Sodium in PDB 1u4j: Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution

Enzymatic activity of Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution

All present enzymatic activity of Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution, PDB code: 1u4j was solved by G.Singh, S.Gourinath, S.Sharma, S.Bhanumathi, C.Betzel, A.Srinivasan, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	14.26 / 2.18
*Space group*	H 3
*Cell size a, b, c (Å), α, β, γ (°)*	80.360, 80.360, 99.440, 90.00, 90.00, 120.00
*R / R_free (%)*	19.4 / 22

Other elements in 1u4j:

The structure of Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution (pdb code 1u4j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution, PDB code: 1u4j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1u4j

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Sodium Binding Sites List in 1u4j

Sodium binding site 1 out of 2 in the Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1002 b:43.8 occ:1.00	OD1	A:ASP49	2.5	45.2	1.0
	O	A:TYR28	2.5	23.4	1.0
	O	A:GLY30	2.5	36.3	1.0
	O	A:GLY32	2.5	39.5	1.0
	CG	A:ASP49	3.1	37.7	1.0
	O6	B:MAN1008	3.1	26.2	0.8
	OD2	A:ASP49	3.2	43.8	1.0
	N	A:GLY32	3.4	39.2	1.0
	C	A:GLY32	3.4	38.0	1.0
	C	A:TYR31	3.5	39.4	1.0
	C	A:GLY30	3.6	34.7	1.0
	C	A:TYR28	3.6	22.6	1.0
	O	A:HOH1067	3.6	56.5	1.0
	CA	A:GLY32	3.7	38.2	1.0
	O	A:TYR31	3.8	42.7	1.0
	CA	A:TYR31	4.1	38.5	1.0
	C6	B:MAN1008	4.2	25.0	0.8
	N	A:GLY30	4.2	27.7	1.0
	CA	A:TYR28	4.2	22.6	1.0
	N	A:TYR31	4.2	36.6	1.0
	CB	A:ASP49	4.4	30.9	1.0
	C	A:CYS29	4.5	23.9	1.0
	N	A:CYS29	4.6	21.0	1.0
	CA	A:GLY30	4.6	31.4	1.0
	CB	A:TYR28	4.6	22.2	1.0
	O	A:HOH1097	4.6	40.1	1.0
	N	A:GLY33	4.7	36.8	1.0
	CA	A:CYS29	4.7	21.5	1.0
	OH	B:TYR31	4.9	47.3	1.0
	O	A:CYS45	4.9	17.8	1.0

Sodium binding site 2 out of 2 in 1u4j

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Sodium Binding Sites List in 1u4j

Sodium binding site 2 out of 2 in the Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Carbohydrate Induced Dimer of Group I Phospholipase A2 From Bungarus Caeruleus at 2.1 A Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na1001 b:33.6 occ:1.00	O	B:GLY30	2.3	33.5	1.0
	O	B:TYR28	2.5	23.2	1.0
	OD1	B:ASP49	2.5	43.7	1.0
	O	B:GLY32	2.6	36.6	1.0
	OD2	B:ASP49	2.8	42.6	1.0
	CG	B:ASP49	2.9	37.4	1.0
	O1	B:MAN1008	3.3	24.0	0.8
	C	B:TYR31	3.4	39.6	1.0
	N	B:GLY32	3.4	38.5	1.0
	C	B:GLY32	3.4	37.2	1.0
	C	B:GLY30	3.5	34.1	1.0
	C	B:TYR28	3.5	21.5	1.0
	O	B:TYR31	3.6	43.6	1.0
	CA	B:GLY32	3.7	36.7	1.0
	CA	B:TYR31	4.1	38.5	1.0
	N	B:GLY30	4.1	26.3	1.0
	C1	B:MAN1008	4.2	21.9	0.8
	CA	B:TYR28	4.2	22.2	1.0
	N	B:TYR31	4.3	36.9	1.0
	CB	B:ASP49	4.3	28.5	1.0
	C	B:CYS29	4.4	23.8	1.0
	N	B:CYS29	4.5	21.4	1.0
	CA	B:GLY30	4.5	30.6	1.0
	CB	B:TYR28	4.6	19.8	1.0
	CA	B:CYS29	4.7	20.7	1.0
	N	B:GLY33	4.7	36.8	1.0
	C2	B:MAN1008	4.7	24.2	0.8
	O	B:CYS45	4.9	17.7	1.0
	CD2	B:TYR28	5.0	22.9	1.0
	O	B:CYS29	5.0	27.4	1.0

Reference:

G.Singh, S.Gourinath, K.Sarvanan, S.Sharma, S.Bhanumathi, C.Betzel, S.Yadav, A.Srinivasan, T.P.Singh. Crystal Structure of A Carbohydrate Induced Homodimer of Phospholipase A(2) From Bungarus Caeruleus at 2.1A Resolution J.Struct.Biol. V. 149 264 2005.
ISSN: ISSN 1047-8477
PubMed: 15721580
DOI: 10.1016/J.JSB.2004.11.011

Page generated: Sun Oct 6 22:42:57 2024

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