Magnesium in PDB 4elv: Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines

Enzymatic activity of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines

All present enzymatic activity of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines:
2.7.7.7;

Protein crystallography data

The structure of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines, PDB code: 4elv was solved by A.Marx, K.Diederichs, S.Obeid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	47.29 / 1.90
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	109.213, 109.213, 91.047, 90.00, 90.00, 120.00
*R / R_free (%)*	17.6 / 21.6

Other elements in 4elv:

The structure of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines (pdb code 4elv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines, PDB code: 4elv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4elv

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Magnesium Binding Sites List in 4elv

Magnesium binding site 1 out of 3 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg901 b:42.4 occ:1.00	O	A:HOH1196	2.0	44.3	1.0
	O	A:HOH1048	2.1	31.0	1.0
	O	A:HOH1129	2.1	43.5	1.0
	OE2	A:GLU786	2.1	30.3	0.5
	O	A:HOH1019	2.1	29.8	1.0
	OD2	A:ASP610	2.2	31.6	1.0
	CG	A:ASP610	3.1	36.0	1.0
	CD	A:GLU786	3.1	34.6	0.5
	OD1	A:ASP610	3.4	41.6	1.0
	O11	A:0R7902	3.5	28.6	1.0
	O	A:HOH1199	3.6	88.9	1.0
	CG	A:GLU786	3.6	27.6	0.5
	O	A:HOH1200	4.0	44.8	1.0
	CA	A:CA908	4.1	26.9	1.0
	OD1	A:ASP785	4.2	26.6	1.0
	OE1	A:GLU786	4.3	36.3	0.5
	O7	A:0R7902	4.4	32.7	1.0
	O	A:HOH1225	4.4	60.5	1.0
	CB	A:ASP610	4.5	24.8	1.0
	O10	A:0R7902	4.6	39.2	1.0
	P1	A:0R7902	4.6	29.9	1.0
	OP1	B:0R8112	4.8	28.4	1.0
	C5'	B:0R8112	4.8	27.2	1.0
	C3'	B:0R8112	4.8	25.5	1.0
	OD2	A:ASP785	4.9	36.0	1.0
	O5'	B:0R8112	4.9	25.4	1.0
	OE1	A:GLU786	4.9	49.6	0.5
	CG	A:ASP785	5.0	30.0	1.0
	NZ	A:LYS663	5.0	35.8	1.0

Magnesium binding site 2 out of 3 in 4elv

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Magnesium Binding Sites List in 4elv

Magnesium binding site 2 out of 3 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg201 b:67.8 occ:1.00	O	B:HOH337	2.2	34.6	1.0
	O	B:HOH338	2.2	69.9	1.0
	O	B:HOH335	2.2	20.2	1.0
	O	C:HOH444	2.2	82.0	1.0
	O	B:HOH336	2.2	39.7	1.0
	O	C:HOH437	2.9	67.6	1.0
	O6	B:DG108	4.1	16.9	1.0
	O	B:HOH316	4.1	31.6	1.0
	N7	B:DG107	4.3	16.0	1.0
	O6	B:DG107	4.4	12.5	1.0
	O	C:HOH430	4.4	34.7	1.0
	O	C:HOH409	4.5	24.6	1.0
	N4	C:DC209	4.6	14.9	1.0
	O	B:HOH315	4.8	33.4	1.0
	C5	B:DC106	4.9	18.9	1.0

Magnesium binding site 3 out of 3 in 4elv

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Magnesium Binding Sites List in 4elv

Magnesium binding site 3 out of 3 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg302 b:75.7 occ:1.00	O	C:HOH440	2.2	42.4	1.0
	O	C:HOH442	2.2	63.2	1.0
	O	C:HOH439	2.2	0.8	1.0
	O	C:HOH441	2.2	45.5	1.0
	O	C:HOH443	2.2	51.2	1.0
	O6	C:DG214	3.5	29.7	1.0
	O	B:HOH330	3.5	49.1	1.0
	N7	C:DG213	3.8	28.6	1.0
	N7	C:DG214	4.1	27.7	1.0
	O6	C:DG213	4.3	25.3	1.0
	C6	C:DG214	4.4	23.4	1.0
	C5	C:DG213	4.6	22.9	1.0
	C5	C:DG214	4.6	24.8	1.0
	C8	C:DG213	4.7	29.9	1.0
	C6	C:DG213	4.8	19.0	1.0
	O	C:HOH427	4.9	37.4	1.0

Reference:

S.Obeid, H.Bu Kamp, W.Welte, K.Diederichs, A.Marx. Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines To Be Published.

Page generated: Mon Dec 14 14:09:03 2020

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