

Page generated: Thu Oct 3 13:25:03 2024

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