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Calcium in PDB 4kpo: Plant Nucleoside Hydrolase - ZMNRH3 Enzyme

Protein crystallography data

The structure of Plant Nucleoside Hydrolase - ZMNRH3 Enzyme, PDB code: 4kpo 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) 43.69 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.440, 85.780, 87.390, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Plant Nucleoside Hydrolase - ZMNRH3 Enzyme (pdb code 4kpo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Plant Nucleoside Hydrolase - ZMNRH3 Enzyme, PDB code: 4kpo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4kpo

Go back to Calcium Binding Sites List in 4kpo
Calcium binding site 1 out of 2 in the Plant Nucleoside Hydrolase - ZMNRH3 Enzyme


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 - ZMNRH3 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:57.9
occ:1.00
O A:LEU123 2.3 50.9 1.0
OD1 A:ASP13 2.5 58.3 1.0
OD2 A:ASP13 2.5 63.4 1.0
OD1 A:ASP8 2.6 57.3 1.0
O A:HOH507 2.7 45.3 1.0
OD2 A:ASP240 2.8 74.5 1.0
CG A:ASP13 2.8 58.2 1.0
ND2 A:ASN37 3.4 47.2 1.0
C A:LEU123 3.4 50.7 1.0
OD1 A:ASP240 3.5 72.8 1.0
CG A:ASP240 3.5 69.9 1.0
CG A:ASP8 3.6 57.0 1.0
OD2 A:ASP8 3.9 60.3 1.0
CB A:LEU123 4.2 48.8 1.0
N A:GLY124 4.2 46.1 1.0
CA A:GLY124 4.3 45.3 1.0
CB A:ASP13 4.3 49.8 1.0
CG A:ASN37 4.3 56.7 1.0
CA A:LEU123 4.3 48.2 1.0
OD1 A:ASN166 4.5 52.3 1.0
CD2 A:LEU149 4.5 58.7 1.0
ND2 A:ASN166 4.6 56.3 1.0
OD1 A:ASP12 4.6 72.8 1.0
OD1 A:ASN37 4.6 49.2 1.0
O A:ASP8 4.6 52.6 1.0
N A:ASP8 4.8 49.2 1.0
CB A:ASP8 4.9 50.5 1.0
CB A:ASP240 5.0 57.6 1.0
CG A:ASN166 5.0 61.2 1.0

Calcium binding site 2 out of 2 in 4kpo

Go back to Calcium Binding Sites List in 4kpo
Calcium binding site 2 out of 2 in the Plant Nucleoside Hydrolase - ZMNRH3 Enzyme


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 - ZMNRH3 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:62.9
occ:1.00
O B:LEU123 2.3 49.9 1.0
OD2 B:ASP13 2.5 65.1 1.0
OD1 B:ASP8 2.5 59.8 1.0
OD1 B:ASP13 2.5 64.7 1.0
OD2 B:ASP240 2.8 71.9 1.0
CG B:ASP13 2.9 63.4 1.0
C B:LEU123 3.4 49.2 1.0
ND2 B:ASN37 3.4 51.3 1.0
OD1 B:ASP240 3.5 70.3 1.0
CG B:ASP240 3.5 69.2 1.0
CG B:ASP8 3.5 59.6 1.0
OD2 B:ASP8 3.9 66.1 1.0
CB B:LEU123 4.2 45.8 1.0
N B:GLY124 4.2 45.9 1.0
CA B:GLY124 4.3 45.8 1.0
CG B:ASN37 4.3 61.6 1.0
CA B:LEU123 4.3 45.1 1.0
CB B:ASP13 4.4 55.9 1.0
CD2 B:LEU149 4.5 55.2 1.0
OD1 B:ASN166 4.5 48.1 1.0
OD1 B:ASN37 4.6 54.5 1.0
ND2 B:ASN166 4.6 47.3 1.0
O B:ASP8 4.6 53.6 1.0
OD1 B:ASP12 4.6 81.8 1.0
N B:ASP8 4.8 48.5 1.0
CB B:ASP8 4.9 50.2 1.0
CB B:ASP240 5.0 60.0 1.0

Reference:

M.Kopecna, H.Blaschke, D.Kopecny, A.Vigouroux, R.Koncitikova, O.Novak, O.Kotland, M.Strnad, S.Morera, K.Von Schwartzenberg. Structure and Function of Nucleoside Hydrolases From Physcomitrella Patens and Maize Catalyzing the Hydrolysis of Purine, Pyrimidine, and Cytokinin Ribosides. Plant Physiol. V. 163 1568 2013.
ISSN: ISSN 0032-0889
PubMed: 24170203
DOI: 10.1104/PP.113.228775
Page generated: Tue Jul 8 23:39:42 2025

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