Calcium in PDB 1q8f: Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik
Enzymatic activity of Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik
All present enzymatic activity of Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik:
3.2.2.8;
Protein crystallography data
The structure of Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik, PDB code: 1q8f
was solved by
B.Giabbai,
M.Degano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.83 /
1.70
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.808,
85.707,
90.678,
112.95,
101.95,
85.92
|
R / Rfree (%)
|
15.3 /
17
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik
(pdb code 1q8f). 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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik, PDB code: 1q8f:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1q8f
Go back to
Calcium Binding Sites List in 1q8f
Calcium binding site 1 out
of 4 in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik
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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2001
b:13.2
occ:1.00
|
OD2
|
A:ASP240
|
2.3
|
9.8
|
1.0
|
O
|
A:VAL124
|
2.4
|
9.1
|
1.0
|
OD1
|
A:ASP11
|
2.5
|
10.3
|
1.0
|
O
|
A:HOH3022
|
2.5
|
11.2
|
1.0
|
OD1
|
A:ASP16
|
2.5
|
10.7
|
1.0
|
OD2
|
A:ASP16
|
2.5
|
10.9
|
1.0
|
O
|
A:HOH3026
|
2.5
|
12.2
|
1.0
|
O3
|
A:GOL3001
|
2.6
|
13.9
|
1.0
|
CG
|
A:ASP16
|
2.9
|
10.3
|
1.0
|
CG
|
A:ASP240
|
3.4
|
9.9
|
1.0
|
C
|
A:VAL124
|
3.5
|
9.3
|
1.0
|
CG
|
A:ASP11
|
3.6
|
11.4
|
1.0
|
OD1
|
A:ASP240
|
3.6
|
9.7
|
1.0
|
C3
|
A:GOL3001
|
3.8
|
20.0
|
1.0
|
OD1
|
A:ASN40
|
3.8
|
13.4
|
1.0
|
OD2
|
A:ASP11
|
3.9
|
11.1
|
1.0
|
CA
|
A:GLY125
|
4.2
|
9.7
|
1.0
|
N
|
A:GLY125
|
4.3
|
9.5
|
1.0
|
CB
|
A:ASP16
|
4.3
|
10.2
|
1.0
|
O2
|
A:GOL3001
|
4.4
|
22.9
|
1.0
|
OD1
|
A:ASN166
|
4.4
|
9.4
|
1.0
|
CG2
|
A:VAL124
|
4.5
|
9.9
|
1.0
|
ND2
|
A:ASN166
|
4.5
|
8.7
|
1.0
|
CB
|
A:VAL124
|
4.5
|
9.7
|
1.0
|
OD1
|
A:ASP15
|
4.5
|
13.2
|
1.0
|
N
|
A:ASP11
|
4.6
|
10.3
|
1.0
|
OD2
|
A:ASP15
|
4.6
|
13.2
|
1.0
|
C2
|
A:GOL3001
|
4.6
|
19.5
|
1.0
|
CA
|
A:VAL124
|
4.6
|
9.7
|
1.0
|
O
|
A:ASP11
|
4.6
|
11.4
|
1.0
|
CG
|
A:ASN40
|
4.7
|
11.9
|
1.0
|
CB
|
A:ASP240
|
4.7
|
8.2
|
1.0
|
N
|
A:ASP16
|
4.8
|
10.6
|
1.0
|
CB
|
A:ASP11
|
4.9
|
11.0
|
1.0
|
CG
|
A:ASP15
|
4.9
|
12.9
|
1.0
|
CA
|
A:ASP16
|
4.9
|
10.4
|
1.0
|
C
|
A:ASP11
|
4.9
|
11.4
|
1.0
|
CG
|
A:ASN166
|
4.9
|
10.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1q8f
Go back to
Calcium Binding Sites List in 1q8f
Calcium binding site 2 out
of 4 in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik
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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2002
b:19.4
occ:1.00
|
OD2
|
B:ASP240
|
2.3
|
12.6
|
1.0
|
O
|
B:VAL124
|
2.4
|
12.7
|
1.0
|
O
|
B:HOH3041
|
2.5
|
18.9
|
1.0
|
OD2
|
B:ASP16
|
2.5
|
12.7
|
1.0
|
OD1
|
B:ASP11
|
2.5
|
11.8
|
1.0
|
O3
|
B:GOL3002
|
2.5
|
18.8
|
1.0
|
OD1
|
B:ASP16
|
2.6
|
13.7
|
1.0
|
O
|
B:HOH3028
|
2.6
|
17.1
|
1.0
|
CG
|
B:ASP16
|
2.9
|
12.2
|
1.0
|
CG
|
B:ASP240
|
3.3
|
12.1
|
1.0
|
C
|
B:VAL124
|
3.5
|
11.6
|
1.0
|
OD1
|
B:ASP240
|
3.6
|
14.3
|
1.0
|
CG
|
B:ASP11
|
3.6
|
12.9
|
1.0
|
C3
|
B:GOL3002
|
3.7
|
24.1
|
1.0
|
OD1
|
B:ASN40
|
3.8
|
17.2
|
1.0
|
OD2
|
B:ASP11
|
3.9
|
12.8
|
1.0
|
CA
|
B:GLY125
|
4.2
|
11.6
|
1.0
|
N
|
B:GLY125
|
4.2
|
11.6
|
1.0
|
CB
|
B:ASP16
|
4.3
|
11.5
|
1.0
|
O2
|
B:GOL3002
|
4.4
|
26.1
|
1.0
|
OD1
|
B:ASN166
|
4.4
|
13.1
|
1.0
|
OD1
|
B:ASP15
|
4.5
|
14.7
|
1.0
|
ND2
|
B:ASN166
|
4.5
|
11.3
|
1.0
|
CG2
|
B:VAL124
|
4.6
|
11.0
|
1.0
|
N
|
B:ASP11
|
4.6
|
12.3
|
1.0
|
OD2
|
B:ASP15
|
4.6
|
14.6
|
1.0
|
CB
|
B:VAL124
|
4.6
|
11.0
|
1.0
|
C2
|
B:GOL3002
|
4.6
|
24.3
|
1.0
|
O
|
B:ASP11
|
4.6
|
12.5
|
1.0
|
CA
|
B:VAL124
|
4.6
|
11.4
|
1.0
|
CG
|
B:ASN40
|
4.7
|
13.3
|
1.0
|
N
|
B:ASP16
|
4.7
|
12.7
|
1.0
|
CB
|
B:ASP240
|
4.7
|
11.7
|
1.0
|
CG
|
B:ASP15
|
4.8
|
15.2
|
1.0
|
CA
|
B:ASP16
|
4.9
|
12.1
|
1.0
|
CB
|
B:ASP11
|
4.9
|
12.2
|
1.0
|
CG
|
B:ASN166
|
4.9
|
11.3
|
1.0
|
C
|
B:ASP11
|
4.9
|
12.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1q8f
Go back to
Calcium Binding Sites List in 1q8f
Calcium binding site 3 out
of 4 in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik
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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2003
b:11.9
occ:1.00
|
O
|
C:VAL124
|
2.4
|
8.6
|
1.0
|
OD2
|
C:ASP240
|
2.4
|
9.1
|
1.0
|
OD2
|
C:ASP16
|
2.5
|
9.7
|
1.0
|
O
|
C:HOH3047
|
2.5
|
12.9
|
1.0
|
OD1
|
C:ASP11
|
2.5
|
9.1
|
1.0
|
OD1
|
C:ASP16
|
2.5
|
10.6
|
1.0
|
O
|
C:HOH3027
|
2.5
|
10.7
|
1.0
|
O3
|
C:GOL3003
|
2.7
|
12.5
|
1.0
|
CG
|
C:ASP16
|
2.9
|
9.2
|
1.0
|
CG
|
C:ASP240
|
3.4
|
9.0
|
1.0
|
C
|
C:VAL124
|
3.5
|
8.3
|
1.0
|
CG
|
C:ASP11
|
3.6
|
11.1
|
1.0
|
OD1
|
C:ASP240
|
3.7
|
8.5
|
1.0
|
OD1
|
C:ASN40
|
3.7
|
13.4
|
1.0
|
C3
|
C:GOL3003
|
3.8
|
19.0
|
1.0
|
OD2
|
C:ASP11
|
4.0
|
9.5
|
1.0
|
CA
|
C:GLY125
|
4.2
|
8.1
|
1.0
|
N
|
C:GLY125
|
4.3
|
8.8
|
1.0
|
CB
|
C:ASP16
|
4.3
|
9.0
|
1.0
|
O2
|
C:GOL3003
|
4.3
|
21.4
|
1.0
|
OD1
|
C:ASN166
|
4.4
|
9.4
|
1.0
|
OD1
|
C:ASP15
|
4.5
|
11.9
|
1.0
|
CB
|
C:VAL124
|
4.5
|
8.2
|
1.0
|
ND2
|
C:ASN166
|
4.5
|
8.0
|
1.0
|
CG2
|
C:VAL124
|
4.5
|
8.8
|
1.0
|
N
|
C:ASP11
|
4.6
|
8.3
|
1.0
|
O
|
C:ASP11
|
4.6
|
9.3
|
1.0
|
C2
|
C:GOL3003
|
4.6
|
18.3
|
1.0
|
CA
|
C:VAL124
|
4.6
|
8.0
|
1.0
|
CG
|
C:ASN40
|
4.7
|
10.2
|
1.0
|
OD2
|
C:ASP15
|
4.7
|
11.7
|
1.0
|
N
|
C:ASP16
|
4.7
|
10.0
|
1.0
|
CB
|
C:ASP240
|
4.8
|
8.7
|
1.0
|
CA
|
C:ASP16
|
4.9
|
9.7
|
1.0
|
CG
|
C:ASP15
|
4.9
|
12.1
|
1.0
|
CB
|
C:ASP11
|
4.9
|
9.5
|
1.0
|
C
|
C:ASP11
|
4.9
|
9.6
|
1.0
|
CG
|
C:ASN166
|
4.9
|
8.3
|
1.0
|
ND2
|
C:ASN40
|
5.0
|
7.8
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1q8f
Go back to
Calcium Binding Sites List in 1q8f
Calcium binding site 4 out
of 4 in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik
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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca2004
b:11.9
occ:1.00
|
O
|
D:VAL124
|
2.4
|
7.4
|
1.0
|
O
|
D:HOH3039
|
2.4
|
11.4
|
1.0
|
OD2
|
D:ASP240
|
2.4
|
8.3
|
1.0
|
OD1
|
D:ASP11
|
2.5
|
11.3
|
1.0
|
OD2
|
D:ASP16
|
2.5
|
8.7
|
1.0
|
O
|
D:HOH3023
|
2.5
|
10.1
|
1.0
|
OD1
|
D:ASP16
|
2.5
|
10.0
|
1.0
|
O3
|
D:GOL3004
|
2.7
|
12.7
|
1.0
|
CG
|
D:ASP16
|
2.9
|
8.7
|
1.0
|
CG
|
D:ASP240
|
3.4
|
8.7
|
1.0
|
C
|
D:VAL124
|
3.6
|
8.0
|
1.0
|
CG
|
D:ASP11
|
3.6
|
11.3
|
1.0
|
OD1
|
D:ASP240
|
3.7
|
8.1
|
1.0
|
OD1
|
D:ASN40
|
3.7
|
12.5
|
1.0
|
C3
|
D:GOL3004
|
3.8
|
18.6
|
1.0
|
OD2
|
D:ASP11
|
3.9
|
10.6
|
1.0
|
CA
|
D:GLY125
|
4.3
|
7.2
|
1.0
|
N
|
D:GLY125
|
4.3
|
7.5
|
1.0
|
CB
|
D:ASP16
|
4.3
|
8.4
|
1.0
|
O2
|
D:GOL3004
|
4.4
|
20.7
|
1.0
|
OD1
|
D:ASP15
|
4.4
|
10.6
|
1.0
|
OD1
|
D:ASN166
|
4.5
|
9.0
|
1.0
|
CG2
|
D:VAL124
|
4.5
|
8.8
|
1.0
|
CB
|
D:VAL124
|
4.5
|
6.8
|
1.0
|
N
|
D:ASP11
|
4.5
|
8.3
|
1.0
|
ND2
|
D:ASN166
|
4.6
|
8.2
|
1.0
|
O
|
D:ASP11
|
4.6
|
9.1
|
1.0
|
OD2
|
D:ASP15
|
4.6
|
10.6
|
1.0
|
C2
|
D:GOL3004
|
4.6
|
17.8
|
1.0
|
CA
|
D:VAL124
|
4.6
|
7.7
|
1.0
|
CG
|
D:ASN40
|
4.7
|
9.6
|
1.0
|
CB
|
D:ASP240
|
4.7
|
8.2
|
1.0
|
N
|
D:ASP16
|
4.8
|
9.3
|
1.0
|
CG
|
D:ASP15
|
4.8
|
12.0
|
1.0
|
CB
|
D:ASP11
|
4.9
|
9.0
|
1.0
|
CA
|
D:ASP16
|
4.9
|
8.8
|
1.0
|
C
|
D:ASP11
|
4.9
|
9.0
|
1.0
|
ND2
|
D:ASN40
|
5.0
|
6.1
|
1.0
|
CG
|
D:ASN166
|
5.0
|
8.4
|
1.0
|
|
Reference:
B.Giabbai,
M.Degano.
Crystal Structure to 1.7 A of the Escherichia Coli Pyrimidine Nucleoside Hydrolase Yeik, A Novel Candidate For Cancer Gene Therapy. Structure V. 12 739 2004.
ISSN: ISSN 0969-2126
PubMed: 15130467
DOI: 10.1016/J.STR.2004.03.018
Page generated: Thu Jul 11 14:03:11 2024
|