Calcium in PDB 6prm: Crystal Structure of Apo PSS1_19B
Protein crystallography data
The structure of Crystal Structure of Apo PSS1_19B, PDB code: 6prm
was solved by
A.G.Hettle,
A.B.Boraston,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.60 /
2.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.510,
88.580,
106.600,
82.22,
79.85,
84.20
|
R / Rfree (%)
|
23.8 /
27.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Apo PSS1_19B
(pdb code 6prm). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Crystal Structure of Apo PSS1_19B, PDB code: 6prm:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6prm
Go back to
Calcium Binding Sites List in 6prm
Calcium binding site 1 out
of 4 in the Crystal Structure of Apo PSS1_19B
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 Apo PSS1_19B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:36.2
occ:1.00
|
OD1
|
A:ASP37
|
2.1
|
41.4
|
1.0
|
OD2
|
A:ASP290
|
2.2
|
25.8
|
1.0
|
OD1
|
A:ASP38
|
2.5
|
43.2
|
1.0
|
OD1
|
A:ASN291
|
2.5
|
35.4
|
1.0
|
SG
|
A:CYS77
|
2.5
|
42.6
|
1.0
|
OD1
|
A:ASP290
|
2.6
|
24.5
|
1.0
|
CG
|
A:ASP290
|
2.7
|
25.7
|
1.0
|
CG
|
A:ASP37
|
3.2
|
39.6
|
1.0
|
CG
|
A:ASP38
|
3.5
|
39.5
|
1.0
|
CG
|
A:ASN291
|
3.5
|
30.2
|
1.0
|
CB
|
A:CYS77
|
3.5
|
35.8
|
1.0
|
CA
|
A:CYS77
|
3.7
|
32.9
|
1.0
|
N
|
A:ASP38
|
3.7
|
35.0
|
1.0
|
ND2
|
A:ASN291
|
3.8
|
25.1
|
1.0
|
OD2
|
A:ASP37
|
3.9
|
42.5
|
1.0
|
NZ
|
A:LYS140
|
4.1
|
46.5
|
1.0
|
OD2
|
A:ASP38
|
4.1
|
38.9
|
1.0
|
N
|
A:CYS77
|
4.1
|
33.3
|
1.0
|
CB
|
A:ASP290
|
4.2
|
24.9
|
1.0
|
CD2
|
A:HIS233
|
4.2
|
35.2
|
1.0
|
CA
|
A:ASP37
|
4.2
|
32.6
|
1.0
|
CE
|
A:LYS309
|
4.3
|
28.7
|
1.0
|
CB
|
A:ASP37
|
4.3
|
37.3
|
1.0
|
NZ
|
A:LYS309
|
4.3
|
30.8
|
1.0
|
C
|
A:ASP37
|
4.4
|
34.1
|
1.0
|
CA
|
A:ASP38
|
4.4
|
36.6
|
1.0
|
CB
|
A:ASP38
|
4.4
|
39.4
|
1.0
|
NH2
|
A:ARG81
|
4.5
|
32.7
|
1.0
|
N
|
A:ASN291
|
4.8
|
25.4
|
1.0
|
CB
|
A:ASN291
|
4.8
|
29.8
|
1.0
|
NE
|
A:ARG81
|
4.9
|
31.3
|
1.0
|
NE2
|
A:HIS233
|
4.9
|
33.8
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6prm
Go back to
Calcium Binding Sites List in 6prm
Calcium binding site 2 out
of 4 in the Crystal Structure of Apo PSS1_19B
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 Apo PSS1_19B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca501
b:35.5
occ:1.00
|
OD1
|
B:ASP37
|
2.1
|
33.0
|
1.0
|
OD2
|
B:ASP290
|
2.3
|
29.6
|
1.0
|
OD1
|
B:ASP38
|
2.4
|
31.0
|
1.0
|
OD1
|
B:ASN291
|
2.5
|
24.9
|
1.0
|
OD1
|
B:ASP290
|
2.6
|
29.8
|
1.0
|
SG
|
B:CYS77
|
2.6
|
36.5
|
1.0
|
CG
|
B:ASP290
|
2.7
|
29.0
|
1.0
|
CG
|
B:ASP37
|
3.3
|
31.4
|
1.0
|
CG
|
B:ASN291
|
3.4
|
26.6
|
1.0
|
CG
|
B:ASP38
|
3.4
|
33.5
|
1.0
|
CB
|
B:CYS77
|
3.6
|
30.9
|
1.0
|
N
|
B:ASP38
|
3.7
|
33.5
|
1.0
|
ND2
|
B:ASN291
|
3.7
|
26.6
|
1.0
|
CA
|
B:CYS77
|
3.8
|
29.3
|
1.0
|
OD2
|
B:ASP37
|
4.0
|
36.9
|
1.0
|
OD2
|
B:ASP38
|
4.1
|
33.6
|
1.0
|
N
|
B:CYS77
|
4.1
|
25.8
|
1.0
|
NZ
|
B:LYS140
|
4.2
|
48.6
|
1.0
|
CB
|
B:ASP290
|
4.2
|
27.9
|
1.0
|
CE
|
B:LYS309
|
4.2
|
24.1
|
1.0
|
CA
|
B:ASP37
|
4.2
|
30.7
|
1.0
|
CD2
|
B:HIS233
|
4.3
|
29.0
|
1.0
|
NZ
|
B:LYS309
|
4.3
|
25.3
|
1.0
|
CB
|
B:ASP37
|
4.3
|
31.0
|
1.0
|
CA
|
B:ASP38
|
4.3
|
31.2
|
1.0
|
C
|
B:ASP37
|
4.3
|
31.3
|
1.0
|
CB
|
B:ASP38
|
4.4
|
31.6
|
1.0
|
NH2
|
B:ARG81
|
4.5
|
29.7
|
1.0
|
N
|
B:ASN291
|
4.7
|
25.0
|
1.0
|
CB
|
B:ASN291
|
4.7
|
25.5
|
1.0
|
C
|
B:ASP290
|
5.0
|
25.3
|
1.0
|
NE
|
B:ARG81
|
5.0
|
30.5
|
1.0
|
NE2
|
B:HIS233
|
5.0
|
27.9
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6prm
Go back to
Calcium Binding Sites List in 6prm
Calcium binding site 3 out
of 4 in the Crystal Structure of Apo PSS1_19B
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 Apo PSS1_19B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca501
b:44.2
occ:1.00
|
OD1
|
C:ASP37
|
2.0
|
38.0
|
1.0
|
OD2
|
C:ASP290
|
2.3
|
29.7
|
1.0
|
OD1
|
C:ASP38
|
2.4
|
28.2
|
1.0
|
OD1
|
C:ASP290
|
2.6
|
21.3
|
1.0
|
OD1
|
C:ASN291
|
2.6
|
36.3
|
1.0
|
SG
|
C:CYS77
|
2.7
|
45.1
|
1.0
|
CG
|
C:ASP290
|
2.7
|
24.1
|
1.0
|
CG
|
C:ASP37
|
3.2
|
36.7
|
1.0
|
CG
|
C:ASP38
|
3.4
|
28.7
|
1.0
|
CG
|
C:ASN291
|
3.5
|
30.7
|
1.0
|
N
|
C:ASP38
|
3.6
|
28.9
|
1.0
|
CB
|
C:CYS77
|
3.7
|
37.6
|
1.0
|
ND2
|
C:ASN291
|
3.8
|
31.3
|
1.0
|
OD2
|
C:ASP37
|
3.9
|
43.0
|
1.0
|
CA
|
C:CYS77
|
3.9
|
35.5
|
1.0
|
OD2
|
C:ASP38
|
4.0
|
31.6
|
1.0
|
NZ
|
C:LYS140
|
4.1
|
38.1
|
1.0
|
CA
|
C:ASP37
|
4.1
|
31.4
|
1.0
|
CD2
|
C:HIS233
|
4.2
|
33.4
|
1.0
|
CB
|
C:ASP37
|
4.2
|
33.9
|
1.0
|
CB
|
C:ASP290
|
4.2
|
24.4
|
1.0
|
C
|
C:ASP37
|
4.2
|
32.8
|
1.0
|
CA
|
C:ASP38
|
4.3
|
29.3
|
1.0
|
CB
|
C:ASP38
|
4.3
|
28.7
|
1.0
|
CE
|
C:LYS309
|
4.3
|
22.0
|
1.0
|
N
|
C:CYS77
|
4.3
|
34.0
|
1.0
|
NZ
|
C:LYS309
|
4.4
|
20.2
|
1.0
|
NH2
|
C:ARG81
|
4.4
|
31.0
|
1.0
|
N
|
C:ASN291
|
4.8
|
25.0
|
1.0
|
CB
|
C:ASN291
|
4.9
|
27.5
|
1.0
|
NE2
|
C:HIS233
|
4.9
|
38.1
|
1.0
|
NE
|
C:ARG81
|
5.0
|
28.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6prm
Go back to
Calcium Binding Sites List in 6prm
Calcium binding site 4 out
of 4 in the Crystal Structure of Apo PSS1_19B
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 Apo PSS1_19B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca501
b:32.9
occ:1.00
|
OD1
|
D:ASP37
|
2.0
|
38.1
|
1.0
|
OD2
|
D:ASP290
|
2.2
|
29.1
|
1.0
|
OD1
|
D:ASP38
|
2.4
|
22.2
|
1.0
|
OD1
|
D:ASP290
|
2.5
|
36.3
|
1.0
|
OD1
|
D:ASN291
|
2.5
|
22.3
|
1.0
|
CG
|
D:ASP290
|
2.6
|
31.6
|
1.0
|
SG
|
D:CYS77
|
2.8
|
30.6
|
1.0
|
CG
|
D:ASP37
|
3.2
|
38.1
|
1.0
|
CG
|
D:ASP38
|
3.4
|
23.9
|
1.0
|
CG
|
D:ASN291
|
3.5
|
21.2
|
1.0
|
N
|
D:ASP38
|
3.5
|
27.1
|
1.0
|
CB
|
D:CYS77
|
3.7
|
30.3
|
1.0
|
ND2
|
D:ASN291
|
3.8
|
18.9
|
1.0
|
CA
|
D:CYS77
|
3.9
|
30.4
|
1.0
|
OD2
|
D:ASP37
|
3.9
|
40.2
|
1.0
|
CA
|
D:ASP37
|
4.1
|
33.6
|
1.0
|
OD2
|
D:ASP38
|
4.1
|
24.6
|
1.0
|
CB
|
D:ASP290
|
4.1
|
29.3
|
1.0
|
C
|
D:ASP37
|
4.2
|
29.6
|
1.0
|
CB
|
D:ASP37
|
4.2
|
34.3
|
1.0
|
NZ
|
D:LYS140
|
4.2
|
57.3
|
1.0
|
CA
|
D:ASP38
|
4.2
|
27.6
|
1.0
|
N
|
D:CYS77
|
4.3
|
30.0
|
1.0
|
CD2
|
D:HIS233
|
4.3
|
29.4
|
1.0
|
CB
|
D:ASP38
|
4.3
|
25.7
|
1.0
|
CE
|
D:LYS309
|
4.4
|
17.2
|
1.0
|
NZ
|
D:LYS309
|
4.4
|
17.7
|
1.0
|
NH2
|
D:ARG81
|
4.4
|
29.7
|
1.0
|
N
|
D:ASN291
|
4.7
|
27.7
|
1.0
|
CB
|
D:ASN291
|
4.8
|
22.5
|
1.0
|
C
|
D:ASP290
|
4.9
|
30.1
|
1.0
|
CA
|
D:ASP290
|
5.0
|
30.5
|
1.0
|
NE
|
D:ARG81
|
5.0
|
35.3
|
1.0
|
|
Reference:
A.G.Hettle,
J.K.Hobbs,
B.Pluvinage,
C.Vickers,
K.Abe,
O.Salama-Alber,
B.Mcguire,
J.H.Hehemann,
J.P.M.Hui,
F.Berrue,
A.Banskota,
J.Zhang,
E.Bottos,
J.Van Hamme,
A.B.Boraston.
The Carrageenan Metabolism Pathway of Marine Pseudoalteromonas Species To Be Published.
Page generated: Tue Jul 16 12:58:34 2024
|