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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

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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

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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

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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

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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

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