Calcium in PDB 6zk3: Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose
Protein crystallography data
The structure of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose, PDB code: 6zk3
was solved by
S.Morera,
A.Vigouroux,
D.Kopecny,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.50 /
1.75
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.81,
86.71,
131.91,
90,
99.44,
90
|
|
R / Rfree (%)
|
16.1 /
18.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose
(pdb code 6zk3). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose, PDB code: 6zk3:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 6zk3
Go back to
Calcium Binding Sites List in 6zk3
Calcium binding site 1 out
of 6 in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:17.8
occ:1.00
|
O
|
A:LEU133
|
2.3
|
16.4
|
1.0
|
|
O2
|
A:RIB402
|
2.4
|
18.6
|
1.0
|
|
OD1
|
A:ASP23
|
2.4
|
16.7
|
1.0
|
|
OD1
|
A:ASP18
|
2.4
|
17.5
|
1.0
|
|
OD2
|
A:ASP250
|
2.5
|
20.5
|
1.0
|
|
OD2
|
A:ASP23
|
2.5
|
17.6
|
1.0
|
|
O1
|
A:RIB402
|
2.5
|
21.2
|
1.0
|
|
O3
|
A:RIB402
|
2.6
|
20.2
|
1.0
|
|
CG
|
A:ASP23
|
2.8
|
16.6
|
1.0
|
|
C2
|
A:RIB402
|
3.1
|
25.2
|
1.0
|
|
C1
|
A:RIB402
|
3.3
|
28.3
|
1.0
|
|
C3
|
A:RIB402
|
3.4
|
23.6
|
1.0
|
|
CG
|
A:ASP250
|
3.4
|
22.4
|
1.0
|
|
C
|
A:LEU133
|
3.5
|
17.8
|
1.0
|
|
CG
|
A:ASP18
|
3.5
|
17.2
|
1.0
|
|
ND2
|
A:ASN47
|
3.6
|
15.8
|
1.0
|
|
OD1
|
A:ASP250
|
3.7
|
21.3
|
1.0
|
|
OD2
|
A:ASP18
|
3.9
|
17.9
|
1.0
|
|
CB
|
A:LEU133
|
4.0
|
15.1
|
1.0
|
|
CB
|
A:ASP23
|
4.2
|
15.9
|
1.0
|
|
CA
|
A:LEU133
|
4.3
|
14.9
|
1.0
|
|
OD1
|
A:ASP22
|
4.3
|
20.0
|
1.0
|
|
O4
|
A:RIB402
|
4.3
|
29.0
|
1.0
|
|
N
|
A:GLY134
|
4.4
|
15.9
|
1.0
|
|
C4
|
A:RIB402
|
4.4
|
26.7
|
1.0
|
|
CA
|
A:GLY134
|
4.5
|
16.1
|
1.0
|
|
OD1
|
A:ASN176
|
4.5
|
16.2
|
1.0
|
|
ND2
|
A:ASN176
|
4.6
|
17.8
|
1.0
|
|
O
|
A:ASP18
|
4.6
|
17.4
|
1.0
|
|
N
|
A:ASP18
|
4.6
|
15.7
|
1.0
|
|
CG
|
A:ASN47
|
4.6
|
24.0
|
1.0
|
|
N
|
A:ASP23
|
4.8
|
16.3
|
1.0
|
|
OD2
|
A:ASP22
|
4.8
|
26.4
|
1.0
|
|
CA
|
A:ASP23
|
4.8
|
15.7
|
1.0
|
|
CB
|
A:ASP250
|
4.8
|
17.6
|
1.0
|
|
CB
|
A:ASP18
|
4.8
|
15.5
|
1.0
|
|
CG
|
A:ASP22
|
4.9
|
21.8
|
1.0
|
|
C
|
A:ASP18
|
5.0
|
19.2
|
1.0
|
|
CG
|
A:ASN176
|
5.0
|
20.5
|
1.0
|
|
Calcium binding site 2 out
of 6 in 6zk3
Go back to
Calcium Binding Sites List in 6zk3
Calcium binding site 2 out
of 6 in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:18.4
occ:1.00
|
O
|
B:LEU133
|
2.3
|
17.3
|
1.0
|
|
O2
|
B:RIB402
|
2.4
|
22.8
|
1.0
|
|
OD2
|
B:ASP250
|
2.4
|
18.7
|
1.0
|
|
OD1
|
B:ASP23
|
2.4
|
19.0
|
1.0
|
|
OD2
|
B:ASP23
|
2.5
|
18.6
|
1.0
|
|
OD1
|
B:ASP18
|
2.5
|
16.9
|
1.0
|
|
O3
|
B:RIB402
|
2.6
|
20.0
|
1.0
|
|
O1
|
B:RIB402
|
2.6
|
20.3
|
1.0
|
|
CG
|
B:ASP23
|
2.7
|
20.2
|
1.0
|
|
C2
|
B:RIB402
|
3.1
|
26.6
|
1.0
|
|
C1
|
B:RIB402
|
3.3
|
27.5
|
1.0
|
|
C3
|
B:RIB402
|
3.4
|
25.4
|
1.0
|
|
CG
|
B:ASP250
|
3.4
|
21.6
|
1.0
|
|
C
|
B:LEU133
|
3.5
|
17.2
|
1.0
|
|
CG
|
B:ASP18
|
3.6
|
17.1
|
1.0
|
|
OD1
|
B:ASP250
|
3.6
|
23.4
|
1.0
|
|
ND2
|
B:ASN47
|
3.7
|
19.6
|
1.0
|
|
CB
|
B:LEU133
|
4.0
|
13.8
|
1.0
|
|
OD2
|
B:ASP18
|
4.0
|
21.5
|
1.0
|
|
CB
|
B:ASP23
|
4.2
|
18.4
|
1.0
|
|
CA
|
B:LEU133
|
4.3
|
14.3
|
1.0
|
|
OD1
|
B:ASP22
|
4.3
|
22.2
|
1.0
|
|
O4
|
B:RIB402
|
4.4
|
28.1
|
1.0
|
|
N
|
B:GLY134
|
4.4
|
15.9
|
1.0
|
|
C4
|
B:RIB402
|
4.4
|
25.8
|
1.0
|
|
CA
|
B:GLY134
|
4.5
|
15.8
|
1.0
|
|
OD1
|
B:ASN176
|
4.5
|
18.2
|
1.0
|
|
ND2
|
B:ASN176
|
4.5
|
16.7
|
1.0
|
|
O
|
B:ASP18
|
4.6
|
20.1
|
1.0
|
|
N
|
B:ASP18
|
4.6
|
15.4
|
1.0
|
|
CG
|
B:ASN47
|
4.7
|
23.7
|
1.0
|
|
N
|
B:ASP23
|
4.8
|
18.8
|
1.0
|
|
CA
|
B:ASP23
|
4.8
|
18.2
|
1.0
|
|
OD2
|
B:ASP22
|
4.8
|
23.9
|
1.0
|
|
CB
|
B:ASP250
|
4.8
|
15.5
|
1.0
|
|
CG
|
B:ASP22
|
4.9
|
23.3
|
1.0
|
|
CB
|
B:ASP18
|
4.9
|
16.7
|
1.0
|
|
C
|
B:ASP18
|
5.0
|
20.0
|
1.0
|
|
CG
|
B:ASN176
|
5.0
|
18.9
|
1.0
|
|
Calcium binding site 3 out
of 6 in 6zk3
Go back to
Calcium Binding Sites List in 6zk3
Calcium binding site 3 out
of 6 in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca401
b:17.5
occ:1.00
|
O
|
C:LEU133
|
2.3
|
15.3
|
1.0
|
|
O2
|
C:RIB402
|
2.4
|
19.5
|
1.0
|
|
OD2
|
C:ASP250
|
2.4
|
18.0
|
1.0
|
|
OD1
|
C:ASP23
|
2.4
|
15.2
|
1.0
|
|
OD2
|
C:ASP23
|
2.5
|
17.2
|
1.0
|
|
OD1
|
C:ASP18
|
2.5
|
16.3
|
1.0
|
|
O3
|
C:RIB402
|
2.5
|
18.7
|
1.0
|
|
O1
|
C:RIB402
|
2.6
|
17.4
|
1.0
|
|
CG
|
C:ASP23
|
2.8
|
16.4
|
1.0
|
|
C2
|
C:RIB402
|
3.1
|
23.2
|
1.0
|
|
C1
|
C:RIB402
|
3.3
|
25.9
|
1.0
|
|
C3
|
C:RIB402
|
3.4
|
22.5
|
1.0
|
|
CG
|
C:ASP250
|
3.4
|
18.9
|
1.0
|
|
C
|
C:LEU133
|
3.4
|
15.3
|
1.0
|
|
CG
|
C:ASP18
|
3.6
|
17.6
|
1.0
|
|
OD1
|
C:ASP250
|
3.6
|
18.3
|
1.0
|
|
ND2
|
C:ASN47
|
3.7
|
16.9
|
1.0
|
|
CB
|
C:LEU133
|
4.0
|
12.6
|
1.0
|
|
OD2
|
C:ASP18
|
4.0
|
19.4
|
1.0
|
|
CB
|
C:ASP23
|
4.2
|
14.2
|
1.0
|
|
CA
|
C:LEU133
|
4.2
|
12.4
|
1.0
|
|
OD1
|
C:ASP22
|
4.3
|
21.0
|
1.0
|
|
N
|
C:GLY134
|
4.3
|
13.6
|
1.0
|
|
O4
|
C:RIB402
|
4.4
|
29.3
|
1.0
|
|
C4
|
C:RIB402
|
4.4
|
26.7
|
1.0
|
|
CA
|
C:GLY134
|
4.4
|
12.8
|
1.0
|
|
OD1
|
C:ASN176
|
4.5
|
17.6
|
1.0
|
|
ND2
|
C:ASN176
|
4.5
|
14.5
|
1.0
|
|
O
|
C:ASP18
|
4.6
|
16.2
|
1.0
|
|
N
|
C:ASP18
|
4.6
|
15.1
|
1.0
|
|
CG
|
C:ASN47
|
4.7
|
21.5
|
1.0
|
|
OD2
|
C:ASP22
|
4.8
|
21.7
|
1.0
|
|
CB
|
C:ASP250
|
4.8
|
14.6
|
1.0
|
|
N
|
C:ASP23
|
4.8
|
15.4
|
1.0
|
|
CA
|
C:ASP23
|
4.8
|
14.3
|
1.0
|
|
CG
|
C:ASP22
|
4.9
|
21.8
|
1.0
|
|
CB
|
C:ASP18
|
4.9
|
15.7
|
1.0
|
|
CG
|
C:ASN176
|
5.0
|
16.8
|
1.0
|
|
Calcium binding site 4 out
of 6 in 6zk3
Go back to
Calcium Binding Sites List in 6zk3
Calcium binding site 4 out
of 6 in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca401
b:17.6
occ:1.00
|
O
|
D:LEU133
|
2.3
|
16.2
|
1.0
|
|
O2
|
D:RIB402
|
2.4
|
18.1
|
1.0
|
|
OD1
|
D:ASP23
|
2.4
|
15.9
|
1.0
|
|
OD1
|
D:ASP18
|
2.5
|
17.1
|
1.0
|
|
OD2
|
D:ASP250
|
2.5
|
18.5
|
1.0
|
|
OD2
|
D:ASP23
|
2.5
|
17.0
|
1.0
|
|
O1
|
D:RIB402
|
2.5
|
21.9
|
1.0
|
|
O3
|
D:RIB402
|
2.6
|
19.6
|
1.0
|
|
CG
|
D:ASP23
|
2.8
|
16.8
|
1.0
|
|
C2
|
D:RIB402
|
3.1
|
24.4
|
1.0
|
|
C1
|
D:RIB402
|
3.3
|
27.9
|
1.0
|
|
C3
|
D:RIB402
|
3.4
|
23.2
|
1.0
|
|
CG
|
D:ASP250
|
3.4
|
18.7
|
1.0
|
|
C
|
D:LEU133
|
3.5
|
17.2
|
1.0
|
|
CG
|
D:ASP18
|
3.5
|
17.7
|
1.0
|
|
ND2
|
D:ASN47
|
3.6
|
14.2
|
1.0
|
|
OD1
|
D:ASP250
|
3.7
|
19.1
|
1.0
|
|
OD2
|
D:ASP18
|
4.0
|
17.7
|
1.0
|
|
CB
|
D:LEU133
|
4.0
|
15.2
|
1.0
|
|
CB
|
D:ASP23
|
4.2
|
16.4
|
1.0
|
|
CA
|
D:LEU133
|
4.3
|
14.7
|
1.0
|
|
OD1
|
D:ASP22
|
4.3
|
20.4
|
1.0
|
|
O4
|
D:RIB402
|
4.3
|
28.0
|
1.0
|
|
C4
|
D:RIB402
|
4.4
|
23.8
|
1.0
|
|
N
|
D:GLY134
|
4.4
|
16.1
|
1.0
|
|
CA
|
D:GLY134
|
4.5
|
14.9
|
1.0
|
|
OD1
|
D:ASN176
|
4.5
|
18.1
|
1.0
|
|
ND2
|
D:ASN176
|
4.5
|
18.5
|
1.0
|
|
O
|
D:ASP18
|
4.6
|
17.5
|
1.0
|
|
N
|
D:ASP18
|
4.6
|
15.7
|
1.0
|
|
CG
|
D:ASN47
|
4.7
|
20.7
|
1.0
|
|
OD2
|
D:ASP22
|
4.8
|
23.2
|
1.0
|
|
N
|
D:ASP23
|
4.8
|
15.4
|
1.0
|
|
CB
|
D:ASP250
|
4.8
|
15.8
|
1.0
|
|
CA
|
D:ASP23
|
4.8
|
14.8
|
1.0
|
|
CB
|
D:ASP18
|
4.8
|
15.2
|
1.0
|
|
CG
|
D:ASP22
|
4.9
|
19.3
|
1.0
|
|
C
|
D:ASP18
|
5.0
|
17.9
|
1.0
|
|
CG
|
D:ASN176
|
5.0
|
20.7
|
1.0
|
|
Calcium binding site 5 out
of 6 in 6zk3
Go back to
Calcium Binding Sites List in 6zk3
Calcium binding site 5 out
of 6 in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca401
b:17.5
occ:1.00
|
O
|
E:LEU133
|
2.3
|
17.2
|
1.0
|
|
O2
|
E:RIB402
|
2.4
|
20.1
|
1.0
|
|
OD2
|
E:ASP250
|
2.4
|
21.8
|
1.0
|
|
OD1
|
E:ASP23
|
2.4
|
17.1
|
1.0
|
|
OD2
|
E:ASP23
|
2.5
|
20.4
|
1.0
|
|
OD1
|
E:ASP18
|
2.5
|
17.1
|
1.0
|
|
O3
|
E:RIB402
|
2.5
|
20.7
|
1.0
|
|
O1
|
E:RIB402
|
2.6
|
22.0
|
1.0
|
|
CG
|
E:ASP23
|
2.8
|
17.0
|
1.0
|
|
C2
|
E:RIB402
|
3.1
|
23.7
|
1.0
|
|
C1
|
E:RIB402
|
3.3
|
26.3
|
1.0
|
|
C3
|
E:RIB402
|
3.4
|
21.6
|
1.0
|
|
CG
|
E:ASP250
|
3.4
|
21.7
|
1.0
|
|
C
|
E:LEU133
|
3.4
|
17.9
|
1.0
|
|
CG
|
E:ASP18
|
3.6
|
17.9
|
1.0
|
|
OD1
|
E:ASP250
|
3.6
|
21.2
|
1.0
|
|
ND2
|
E:ASN47
|
3.7
|
17.5
|
1.0
|
|
CB
|
E:LEU133
|
4.0
|
17.8
|
1.0
|
|
OD2
|
E:ASP18
|
4.0
|
16.8
|
1.0
|
|
CB
|
E:ASP23
|
4.2
|
15.8
|
1.0
|
|
CA
|
E:LEU133
|
4.3
|
17.0
|
1.0
|
|
OD1
|
E:ASP22
|
4.3
|
20.3
|
1.0
|
|
N
|
E:GLY134
|
4.4
|
15.6
|
1.0
|
|
O4
|
E:RIB402
|
4.4
|
28.7
|
1.0
|
|
C4
|
E:RIB402
|
4.4
|
26.6
|
1.0
|
|
CA
|
E:GLY134
|
4.5
|
16.1
|
1.0
|
|
ND2
|
E:ASN176
|
4.5
|
16.2
|
1.0
|
|
OD1
|
E:ASN176
|
4.5
|
18.9
|
1.0
|
|
N
|
E:ASP18
|
4.6
|
16.3
|
1.0
|
|
O
|
E:ASP18
|
4.6
|
18.4
|
1.0
|
|
OD2
|
E:ASP22
|
4.7
|
22.4
|
1.0
|
|
CG
|
E:ASN47
|
4.8
|
19.8
|
1.0
|
|
CB
|
E:ASP250
|
4.8
|
19.1
|
1.0
|
|
CA
|
E:ASP23
|
4.8
|
15.7
|
1.0
|
|
N
|
E:ASP23
|
4.8
|
14.9
|
1.0
|
|
CG
|
E:ASP22
|
4.9
|
22.0
|
1.0
|
|
CB
|
E:ASP18
|
4.9
|
16.6
|
1.0
|
|
CG
|
E:ASN176
|
5.0
|
18.0
|
1.0
|
|
Calcium binding site 6 out
of 6 in 6zk3
Go back to
Calcium Binding Sites List in 6zk3
Calcium binding site 6 out
of 6 in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Ribose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca401
b:17.8
occ:1.00
|
O
|
F:LEU133
|
2.3
|
17.6
|
1.0
|
|
O2
|
F:RIB402
|
2.4
|
20.4
|
1.0
|
|
OD1
|
F:ASP23
|
2.4
|
17.6
|
1.0
|
|
OD2
|
F:ASP250
|
2.4
|
22.2
|
1.0
|
|
OD2
|
F:ASP23
|
2.5
|
20.8
|
1.0
|
|
OD1
|
F:ASP18
|
2.5
|
19.6
|
1.0
|
|
O3
|
F:RIB402
|
2.5
|
19.1
|
1.0
|
|
O1
|
F:RIB402
|
2.6
|
20.2
|
1.0
|
|
CG
|
F:ASP23
|
2.8
|
18.3
|
1.0
|
|
C2
|
F:RIB402
|
3.1
|
25.1
|
1.0
|
|
C1
|
F:RIB402
|
3.3
|
27.1
|
1.0
|
|
C3
|
F:RIB402
|
3.4
|
23.8
|
1.0
|
|
CG
|
F:ASP250
|
3.4
|
20.4
|
1.0
|
|
C
|
F:LEU133
|
3.4
|
18.7
|
1.0
|
|
CG
|
F:ASP18
|
3.6
|
19.8
|
1.0
|
|
OD1
|
F:ASP250
|
3.7
|
22.6
|
1.0
|
|
ND2
|
F:ASN47
|
3.7
|
16.5
|
1.0
|
|
CB
|
F:LEU133
|
4.0
|
15.8
|
1.0
|
|
OD2
|
F:ASP18
|
4.0
|
18.7
|
1.0
|
|
CB
|
F:ASP23
|
4.2
|
16.1
|
1.0
|
|
CA
|
F:LEU133
|
4.3
|
16.6
|
1.0
|
|
OD1
|
F:ASP22
|
4.3
|
18.4
|
1.0
|
|
O4
|
F:RIB402
|
4.4
|
29.8
|
1.0
|
|
N
|
F:GLY134
|
4.4
|
17.1
|
1.0
|
|
C4
|
F:RIB402
|
4.4
|
27.2
|
1.0
|
|
CA
|
F:GLY134
|
4.4
|
16.4
|
1.0
|
|
OD1
|
F:ASN176
|
4.5
|
17.1
|
1.0
|
|
ND2
|
F:ASN176
|
4.5
|
18.1
|
1.0
|
|
O
|
F:ASP18
|
4.6
|
19.6
|
1.0
|
|
N
|
F:ASP18
|
4.6
|
17.7
|
1.0
|
|
CG
|
F:ASN47
|
4.7
|
19.0
|
1.0
|
|
OD2
|
F:ASP22
|
4.7
|
23.0
|
1.0
|
|
N
|
F:ASP23
|
4.8
|
14.4
|
1.0
|
|
CA
|
F:ASP23
|
4.8
|
15.4
|
1.0
|
|
CB
|
F:ASP250
|
4.8
|
19.1
|
1.0
|
|
CG
|
F:ASP22
|
4.9
|
22.0
|
1.0
|
|
CB
|
F:ASP18
|
4.9
|
17.9
|
1.0
|
|
C
|
F:ASP18
|
5.0
|
20.7
|
1.0
|
|
Reference:
E.Luptakova,
A.Vigouroux,
R.Koncitikova,
M.Kopecna,
D.Zalabak,
O.Novak,
N.De Digo,
S.Cavar Zeljkovic,
O.Plihal,
M.Strnad,
K.Von Schwartzenberg,
D.Kopecny,
S.Morera.
Plant Nucleoside N-Ribohydrolases: Substrate Binding and Role in Nitrogen Storage Mobilization To Be Published.
Page generated: Wed Jul 9 20:33:37 2025
|
