Calcium in PDB 4r49: Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex
Protein crystallography data
The structure of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex, PDB code: 4r49
was solved by
P.K.Mandal,
G.W.Collie,
B.Kauffmann,
I.Huc,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.25 /
1.28
|
Space group
|
P -1
|
Cell size a, b, c (Å), α, β, γ (°)
|
23.263,
33.604,
36.820,
103.32,
101.02,
109.78
|
R / Rfree (%)
|
21.7 /
26
|
Other elements in 4r49:
The structure of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex
(pdb code 4r49). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex, PDB code: 4r49:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 4r49
Go back to
Calcium Binding Sites List in 4r49
Calcium binding site 1 out
of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca101
b:8.8
occ:1.00
|
O
|
A:HOH201
|
2.3
|
10.0
|
1.0
|
O
|
A:HOH217
|
2.4
|
9.9
|
1.0
|
O
|
A:HOH209
|
2.4
|
10.7
|
1.0
|
O
|
A:HOH202
|
2.5
|
9.7
|
1.0
|
O
|
A:HOH203
|
2.5
|
10.3
|
1.0
|
OP1
|
A:DA6
|
4.3
|
14.2
|
1.0
|
O
|
A:HOH258
|
4.3
|
15.7
|
0.7
|
O
|
A:HOH207
|
4.5
|
11.0
|
0.8
|
O
|
A:HOH212
|
4.7
|
10.9
|
0.9
|
OP2
|
A:DC7
|
4.7
|
11.8
|
1.0
|
O
|
A:HOH257
|
4.8
|
17.7
|
1.0
|
O5'
|
A:DA6
|
4.8
|
13.5
|
1.0
|
P
|
A:DA6
|
5.0
|
12.9
|
1.0
|
|
Calcium binding site 2 out
of 7 in 4r49
Go back to
Calcium Binding Sites List in 4r49
Calcium binding site 2 out
of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca102
b:10.2
occ:1.00
|
O
|
A:HOH295
|
2.3
|
33.6
|
1.0
|
OP1
|
A:DT5
|
2.3
|
9.8
|
1.0
|
O
|
A:HOH216
|
2.4
|
10.8
|
0.9
|
O
|
A:HOH205
|
2.4
|
15.1
|
1.0
|
O
|
A:HOH208
|
2.4
|
13.2
|
1.0
|
P
|
A:DT5
|
3.6
|
9.2
|
1.0
|
O5'
|
A:DT5
|
4.2
|
9.4
|
1.0
|
C5'
|
A:DT5
|
4.3
|
9.0
|
1.0
|
OP2
|
A:DT5
|
4.3
|
11.0
|
1.0
|
O
|
A:HOH264
|
4.3
|
32.2
|
0.5
|
O
|
A:HOH279
|
4.4
|
34.1
|
1.0
|
O
|
A:HOH274
|
4.5
|
25.0
|
1.0
|
O
|
A:HOH271
|
4.7
|
18.4
|
1.0
|
O3'
|
A:DG4
|
4.8
|
8.2
|
1.0
|
|
Calcium binding site 3 out
of 7 in 4r49
Go back to
Calcium Binding Sites List in 4r49
Calcium binding site 3 out
of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca103
b:13.2
occ:0.84
|
O
|
A:HOH233
|
2.3
|
17.6
|
0.6
|
O
|
A:HOH214
|
2.4
|
12.6
|
1.0
|
O
|
A:HOH243
|
2.4
|
22.9
|
0.7
|
O
|
A:HOH239
|
2.4
|
22.0
|
0.7
|
O
|
A:HOH238
|
2.5
|
17.3
|
0.7
|
N4
|
B:DC7
|
4.1
|
8.9
|
1.0
|
O
|
A:HOH227
|
4.5
|
14.6
|
0.7
|
O
|
A:HOH261
|
4.7
|
28.3
|
0.8
|
O
|
B:HOH255
|
4.7
|
23.2
|
0.7
|
O
|
A:HOH262
|
4.7
|
21.8
|
0.6
|
N7
|
A:DG3
|
4.7
|
11.8
|
1.0
|
C6
|
A:DC2
|
4.9
|
11.0
|
1.0
|
O6
|
A:DG3
|
4.9
|
9.1
|
1.0
|
|
Calcium binding site 4 out
of 7 in 4r49
Go back to
Calcium Binding Sites List in 4r49
Calcium binding site 4 out
of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca101
b:10.7
occ:1.00
|
OP1
|
B:DT5
|
2.3
|
10.3
|
1.0
|
O
|
B:HOH216
|
2.4
|
13.0
|
1.0
|
O
|
B:HOH261
|
2.5
|
23.0
|
1.0
|
P
|
B:DT5
|
3.6
|
9.4
|
1.0
|
O5'
|
B:DT5
|
4.2
|
9.4
|
1.0
|
OP2
|
B:DT5
|
4.3
|
11.4
|
1.0
|
O
|
B:HOH240
|
4.3
|
21.1
|
0.6
|
C5'
|
B:DT5
|
4.4
|
10.1
|
1.0
|
O
|
B:HOH231
|
4.7
|
13.3
|
0.6
|
O3'
|
B:DG4
|
4.8
|
9.2
|
1.0
|
|
Calcium binding site 5 out
of 7 in 4r49
Go back to
Calcium Binding Sites List in 4r49
Calcium binding site 5 out
of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca102
b:12.3
occ:0.86
|
O
|
B:HOH220
|
2.4
|
16.5
|
1.0
|
O
|
B:HOH227
|
2.4
|
23.1
|
0.8
|
O
|
B:HOH254
|
2.5
|
12.2
|
1.0
|
O
|
B:HOH250
|
4.4
|
26.6
|
0.8
|
OP1
|
B:DG10
|
4.4
|
12.7
|
1.0
|
OP2
|
B:DG10
|
4.6
|
17.2
|
1.0
|
O
|
B:HOH256
|
4.6
|
22.8
|
1.0
|
O
|
B:HOH246
|
4.6
|
19.3
|
0.8
|
|
Calcium binding site 6 out
of 7 in 4r49
Go back to
Calcium Binding Sites List in 4r49
Calcium binding site 6 out
of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca103
b:9.0
occ:1.00
|
O
|
B:HOH203
|
2.4
|
10.2
|
1.0
|
O
|
B:HOH201
|
2.5
|
10.7
|
1.0
|
O
|
B:HOH205
|
2.5
|
11.7
|
1.0
|
OP1
|
B:DA6
|
4.2
|
28.3
|
1.0
|
O
|
B:HOH207
|
4.5
|
11.9
|
0.9
|
O
|
B:HOH217
|
4.7
|
12.5
|
1.0
|
OP2
|
B:DC7
|
4.7
|
11.1
|
1.0
|
O5'
|
B:DA6
|
4.9
|
12.4
|
1.0
|
P
|
B:DA6
|
4.9
|
16.9
|
1.0
|
|
Calcium binding site 7 out
of 7 in 4r49
Go back to
Calcium Binding Sites List in 4r49
Calcium binding site 7 out
of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca104
b:14.2
occ:0.66
|
O
|
B:HOH245
|
2.9
|
16.1
|
0.8
|
N4
|
B:DC8
|
3.3
|
8.3
|
1.0
|
O
|
A:HOH234
|
3.4
|
21.9
|
0.9
|
O
|
B:HOH248
|
3.4
|
16.8
|
0.6
|
C5
|
B:DC8
|
3.7
|
8.8
|
1.0
|
C6
|
B:DC7
|
3.8
|
8.6
|
1.0
|
N4
|
A:DC2
|
3.9
|
10.4
|
1.0
|
C4
|
B:DC8
|
4.0
|
7.6
|
1.0
|
O
|
B:HOH263
|
4.0
|
33.9
|
1.0
|
C2'
|
B:DC7
|
4.1
|
10.6
|
1.0
|
C5
|
B:DC7
|
4.2
|
8.3
|
1.0
|
O
|
B:HOH207
|
4.3
|
11.9
|
0.9
|
N1
|
B:DC7
|
4.5
|
8.2
|
1.0
|
O6
|
B:DG9
|
4.6
|
10.1
|
1.0
|
C1'
|
B:DC7
|
4.8
|
9.7
|
1.0
|
C6
|
B:DC8
|
5.0
|
9.7
|
1.0
|
|
Reference:
P.K.Mandal,
G.W.Collie,
B.Kauffmann,
I.Huc.
Racemic Dna Crystallography. Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25358289
DOI: 10.1002/ANIE.201409014
Page generated: Sun Jul 14 12:36:05 2024
|