Calcium in PDB 1po7: High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida

Enzymatic activity of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida

All present enzymatic activity of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida:
4.1.1.7;

Protein crystallography data

The structure of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 1po7 was solved by A.K.Bera, M.S.Hasson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.00 / 1.20
*Space group*	I 2 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	81.127, 95.543, 137.388, 90.00, 90.00, 90.00
*R / R_free (%)*	11.3 / 14.3

Other elements in 1po7:

The structure of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida (pdb code 1po7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 1po7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1po7

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Calcium Binding Sites List in 1po7

Calcium binding site 1 out of 3 in the High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca532 b:10.6 occ:0.74	OD1	A:ASN455	2.0	15.2	0.9
	OD1	A:ASP428	2.2	14.7	1.0
	O	A:THR457	2.2	11.3	1.0
	O12	A:TZD530	2.2	10.7	1.0
	O	A:HOH535	2.2	14.0	1.0
	O21	A:TZD530	2.2	10.2	1.0
	CG	A:ASN455	3.0	15.3	1.0
	CG	A:ASP428	3.3	10.9	1.0
	P1	A:TZD530	3.4	9.9	1.0
	C	A:THR457	3.4	11.4	1.0
	P2	A:TZD530	3.5	10.1	1.0
	ND2	A:ASN455	3.5	19.7	1.0
	O11	A:TZD530	3.5	9.7	1.0
	OD2	A:ASP428	3.9	16.0	1.0
	N	A:THR457	3.9	11.9	1.0
	N	A:ASP428	4.1	10.0	1.0
	O5G	A:TZD530	4.1	10.1	1.0
	N	A:GLY459	4.1	10.2	1.0
	N	A:GLY429	4.2	9.4	1.0
	O	A:MET453	4.2	12.2	1.0
	CB	A:ASN455	4.2	16.9	1.0
	CA	A:THR457	4.3	11.5	1.0
	O22	A:TZD530	4.3	10.6	1.0
	N	A:TYR458	4.4	10.2	1.0
	N	A:ASN455	4.4	13.2	1.0
	O	A:HOH542	4.4	12.0	1.0
	CB	A:ASP428	4.5	10.5	1.0
	CG2	A:THR457	4.5	14.0	1.0
	O13	A:TZD530	4.6	10.1	1.0
	CA	A:TYR458	4.6	9.6	1.0
	O23	A:TZD530	4.6	10.1	1.0
	N	A:GLY456	4.7	12.1	1.0
	CA	A:ASN455	4.7	14.4	1.0
	CA	A:GLY427	4.8	10.0	1.0
	CA	A:ASP428	4.8	9.9	1.0
	C	A:ASN455	4.8	14.2	1.0
	C	A:GLY427	4.8	9.2	1.0
	C	A:TYR458	4.9	9.8	1.0
	C	A:ASP428	5.0	9.3	1.0
	CA	A:GLY459	5.0	11.7	1.0

Calcium binding site 2 out of 3 in 1po7

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Calcium Binding Sites List in 1po7

Calcium binding site 2 out of 3 in the High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca533 b:19.5 occ:0.88	OD1	A:ASP364	2.4	19.6	1.0
	O	A:HOH692	2.4	17.8	1.0
	O	A:HOH1115	2.8	32.0	0.8
	O	A:HOH851	3.2	27.8	0.7
	CG	A:ASP364	3.4	18.8	1.0
	OD2	A:ASP364	3.8	22.3	1.0
	O	A:ASP360	4.5	13.5	1.0
	O	A:HOH710	4.6	27.8	0.5
	O	A:HOH695	4.7	26.2	0.7
	CB	A:ASP364	4.7	16.8	1.0
	O	A:HOH682	4.8	16.0	1.0
	ND2	A:ASN363	4.8	17.4	1.0

Calcium binding site 3 out of 3 in 1po7

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Calcium Binding Sites List in 1po7

Calcium binding site 3 out of 3 in the High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca534 b:12.0 occ:0.71	O	A:ALA416	2.3	12.1	1.0
	O	A:HOH994	2.4	28.1	0.8
	O	A:HOH713	2.5	16.6	1.0
	O	A:HOH1014	2.5	20.9	0.7
	O	A:HOH702	2.5	17.2	1.0
	C	A:ALA416	3.4	11.4	1.0
	CA	A:ALA416	4.0	10.3	1.0
	O	A:HOH852	4.2	27.0	0.8
	CD	A:PRO418	4.4	13.6	1.0
	N	A:GLU417	4.6	11.4	1.0
	O	A:HOH919	4.6	32.9	0.5
	O	A:HOH703	4.6	21.0	0.7
	O	A:HOH727	4.6	17.3	0.9
	CB	A:ALA416	4.7	11.3	1.0
	OG	A:SER61	4.7	10.5	0.7
	O	A:LEU415	4.8	11.6	1.0
	CA	A:GLU417	5.0	11.0	1.0

Reference:

A.K.Bera, N.L.Anderson, M.S.Hasson. High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase From Pseudomonas Putida To Be Published.

Page generated: Sat Dec 12 03:14:19 2020

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