Calcium in PDB 1rwy: Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution
Protein crystallography data
The structure of Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution, PDB code: 1rwy
was solved by
C.A.Bottoms,
J.P.Schuermann,
S.Agah,
M.T.Henzl,
J.J.Tanner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.10 /
1.05
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
33.838,
54.708,
153.643,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13.3 /
16.2
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution
(pdb code 1rwy). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution, PDB code: 1rwy:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 1rwy
Go back to
Calcium Binding Sites List in 1rwy
Calcium binding site 1 out
of 6 in the Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca421
b:7.1
occ:1.00
|
OD1
|
A:ASP51
|
2.3
|
7.9
|
1.0
|
OD1
|
A:ASP53
|
2.3
|
8.3
|
1.0
|
O
|
A:PHE57
|
2.3
|
7.2
|
1.0
|
OE1
|
A:GLU59
|
2.4
|
8.6
|
1.0
|
OE1
|
A:GLU62
|
2.4
|
8.0
|
1.0
|
OE2
|
A:GLU62
|
2.5
|
8.2
|
1.0
|
OG
|
A:SER55
|
2.6
|
7.8
|
1.0
|
CD
|
A:GLU62
|
2.8
|
7.2
|
1.0
|
CD
|
A:GLU59
|
3.3
|
8.3
|
1.0
|
CG
|
A:ASP53
|
3.3
|
7.8
|
1.0
|
CG
|
A:ASP51
|
3.4
|
8.6
|
1.0
|
OE2
|
A:GLU59
|
3.5
|
8.9
|
1.0
|
C
|
A:PHE57
|
3.6
|
7.2
|
1.0
|
CB
|
A:SER55
|
3.6
|
8.9
|
1.0
|
OD2
|
A:ASP53
|
3.9
|
9.3
|
1.0
|
N
|
A:SER55
|
3.9
|
9.2
|
1.0
|
CA
|
A:ASP51
|
4.2
|
7.7
|
1.0
|
N
|
A:ASP53
|
4.2
|
8.4
|
1.0
|
CB
|
A:ASP51
|
4.3
|
8.1
|
1.0
|
N
|
A:PHE57
|
4.3
|
7.3
|
1.0
|
C
|
A:ASP51
|
4.3
|
7.7
|
1.0
|
CG
|
A:GLU62
|
4.3
|
7.6
|
1.0
|
OD2
|
A:ASP51
|
4.3
|
9.5
|
1.0
|
CA
|
A:SER55
|
4.4
|
8.6
|
1.0
|
N
|
A:GLU59
|
4.4
|
7.1
|
1.0
|
N
|
A:ILE58
|
4.4
|
6.8
|
1.0
|
CA
|
A:ILE58
|
4.5
|
6.6
|
1.0
|
N
|
A:LYS54
|
4.5
|
8.2
|
1.0
|
N
|
A:LYS52
|
4.5
|
8.4
|
1.0
|
O
|
A:HOH479
|
4.5
|
10.6
|
1.0
|
CA
|
A:PHE57
|
4.5
|
7.2
|
1.0
|
CB
|
A:ASP53
|
4.5
|
9.0
|
1.0
|
CA
|
A:ASP53
|
4.6
|
8.5
|
1.0
|
CG
|
A:GLU59
|
4.6
|
8.5
|
1.0
|
C
|
A:ASP53
|
4.6
|
8.3
|
1.0
|
O
|
A:ASP51
|
4.8
|
8.8
|
1.0
|
N
|
A:GLY56
|
4.8
|
8.5
|
1.0
|
C
|
A:SER55
|
4.9
|
8.9
|
1.0
|
C
|
A:ILE58
|
5.0
|
6.8
|
1.0
|
|
Calcium binding site 2 out
of 6 in 1rwy
Go back to
Calcium Binding Sites List in 1rwy
Calcium binding site 2 out
of 6 in the Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca422
b:11.9
occ:1.00
|
OD1
|
A:ASP90
|
2.3
|
12.5
|
1.0
|
OD1
|
A:ASP92
|
2.3
|
19.1
|
1.0
|
OD1
|
A:ASP94
|
2.3
|
12.3
|
1.0
|
O
|
A:LYS96
|
2.4
|
10.3
|
1.0
|
OE1
|
A:GLU101
|
2.4
|
12.5
|
1.0
|
O
|
A:HOH535
|
2.5
|
13.2
|
1.0
|
OE2
|
A:GLU101
|
2.5
|
13.1
|
1.0
|
CD
|
A:GLU101
|
2.8
|
11.3
|
1.0
|
CG
|
A:ASP94
|
3.3
|
12.4
|
1.0
|
CG
|
A:ASP92
|
3.3
|
21.9
|
1.0
|
CG
|
A:ASP90
|
3.4
|
12.7
|
1.0
|
C
|
A:LYS96
|
3.5
|
9.4
|
1.0
|
OD2
|
A:ASP94
|
3.6
|
13.2
|
1.0
|
OD2
|
A:ASP92
|
3.7
|
23.1
|
1.0
|
CA
|
A:ASP90
|
4.0
|
12.0
|
1.0
|
CB
|
A:ASP90
|
4.2
|
12.6
|
1.0
|
N
|
A:LYS96
|
4.2
|
11.6
|
1.0
|
OD2
|
A:ASP90
|
4.3
|
17.1
|
1.0
|
N
|
A:ASP94
|
4.3
|
14.9
|
1.0
|
CG
|
A:GLU101
|
4.4
|
10.1
|
1.0
|
N
|
A:ASP92
|
4.4
|
16.2
|
1.0
|
N
|
A:ILE97
|
4.4
|
9.1
|
1.0
|
CA
|
A:LYS96
|
4.4
|
10.2
|
1.0
|
CA
|
A:ILE97
|
4.4
|
8.8
|
1.0
|
CB
|
A:ASP94
|
4.4
|
12.7
|
1.0
|
C
|
A:ASP90
|
4.5
|
14.3
|
1.0
|
N
|
A:GLY98
|
4.5
|
9.3
|
1.0
|
O
|
A:HOH557
|
4.5
|
19.7
|
1.0
|
CB
|
A:ASP92
|
4.5
|
22.9
|
1.0
|
N
|
A:GLY93
|
4.5
|
19.4
|
1.0
|
O
|
A:HOH513
|
4.6
|
18.1
|
1.0
|
O
|
B:HOH549
|
4.7
|
13.8
|
1.0
|
N
|
A:LYS91
|
4.7
|
16.1
|
1.0
|
CB
|
A:LYS96
|
4.7
|
13.2
|
1.0
|
CA
|
A:ASP94
|
4.8
|
13.1
|
1.0
|
CA
|
A:ASP92
|
4.8
|
22.0
|
1.0
|
C
|
A:ASP92
|
4.8
|
21.6
|
1.0
|
C
|
A:ILE97
|
4.9
|
8.9
|
1.0
|
N
|
A:GLY95
|
4.9
|
13.5
|
1.0
|
|
Calcium binding site 3 out
of 6 in 1rwy
Go back to
Calcium Binding Sites List in 1rwy
Calcium binding site 3 out
of 6 in the Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca423
b:6.7
occ:1.00
|
OD1
|
B:ASP51
|
2.3
|
7.3
|
1.0
|
OD1
|
B:ASP53
|
2.3
|
9.7
|
1.0
|
O
|
B:PHE57
|
2.3
|
6.5
|
1.0
|
OE1
|
B:GLU59
|
2.3
|
8.6
|
1.0
|
OE1
|
B:GLU62
|
2.4
|
7.9
|
1.0
|
OE2
|
B:GLU62
|
2.5
|
8.4
|
1.0
|
OG
|
B:SER55
|
2.5
|
8.3
|
1.0
|
CD
|
B:GLU62
|
2.8
|
7.1
|
1.0
|
CD
|
B:GLU59
|
3.3
|
7.3
|
1.0
|
CG
|
B:ASP53
|
3.4
|
11.1
|
1.0
|
CG
|
B:ASP51
|
3.4
|
7.0
|
1.0
|
OE2
|
B:GLU59
|
3.5
|
8.6
|
1.0
|
CB
|
B:SER55
|
3.6
|
9.3
|
1.0
|
C
|
B:PHE57
|
3.6
|
5.5
|
1.0
|
OD2
|
B:ASP53
|
3.9
|
14.3
|
1.0
|
N
|
B:SER55
|
3.9
|
9.2
|
1.0
|
N
|
B:ASP53
|
4.1
|
9.9
|
1.0
|
OD2
|
B:ASP51
|
4.2
|
9.0
|
1.0
|
CA
|
B:ASP51
|
4.2
|
6.8
|
1.0
|
CG
|
B:GLU62
|
4.3
|
7.2
|
1.0
|
C
|
B:ASP51
|
4.3
|
7.4
|
1.0
|
N
|
B:GLU59
|
4.3
|
6.4
|
1.0
|
N
|
B:PHE57
|
4.3
|
6.5
|
1.0
|
CA
|
B:SER55
|
4.3
|
9.7
|
1.0
|
N
|
B:LYS52
|
4.3
|
7.7
|
1.0
|
CB
|
B:ASP51
|
4.3
|
7.2
|
1.0
|
O
|
B:HOH479
|
4.4
|
17.6
|
1.0
|
N
|
B:LYS54
|
4.4
|
10.1
|
1.0
|
CA
|
B:ILE58
|
4.4
|
5.4
|
1.0
|
N
|
B:ILE58
|
4.4
|
5.4
|
1.0
|
CB
|
B:ASP53
|
4.5
|
12.8
|
1.0
|
CA
|
B:PHE57
|
4.5
|
6.5
|
1.0
|
O
|
B:HOH559
|
4.6
|
34.5
|
1.0
|
CG
|
B:GLU59
|
4.6
|
8.0
|
1.0
|
CA
|
B:ASP53
|
4.6
|
11.5
|
1.0
|
C
|
B:ASP53
|
4.7
|
10.8
|
1.0
|
N
|
B:GLY56
|
4.8
|
9.1
|
1.0
|
O
|
B:HOH522
|
4.9
|
20.4
|
1.0
|
O
|
B:ASP51
|
4.9
|
8.4
|
1.0
|
C
|
B:ILE58
|
4.9
|
5.6
|
1.0
|
C
|
B:SER55
|
4.9
|
9.3
|
1.0
|
CB
|
B:GLU59
|
5.0
|
7.8
|
1.0
|
|
Calcium binding site 4 out
of 6 in 1rwy
Go back to
Calcium Binding Sites List in 1rwy
Calcium binding site 4 out
of 6 in the Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca424
b:7.0
occ:1.00
|
OD1
|
B:ASP90
|
2.3
|
7.4
|
1.0
|
O
|
B:LYS96
|
2.3
|
7.7
|
1.0
|
OD1
|
B:ASP94
|
2.4
|
7.8
|
1.0
|
O
|
B:HOH523
|
2.4
|
10.5
|
1.0
|
OD1
|
B:ASP92
|
2.4
|
8.6
|
1.0
|
OE1
|
B:GLU101
|
2.5
|
7.0
|
1.0
|
OE2
|
B:GLU101
|
2.5
|
9.0
|
1.0
|
CD
|
B:GLU101
|
2.8
|
6.8
|
1.0
|
CG
|
B:ASP94
|
3.2
|
9.0
|
1.0
|
CG
|
B:ASP92
|
3.4
|
9.3
|
1.0
|
CG
|
B:ASP90
|
3.4
|
7.3
|
1.0
|
C
|
B:LYS96
|
3.5
|
6.1
|
1.0
|
OD2
|
B:ASP94
|
3.7
|
10.4
|
1.0
|
OD2
|
B:ASP92
|
3.9
|
12.1
|
1.0
|
N
|
B:ASP94
|
4.1
|
9.0
|
1.0
|
CA
|
B:ASP90
|
4.1
|
7.7
|
1.0
|
CB
|
B:ASP90
|
4.2
|
8.1
|
1.0
|
N
|
B:ASP92
|
4.2
|
7.7
|
1.0
|
N
|
B:LYS96
|
4.2
|
7.0
|
1.0
|
OD2
|
B:ASP90
|
4.3
|
8.6
|
1.0
|
CB
|
B:ASP94
|
4.3
|
10.4
|
1.0
|
CG
|
B:GLU101
|
4.3
|
7.9
|
1.0
|
C
|
B:ASP90
|
4.4
|
7.8
|
1.0
|
CA
|
B:ILE97
|
4.4
|
6.1
|
1.0
|
N
|
B:ILE97
|
4.4
|
6.3
|
1.0
|
N
|
B:GLY98
|
4.5
|
6.0
|
1.0
|
CB
|
B:ASP92
|
4.5
|
9.3
|
1.0
|
N
|
B:GLY93
|
4.5
|
9.4
|
1.0
|
CA
|
B:LYS96
|
4.5
|
6.5
|
1.0
|
N
|
B:LYS91
|
4.5
|
8.5
|
1.0
|
CA
|
B:ASP94
|
4.6
|
9.8
|
1.0
|
CA
|
B:ASP92
|
4.7
|
8.9
|
1.0
|
N
|
B:GLY95
|
4.7
|
7.7
|
1.0
|
CG
|
B:LYS96
|
4.8
|
8.5
|
1.0
|
C
|
B:ASP92
|
4.8
|
9.4
|
1.0
|
C
|
B:ILE97
|
4.9
|
6.0
|
1.0
|
C
|
B:ASP94
|
4.9
|
9.2
|
1.0
|
O
|
B:ASP90
|
5.0
|
8.9
|
1.0
|
|
Calcium binding site 5 out
of 6 in 1rwy
Go back to
Calcium Binding Sites List in 1rwy
Calcium binding site 5 out
of 6 in the Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca425
b:6.1
occ:1.00
|
OD1
|
C:ASP51
|
2.3
|
6.6
|
1.0
|
OD1
|
C:ASP53
|
2.3
|
8.1
|
1.0
|
O
|
C:PHE57
|
2.3
|
6.9
|
1.0
|
OE1
|
C:GLU59
|
2.4
|
6.8
|
1.0
|
OE1
|
C:GLU62
|
2.4
|
7.0
|
1.0
|
OG
|
C:SER55
|
2.5
|
7.3
|
1.0
|
OE2
|
C:GLU62
|
2.5
|
7.8
|
1.0
|
CD
|
C:GLU62
|
2.8
|
6.0
|
1.0
|
CD
|
C:GLU59
|
3.2
|
6.3
|
1.0
|
CG
|
C:ASP53
|
3.4
|
8.8
|
1.0
|
CG
|
C:ASP51
|
3.4
|
6.7
|
1.0
|
OE2
|
C:GLU59
|
3.5
|
7.8
|
1.0
|
CB
|
C:SER55
|
3.6
|
8.0
|
1.0
|
C
|
C:PHE57
|
3.6
|
5.9
|
1.0
|
OD2
|
C:ASP53
|
3.8
|
13.6
|
1.0
|
N
|
C:SER55
|
4.0
|
8.0
|
1.0
|
CA
|
C:ASP51
|
4.1
|
6.4
|
1.0
|
N
|
C:ASP53
|
4.2
|
8.0
|
1.0
|
OD2
|
C:ASP51
|
4.2
|
9.0
|
1.0
|
CB
|
C:ASP51
|
4.2
|
7.1
|
1.0
|
C
|
C:ASP51
|
4.2
|
6.6
|
1.0
|
O
|
C:HOH490
|
4.3
|
13.6
|
1.0
|
CG
|
C:GLU62
|
4.3
|
7.3
|
1.0
|
CA
|
C:SER55
|
4.3
|
8.6
|
1.0
|
N
|
C:GLU59
|
4.3
|
5.9
|
1.0
|
N
|
C:PHE57
|
4.3
|
6.7
|
1.0
|
N
|
C:LYS52
|
4.4
|
7.0
|
1.0
|
CA
|
C:ILE58
|
4.4
|
5.8
|
1.0
|
N
|
C:ILE58
|
4.4
|
6.2
|
1.0
|
CB
|
C:ASP53
|
4.5
|
9.1
|
1.0
|
N
|
C:LYS54
|
4.5
|
8.6
|
1.0
|
CA
|
C:PHE57
|
4.5
|
6.5
|
1.0
|
O
|
C:HOH518
|
4.6
|
18.5
|
1.0
|
CG
|
C:GLU59
|
4.6
|
6.7
|
1.0
|
CA
|
C:ASP53
|
4.7
|
8.3
|
1.0
|
C
|
C:ASP53
|
4.8
|
8.8
|
1.0
|
O
|
C:ASP51
|
4.8
|
7.2
|
1.0
|
N
|
C:GLY56
|
4.9
|
8.2
|
1.0
|
C
|
C:ILE58
|
4.9
|
5.6
|
1.0
|
C
|
C:SER55
|
4.9
|
8.4
|
1.0
|
|
Calcium binding site 6 out
of 6 in 1rwy
Go back to
Calcium Binding Sites List in 1rwy
Calcium binding site 6 out
of 6 in the Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca426
b:7.2
occ:1.00
|
OD1
|
C:ASP90
|
2.3
|
8.7
|
1.0
|
OD1
|
C:ASP94
|
2.3
|
8.5
|
1.0
|
OD1
|
C:ASP92
|
2.3
|
9.3
|
1.0
|
O
|
C:LYS96
|
2.4
|
7.5
|
1.0
|
O
|
C:HOH534
|
2.4
|
9.2
|
1.0
|
OE1
|
C:GLU101
|
2.4
|
7.6
|
1.0
|
OE2
|
C:GLU101
|
2.5
|
7.5
|
1.0
|
CD
|
C:GLU101
|
2.8
|
6.9
|
1.0
|
CG
|
C:ASP94
|
3.3
|
8.7
|
1.0
|
CG
|
C:ASP90
|
3.4
|
8.7
|
1.0
|
CG
|
C:ASP92
|
3.4
|
10.1
|
1.0
|
C
|
C:LYS96
|
3.5
|
7.2
|
1.0
|
OD2
|
C:ASP94
|
3.6
|
9.4
|
1.0
|
OD2
|
C:ASP92
|
4.0
|
13.2
|
1.0
|
O
|
C:HOH466
|
4.0
|
9.7
|
1.0
|
CA
|
C:ASP90
|
4.1
|
8.6
|
1.0
|
CB
|
C:ASP90
|
4.1
|
8.8
|
1.0
|
N
|
C:ASP92
|
4.2
|
10.5
|
1.0
|
OD2
|
C:ASP90
|
4.3
|
10.1
|
1.0
|
N
|
C:LYS96
|
4.3
|
7.4
|
1.0
|
CA
|
C:ILE97
|
4.3
|
6.7
|
1.0
|
N
|
C:ILE97
|
4.3
|
6.5
|
1.0
|
CG
|
C:GLU101
|
4.3
|
7.1
|
1.0
|
N
|
C:ASP94
|
4.4
|
10.8
|
1.0
|
N
|
C:LYS91
|
4.4
|
9.1
|
1.0
|
CA
|
C:LYS96
|
4.5
|
7.0
|
1.0
|
CB
|
C:ASP94
|
4.5
|
11.5
|
1.0
|
N
|
C:GLY98
|
4.5
|
6.4
|
1.0
|
CB
|
C:ASP92
|
4.5
|
10.1
|
1.0
|
C
|
C:ASP90
|
4.6
|
8.5
|
1.0
|
N
|
C:GLY93
|
4.6
|
12.1
|
1.0
|
CA
|
C:ASP92
|
4.7
|
10.6
|
1.0
|
CG
|
C:LYS96
|
4.8
|
7.9
|
1.0
|
C
|
C:ASP92
|
4.8
|
12.0
|
1.0
|
CA
|
C:ASP94
|
4.9
|
10.8
|
1.0
|
C
|
C:ILE97
|
4.9
|
6.1
|
1.0
|
N
|
C:GLY95
|
4.9
|
9.3
|
1.0
|
|
Reference:
C.A.Bottoms,
J.P.Schuermann,
S.Agah,
M.T.Henzl,
J.J.Tanner.
Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution Protein Sci. V. 13 1724 2004.
ISSN: ISSN 0961-8368
PubMed: 15169955
DOI: 10.1110/PS.03571004
Page generated: Thu Jul 11 22:18:07 2024
|