Magnesium in PDB 7y3s: 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: 7y3s 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)*	41.25 / 2.60
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	71.897, 92.017, 87.326, 90, 108.16, 90
*R / R_free (%)*	20.3 / 25

Other elements in 7y3s:

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

Bromine	(Br)	2 atoms
Zinc	(Zn)	1 atom

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 7y3s). 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: 7y3s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7y3s

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Magnesium Binding Sites List in 7y3s

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:Mg2603 b:21.6 occ:1.00	O1B	A:ATP2602	2.6	26.9	1.0
	O1G	A:ATP2602	2.9	31.5	1.0
	O2B	A:ATP2602	3.4	62.0	1.0
	PB	A:ATP2602	3.4	44.1	1.0
	OE2	A:GLU1154	3.7	47.1	1.0
	NH1	A:ARG1152	3.8	34.3	1.0
	O3B	A:ATP2602	3.9	112.5	1.0
	PG	A:ATP2602	4.0	59.0	1.0
	OE1	A:GLU1100	4.2	39.8	1.0
	N1	A:F9C2601	4.3	39.4	1.0
	CE1	A:PHE1097	4.3	42.0	1.0
	NH1	A:ARG1163	4.3	31.4	1.0
	OE2	A:GLU1100	4.4	37.5	1.0
	OE1	A:GLU1154	4.4	45.4	1.0
	CD	A:GLU1154	4.5	40.9	1.0
	C6	A:F9C2601	4.7	41.7	1.0
	N7	A:ATP2602	4.7	23.8	1.0
	CD	A:GLU1100	4.8	38.8	1.0
	CD	A:ARG1152	4.8	30.6	1.0
	CZ	A:ARG1152	4.9	35.7	1.0
	O3A	A:ATP2602	4.9	36.8	1.0
	O3G	A:ATP2602	4.9	34.1	1.0
	CZ	A:PHE1097	5.0	43.0	1.0
	O2G	A:ATP2602	5.0	73.4	1.0

Magnesium binding site 2 out of 4 in 7y3s

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Magnesium Binding Sites List in 7y3s

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:Mg2604 b:28.8 occ:1.00	O2G	A:ATP2602	2.5	73.4	1.0
	O3B	A:ATP2602	2.7	112.5	1.0
	OE1	A:GLN1237	2.9	39.7	1.0
	PG	A:ATP2602	3.2	59.0	1.0
	PB	A:ATP2602	3.7	44.1	1.0
	CD	A:GLN1237	3.9	31.9	1.0
	O3A	A:ATP2602	4.0	36.8	1.0
	O1B	A:ATP2602	4.1	26.9	1.0
	NE2	A:GLN1237	4.1	35.4	1.0
	O1G	A:ATP2602	4.3	31.5	1.0
	OE1	A:GLU1214	4.3	58.2	1.0
	O3G	A:ATP2602	4.3	34.1	1.0
	O	A:GLU1214	4.6	65.4	1.0
	O2B	A:ATP2602	4.9	62.0	1.0

Magnesium binding site 3 out of 4 in 7y3s

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Magnesium Binding Sites List in 7y3s

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:40.5 occ:1.00	O2B	B:ATP2602	2.2	53.9	1.0
	O	B:HOH2719	2.4	33.4	1.0
	O3G	B:ATP2602	3.1	74.7	1.0
	PB	B:ATP2602	3.5	69.7	1.0
	O3B	B:ATP2602	3.7	73.2	1.0
	PG	B:ATP2602	3.7	69.3	1.0
	O1G	B:ATP2602	3.8	75.9	1.0
	NH1	B:ARG1163	4.1	50.7	1.0
	O1B	B:ATP2602	4.2	58.8	1.0
	OE2	B:GLU1154	4.3	56.4	1.0
	NH1	B:ARG1152	4.4	41.7	1.0
	OE2	B:GLU1100	4.4	61.2	1.0
	OE1	B:GLU1154	4.4	56.6	1.0
	N7	B:ATP2602	4.5	40.0	1.0
	O3A	B:ATP2602	4.7	64.1	1.0
	N1	B:F9C2601	4.8	41.1	1.0
	CD	B:GLU1154	4.8	58.0	1.0
	CE1	B:PHE1097	4.8	45.9	1.0
	C8	B:ATP2602	4.9	49.4	1.0
	NZ	B:LYS1156	4.9	68.2	1.0
	OE1	B:GLU1100	5.0	55.3	1.0

Magnesium binding site 4 out of 4 in 7y3s

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Magnesium Binding Sites List in 7y3s

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:53.6 occ:1.00	O1B	B:ATP2602	2.5	58.8	1.0
	OE1	B:GLU1214	3.0	53.0	1.0
	O	B:HOH2709	3.0	38.1	1.0
	NE2	B:GLN1237	3.3	39.0	1.0
	O1G	B:ATP2602	3.5	75.9	1.0
	PB	B:ATP2602	3.8	69.7	1.0
	CE	B:LYS1210	4.0	49.3	1.0
	O3B	B:ATP2602	4.0	73.2	1.0
	O	B:GLU1214	4.1	45.1	1.0
	CD	B:GLU1214	4.1	59.4	1.0
	PG	B:ATP2602	4.3	69.3	1.0
	NZ	B:LYS1210	4.3	49.8	1.0
	CD	B:GLN1237	4.4	38.1	1.0
	CD	B:LYS1210	4.4	46.8	1.0
	OE1	B:GLN1237	4.6	45.0	1.0
	OE2	B:GLU1214	4.7	65.9	1.0
	O2B	B:ATP2602	4.8	53.9	1.0
	O3A	B:ATP2602	4.9	64.1	1.0
	O2G	B:ATP2602	4.9	59.6	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 Aug 14 18:58:54 2025

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