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Barium in PDB 3ulg: Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium

Protein crystallography data

The structure of Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium, PDB code: 3ulg was solved by S.Kumar, S.Gourinath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.20
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 95.210, 95.210, 62.986, 90.00, 90.00, 120.00
R / Rfree (%) 24.7 / 31.4

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium (pdb code 3ulg). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 6 binding sites of Barium where determined in the Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium, PDB code: 3ulg:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6;

Barium binding site 1 out of 6 in 3ulg

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Barium binding site 1 out of 6 in the Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba135

b:1.0
occ:1.00
OD1 A:ASN12 2.2 98.0 1.0
O A:HOH147 2.7 88.6 1.0
O A:ALA16 2.7 91.3 1.0
OD1 A:ASP14 2.8 99.0 1.0
CG A:ASN12 3.0 0.1 1.0
OD1 A:ASP10 3.0 89.4 1.0
OE1 A:GLU21 3.1 0.6 1.0
OE2 A:GLU21 3.1 0.9 1.0
ND2 A:ASN12 3.3 86.1 1.0
CG A:ASP14 3.3 0.3 1.0
OD2 A:ASP14 3.3 0.6 1.0
CD A:GLU21 3.4 0.2 1.0
C A:ALA16 3.6 0.8 1.0
CG A:ASP10 4.1 0.5 1.0
CB A:ASN12 4.3 0.1 1.0
CB A:ALA16 4.3 74.4 1.0
CA A:ALA16 4.3 92.5 1.0
N A:ALA16 4.4 93.3 1.0
N A:VAL17 4.4 0.9 1.0
CA A:VAL17 4.5 0.9 1.0
N A:SER18 4.5 0.7 1.0
N A:ASP14 4.5 0.5 1.0
CB A:ASP14 4.5 0.8 1.0
CA A:ASP10 4.6 0.6 1.0
N A:ASN12 4.7 0.4 1.0
N A:GLY13 4.7 0.3 1.0
CB A:ASP10 4.8 0.5 1.0
CG A:GLU21 4.8 0.3 1.0
C A:ASP10 4.9 0.6 1.0
CA A:ASN12 4.9 0.4 1.0
CA A:ASP14 5.0 97.0 1.0
C A:VAL17 5.0 0.9 1.0

Barium binding site 2 out of 6 in 3ulg

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Barium binding site 2 out of 6 in the Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba136

b:98.7
occ:0.50
O A:GLU52 2.5 95.0 1.0
OD1 A:ASP48 2.6 89.9 1.0
OD2 A:ASP48 2.6 0.7 1.0
OE1 A:GLU57 2.7 0.8 1.0
OD1 A:ASN50 2.7 83.0 1.0
OE2 A:GLU57 2.8 1.0 1.0
ND2 A:ASN50 2.8 95.9 1.0
CG A:ASP48 2.9 0.2 1.0
CG A:ASN50 2.9 95.2 1.0
OD1 A:ASP46 3.0 94.4 1.0
CD A:GLU57 3.0 0.8 1.0
OD2 A:ASP54 3.7 1.0 1.0
C A:GLU52 3.8 0.2 1.0
CG A:ASP46 3.8 0.1 1.0
CB A:ASN50 4.2 0.4 1.0
CA A:ILE53 4.3 0.8 1.0
CB A:ASP48 4.4 0.8 1.0
N A:ASP54 4.4 0.1 1.0
CG A:GLU57 4.5 98.5 1.0
N A:ASN50 4.5 0.4 1.0
N A:ILE53 4.5 0.4 1.0
CB A:ASP46 4.5 0.6 1.0
OD2 A:ASP46 4.5 0.9 1.0
CG A:ASP54 4.5 0.0 1.0
CA A:ASP46 4.6 0.9 1.0
N A:ASP48 4.6 0.8 1.0
N A:GLU52 4.7 0.3 1.0
N A:ALA47 4.8 0.3 1.0
CA A:GLU52 4.8 0.7 1.0
C A:ILE53 4.8 0.3 1.0
CA A:ASN50 4.9 0.9 1.0
CA A:ASP48 4.9 0.8 1.0
CG A:GLU52 4.9 0.3 1.0
C A:ASP46 5.0 0.1 1.0

Barium binding site 3 out of 6 in 3ulg

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Barium binding site 3 out of 6 in the Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba137

b:0.2
occ:0.50
O A:HOH145 2.7 73.2 1.0
O A:ASP46 2.8 1.0 1.0
O A:LYS43 2.9 0.8 1.0
O A:HOH140 3.4 87.8 1.0
O A:ALA47 3.4 0.6 1.0
O A:HOH141 3.7 98.8 1.0
O A:HOH138 3.8 77.0 1.0
C A:ASP46 4.0 0.1 1.0
C A:LYS43 4.0 1.0 1.0
C A:ALA47 4.0 0.3 1.0
CA A:ALA47 4.1 0.4 1.0
N A:GLY49 4.3 96.9 1.0
CB A:LYS43 4.5 0.7 1.0
N A:ALA47 4.5 0.3 1.0
CA A:LYS43 4.6 0.4 1.0
CA A:GLY49 4.6 0.1 1.0

Barium binding site 4 out of 6 in 3ulg

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Barium binding site 4 out of 6 in the Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba135

b:0.9
occ:1.00
OD1 B:ASN12 2.4 0.5 1.0
O B:ALA16 2.4 75.1 1.0
OD1 B:ASP10 2.7 87.6 1.0
OE2 B:GLU21 2.8 0.4 1.0
OD1 B:ASP14 2.8 0.9 1.0
O B:HOH144 2.9 0.0 1.0
OE1 B:GLU21 3.1 0.9 1.0
CG B:ASN12 3.2 0.6 1.0
CD B:GLU21 3.3 0.5 1.0
C B:ALA16 3.3 96.6 1.0
ND2 B:ASN12 3.4 0.0 1.0
CG B:ASP10 3.5 0.9 1.0
CG B:ASP14 3.5 0.2 1.0
OD2 B:ASP14 3.7 0.6 1.0
N B:VAL17 4.1 0.9 1.0
CA B:ALA16 4.1 96.3 1.0
CB B:ALA16 4.1 82.0 1.0
CA B:VAL17 4.2 0.9 1.0
CB B:ASP10 4.3 0.4 1.0
CA B:ASP10 4.3 0.1 1.0
OD2 B:ASP10 4.3 0.8 1.0
N B:SER18 4.3 0.8 1.0
N B:ALA16 4.3 95.7 1.0
N B:ASP14 4.6 95.0 1.0
CB B:ASN12 4.6 0.5 1.0
C B:ASP10 4.6 0.0 1.0
N B:ASN12 4.7 0.8 1.0
CG B:GLU21 4.7 0.8 1.0
N B:GLY13 4.7 0.1 1.0
C B:VAL17 4.8 0.9 1.0
N B:VAL11 4.8 0.1 1.0
CB B:ASP14 4.8 0.6 1.0

Barium binding site 5 out of 6 in 3ulg

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Barium binding site 5 out of 6 in the Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba136

b:97.5
occ:0.50
OE1 B:GLU57 2.3 0.2 1.0
OD2 B:ASP48 2.4 0.4 1.0
OD1 B:ASP48 2.5 79.9 1.0
O B:GLU52 2.5 0.1 1.0
OD1 B:ASP46 2.7 83.8 1.0
CG B:ASP48 2.7 0.6 1.0
OE2 B:GLU57 2.8 99.0 1.0
OD1 B:ASN50 2.8 82.2 1.0
CD B:GLU57 2.9 0.7 1.0
CG B:ASN50 3.1 92.2 1.0
ND2 B:ASN50 3.1 0.6 1.0
CG B:ASP46 3.6 0.5 1.0
C B:GLU52 3.7 0.5 1.0
CA B:ILE53 4.2 0.5 1.0
CB B:ASP48 4.2 0.1 1.0
N B:ASP54 4.2 0.8 1.0
OD2 B:ASP54 4.2 0.2 1.0
CB B:ASN50 4.3 99.3 1.0
OD2 B:ASP46 4.3 0.4 1.0
N B:ASN50 4.3 0.7 1.0
CB B:ASP46 4.4 0.6 1.0
N B:ILE53 4.4 0.2 1.0
CG B:GLU57 4.4 0.4 1.0
CA B:ASP46 4.4 0.3 1.0
N B:ASP48 4.4 0.1 1.0
N B:GLU52 4.7 0.5 1.0
N B:ALA47 4.7 0.3 1.0
CA B:ASP48 4.7 0.6 1.0
CG B:ASP54 4.7 0.9 1.0
C B:ILE53 4.7 0.3 1.0
C B:ASP46 4.7 0.6 1.0
CA B:GLU52 4.8 0.8 1.0
N B:GLY49 4.8 0.8 1.0
CA B:ASN50 4.8 0.7 1.0
C B:ASP48 4.9 0.8 1.0

Barium binding site 6 out of 6 in 3ulg

Go back to Barium Binding Sites List in 3ulg
Barium binding site 6 out of 6 in the Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of Calcium-Binding Protein-1 From Entamoeba Histolytica in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba137

b:0.9
occ:0.50
O B:LYS43 2.7 0.9 1.0
O B:HOH142 2.8 96.8 1.0
O B:ASP46 3.0 0.7 1.0
O B:HOH140 3.2 0.3 1.0
O B:ALA47 3.5 1.0 1.0
C B:LYS43 3.8 0.8 1.0
C B:ALA47 4.1 0.1 1.0
C B:ASP46 4.1 0.6 1.0
CA B:ALA47 4.1 0.9 1.0
O A:HOH138 4.3 77.0 1.0
CA B:LYS43 4.5 0.0 1.0
N B:GLY49 4.6 0.8 1.0
N B:ALA47 4.6 0.3 1.0
CB B:LYS43 4.6 0.2 1.0
N B:SER44 4.8 0.5 1.0
CA B:GLY49 4.9 0.4 1.0
CA B:SER44 5.0 0.1 1.0

Reference:

S.Kumar, E.Ahmed, S.Kumar, R.H.Khan, S.Gourinath. Flexibility of Ef-Hand Motifs: Structural and Thermodynamic Studies of Calcium Binding Protein- 1 From Entamoeba Histolytica with PB2+, BA2+, and SR2+ Bmc Biophys V. 5 15 2012.
ISSN: ISSN 2046-1682
PubMed: 22906057
DOI: 10.1186/2046-1682-5-15
Page generated: Sat Dec 12 01:55:57 2020

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