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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 / Rfree (%) 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

Go back to 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

Go back to 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: Tue Dec 15 05:36:47 2020

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