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
Go back to
Barium Binding Sites List in 3ulg
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
Go back to
Barium Binding Sites List in 3ulg
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
Go back to
Barium Binding Sites List in 3ulg
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
Go back to
Barium Binding Sites List in 3ulg
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
Go back to
Barium Binding Sites List in 3ulg
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
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