Calcium in PDB 2b01: Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate

Enzymatic activity of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate

All present enzymatic activity of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate, PDB code: 2b01 was solved by Y.H.Pan, B.J.Bahnson, M.K.Jain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	27.08 / 2.20
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	68.346, 68.346, 67.070, 90.00, 90.00, 120.00
*R / R_free (%)*	20.3 / 23.3

Other elements in 2b01:

The structure of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate (pdb code 2b01). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate, PDB code: 2b01:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2b01

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Calcium Binding Sites List in 2b01

Calcium binding site 1 out of 3 in the Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca130 b:35.9 occ:1.00	O	A:HOH213	2.3	42.8	1.0
	OD1	A:ASP49	2.3	31.8	1.0
	O	A:GLY30	2.3	35.8	1.0
	O	A:TYR28	2.3	33.4	1.0
	O	A:GLY32	2.4	36.6	1.0
	O	A:HOH156	2.5	31.6	1.0
	OD2	A:ASP49	2.6	32.3	1.0
	CG	A:ASP49	2.8	32.0	1.0
	C	A:GLY32	3.5	36.2	1.0
	C	A:TYR28	3.5	33.7	1.0
	C	A:GLY30	3.5	35.4	1.0
	N	A:GLY32	3.7	38.2	1.0
	N	A:GLY30	3.8	33.8	1.0
	O	A:HOH235	4.0	41.2	1.0
	CA	A:GLY32	4.1	36.3	1.0
	CA	A:TYR28	4.2	31.6	1.0
	C	A:LEU31	4.2	37.9	1.0
	O	A:HOH154	4.2	35.9	1.0
	CB	A:ASP49	4.3	30.9	1.0
	CA	A:GLY30	4.3	34.4	1.0
	O	A:HOH155	4.4	31.6	1.0
	N	A:LEU31	4.5	36.8	1.0
	CL	A:CL133	4.5	34.3	1.0
	N	A:CYS29	4.5	33.6	1.0
	N	A:GLY33	4.6	36.4	1.0
	CA	A:LEU31	4.6	37.6	1.0
	CB	A:TYR28	4.6	30.9	1.0
	O	A:HOH182	4.6	41.6	1.0
	C	A:CYS29	4.6	33.5	1.0
	CA	A:CYS29	4.7	33.5	1.0
	CD1	A:TYR28	4.8	29.9	1.0
	O	A:CYS45	4.9	34.5	1.0
	O	A:LEU31	4.9	38.3	1.0
	CA	A:GLY33	4.9	35.1	1.0

Calcium binding site 2 out of 3 in 2b01

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Calcium Binding Sites List in 2b01

Calcium binding site 2 out of 3 in the Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca131 b:13.0 occ:0.50	OE1	A:GLU71	2.3	30.9	1.0
	OE1	A:GLU92	2.3	32.2	1.0
	O	A:SER72	2.4	28.2	1.0
	CD	A:GLU92	3.3	30.1	1.0
	CD	A:GLU71	3.4	29.4	1.0
	C	A:SER72	3.4	28.5	1.0
	N	A:SER72	3.5	28.7	1.0
	CG	A:GLU92	3.7	30.0	1.0
	O	A:HOH146	3.8	24.4	1.0
	CA	A:SER72	3.9	28.4	1.0
	CB	A:SER72	4.0	28.8	1.0
	OE2	A:GLU71	4.1	30.3	1.0
	CG	A:GLU71	4.4	27.1	1.0
	C	A:GLU71	4.4	28.8	1.0
	OE2	A:GLU92	4.4	33.8	1.0
	N	A:TYR73	4.6	28.5	1.0
	CA	A:GLU71	4.7	29.0	1.0
	OG	A:SER72	5.0	28.9	1.0

Calcium binding site 3 out of 3 in 2b01

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Calcium Binding Sites List in 2b01

Calcium binding site 3 out of 3 in the Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca132 b:30.0 occ:0.50	O	A:LYS62	2.2	37.8	1.0
	CL	A:CL135	2.6	18.9	0.5
	O	A:HOH138	2.9	38.4	1.0
	CL	A:CL134	3.0	61.6	1.0
	C	A:LYS62	3.4	38.5	1.0
	CB	A:LYS62	4.0	42.0	1.0
	CA	A:LYS62	4.2	39.7	1.0
	N	A:LYS62	4.2	38.5	1.0
	N	A:PHE63	4.5	37.9	1.0
	CA	A:PHE63	4.7	36.3	1.0
	CG	A:LYS62	4.7	45.0	1.0

Reference:

Y.H.Pan, B.J.Bahnson. Structural Basis For Bile Salt Inhibition of Pancreatic Phospholipase A2. J.Mol.Biol. V. 369 439 2007.
ISSN: ISSN 0022-2836
PubMed: 17434532
DOI: 10.1016/J.JMB.2007.03.034

Page generated: Fri Jul 12 08:54:25 2024

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