Calcium in PDB 3gg1: Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex
Protein crystallography data
The structure of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex, PDB code: 3gg1
was solved by
T.Barends,
E.Hartmann,
J.Griese,
T.Beitlich,
N.Kirienko,
D.Ryjenkov,
J.Reinstein,
R.Shoeman,
M.Gomelsky,
I.Schlichting,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.850,
96.690,
127.040,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.4 /
29.6
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex
(pdb code 3gg1). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex, PDB code: 3gg1:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 3gg1
Go back to
Calcium Binding Sites List in 3gg1
Calcium binding site 1 out
of 4 in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:17.6
occ:1.00
|
OE2
|
A:GLU272
|
2.2
|
27.6
|
1.0
|
OD1
|
A:ASN239
|
2.2
|
22.9
|
1.0
|
OD2
|
A:ASP302
|
2.3
|
30.5
|
1.0
|
O2P
|
A:C2E501
|
2.3
|
24.0
|
1.0
|
OE2
|
A:GLU188
|
2.3
|
25.0
|
1.0
|
O
|
A:HOH406
|
2.4
|
11.0
|
1.0
|
CG
|
A:ASN239
|
3.2
|
23.8
|
1.0
|
CG
|
A:ASP302
|
3.3
|
30.7
|
1.0
|
CD
|
A:GLU188
|
3.4
|
24.9
|
1.0
|
CD
|
A:GLU272
|
3.4
|
29.1
|
1.0
|
ND2
|
A:ASN239
|
3.6
|
22.9
|
1.0
|
P1
|
A:C2E501
|
3.6
|
23.5
|
1.0
|
OE1
|
A:GLU188
|
3.8
|
24.1
|
1.0
|
OD1
|
A:ASP302
|
3.9
|
30.1
|
1.0
|
CB
|
A:GLU272
|
4.0
|
29.3
|
1.0
|
O5'
|
A:C2E501
|
4.1
|
23.3
|
1.0
|
O
|
A:HOH481
|
4.2
|
33.3
|
1.0
|
O1P
|
A:C2E501
|
4.2
|
23.2
|
1.0
|
OE1
|
A:GLU272
|
4.3
|
28.4
|
1.0
|
CB
|
A:ASP302
|
4.3
|
30.7
|
1.0
|
CG
|
A:GLU272
|
4.3
|
29.2
|
1.0
|
OE2
|
A:GLU359
|
4.5
|
26.1
|
1.0
|
NZ
|
A:LYS323
|
4.5
|
26.1
|
1.0
|
O
|
A:HOH425
|
4.6
|
40.5
|
1.0
|
CG
|
A:GLU188
|
4.6
|
25.0
|
1.0
|
CB
|
A:ASN239
|
4.6
|
24.3
|
1.0
|
C2A
|
A:C2E501
|
4.8
|
23.2
|
1.0
|
O3A
|
A:C2E501
|
4.8
|
23.1
|
1.0
|
CA
|
A:CA503
|
4.9
|
30.8
|
1.0
|
|
Calcium binding site 2 out
of 4 in 3gg1
Go back to
Calcium Binding Sites List in 3gg1
Calcium binding site 2 out
of 4 in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:30.8
occ:1.00
|
OD1
|
A:ASP303
|
2.3
|
33.5
|
1.0
|
OE1
|
A:GLU359
|
2.3
|
26.0
|
1.0
|
O1P
|
A:C2E501
|
2.3
|
23.2
|
1.0
|
OD1
|
A:ASP302
|
2.8
|
30.1
|
1.0
|
CD
|
A:GLU359
|
2.9
|
24.9
|
1.0
|
OE2
|
A:GLU359
|
3.0
|
26.1
|
1.0
|
CG
|
A:ASP303
|
3.5
|
33.3
|
1.0
|
CG
|
A:ASP302
|
3.5
|
30.7
|
1.0
|
OD2
|
A:ASP302
|
3.7
|
30.5
|
1.0
|
P1
|
A:C2E501
|
3.7
|
23.5
|
1.0
|
N
|
A:ASP303
|
4.0
|
32.1
|
1.0
|
O
|
A:HOH406
|
4.1
|
11.0
|
1.0
|
O
|
A:HOH481
|
4.2
|
33.3
|
1.0
|
O2P
|
A:C2E501
|
4.2
|
24.0
|
1.0
|
CA
|
A:ASP303
|
4.2
|
33.0
|
1.0
|
OD2
|
A:ASP303
|
4.3
|
34.4
|
1.0
|
CG
|
A:GLU359
|
4.4
|
24.7
|
1.0
|
OD1
|
A:ASP325
|
4.4
|
30.0
|
1.0
|
CB
|
A:ASP303
|
4.5
|
33.0
|
1.0
|
O5'
|
A:C2E501
|
4.6
|
23.3
|
1.0
|
O3A
|
A:C2E501
|
4.7
|
23.1
|
1.0
|
C5'
|
A:C2E501
|
4.7
|
23.2
|
1.0
|
CB
|
A:ASP302
|
4.8
|
30.7
|
1.0
|
CA
|
A:CA502
|
4.9
|
17.6
|
1.0
|
CB
|
A:GLU359
|
5.0
|
23.9
|
1.0
|
|
Calcium binding site 3 out
of 4 in 3gg1
Go back to
Calcium Binding Sites List in 3gg1
Calcium binding site 3 out
of 4 in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca502
b:18.9
occ:1.00
|
OD1
|
B:ASP302
|
2.2
|
30.4
|
1.0
|
O2P
|
B:C2E501
|
2.2
|
24.4
|
1.0
|
OE2
|
B:GLU188
|
2.2
|
24.5
|
1.0
|
OE2
|
B:GLU272
|
2.3
|
28.3
|
1.0
|
O
|
B:HOH483
|
2.4
|
22.9
|
1.0
|
OD1
|
B:ASN239
|
2.4
|
22.1
|
1.0
|
CG
|
B:ASP302
|
3.1
|
31.1
|
1.0
|
CD
|
B:GLU188
|
3.3
|
24.8
|
1.0
|
CG
|
B:ASN239
|
3.3
|
23.5
|
1.0
|
OD2
|
B:ASP302
|
3.3
|
30.9
|
1.0
|
CD
|
B:GLU272
|
3.5
|
29.2
|
1.0
|
P1
|
B:C2E501
|
3.6
|
24.3
|
1.0
|
ND2
|
B:ASN239
|
3.6
|
22.0
|
1.0
|
OE1
|
B:GLU188
|
3.9
|
23.9
|
1.0
|
O
|
B:HOH429
|
4.0
|
28.7
|
1.0
|
CB
|
B:GLU272
|
4.0
|
29.5
|
1.0
|
NZ
|
B:LYS323
|
4.1
|
26.6
|
1.0
|
O5'
|
B:C2E501
|
4.2
|
23.8
|
1.0
|
CG
|
B:GLU272
|
4.3
|
29.4
|
1.0
|
O1P
|
B:C2E501
|
4.4
|
24.1
|
1.0
|
OE1
|
B:GLU272
|
4.4
|
29.2
|
1.0
|
CB
|
B:ASP302
|
4.4
|
31.1
|
1.0
|
CG
|
B:GLU188
|
4.4
|
24.5
|
1.0
|
CB
|
B:ASN239
|
4.7
|
24.2
|
1.0
|
OE2
|
B:GLU359
|
4.8
|
26.2
|
1.0
|
O3A
|
B:C2E501
|
4.8
|
23.9
|
1.0
|
C2A
|
B:C2E501
|
4.8
|
23.9
|
1.0
|
CD
|
B:LYS323
|
4.8
|
27.2
|
1.0
|
CE
|
B:LYS323
|
5.0
|
26.8
|
1.0
|
|
Calcium binding site 4 out
of 4 in 3gg1
Go back to
Calcium Binding Sites List in 3gg1
Calcium binding site 4 out
of 4 in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca503
b:35.0
occ:1.00
|
OD1
|
B:ASP303
|
2.3
|
33.8
|
1.0
|
O1P
|
B:C2E501
|
2.3
|
24.1
|
1.0
|
OD1
|
B:ASP325
|
2.6
|
29.0
|
1.0
|
OE1
|
B:GLU359
|
2.7
|
26.8
|
1.0
|
CD
|
B:GLU359
|
3.2
|
25.7
|
1.0
|
CG
|
B:ASP303
|
3.4
|
33.6
|
1.0
|
OE2
|
B:GLU359
|
3.6
|
26.2
|
1.0
|
CG
|
B:ASP325
|
3.8
|
28.5
|
1.0
|
P1
|
B:C2E501
|
3.8
|
24.3
|
1.0
|
CG
|
B:GLU359
|
4.1
|
24.7
|
1.0
|
CA
|
B:ASP303
|
4.2
|
33.2
|
1.0
|
OD2
|
B:ASP303
|
4.2
|
34.5
|
1.0
|
OD2
|
B:ASP302
|
4.3
|
30.9
|
1.0
|
CB
|
B:ASP303
|
4.3
|
33.2
|
1.0
|
O3A
|
B:C2E501
|
4.5
|
23.9
|
1.0
|
N
|
B:ASP303
|
4.5
|
32.4
|
1.0
|
OD2
|
B:ASP325
|
4.6
|
28.8
|
1.0
|
O2P
|
B:C2E501
|
4.6
|
24.4
|
1.0
|
CB
|
B:ASP325
|
4.7
|
28.0
|
1.0
|
CA
|
B:ASP325
|
4.7
|
28.0
|
1.0
|
O
|
B:HOH483
|
4.7
|
22.9
|
1.0
|
N
|
B:ALA326
|
4.8
|
28.2
|
1.0
|
C5'
|
B:C2E501
|
4.8
|
23.8
|
1.0
|
O5'
|
B:C2E501
|
4.8
|
23.8
|
1.0
|
O
|
B:HOH429
|
4.9
|
28.7
|
1.0
|
|
Reference:
T.R.Barends,
E.Hartmann,
J.J.Griese,
T.Beitlich,
N.V.Kirienko,
D.A.Ryjenkov,
J.Reinstein,
R.L.Shoeman,
M.Gomelsky,
I.Schlichting.
Structure and Mechanism of A Bacterial Light-Regulated Cyclic Nucleotide Phosphodiesterase. Nature V. 459 1015 2009.
ISSN: ISSN 0028-0836
PubMed: 19536266
DOI: 10.1038/NATURE07966
Page generated: Sat Jul 13 10:37:04 2024
|