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Calcium in PDB 4kpn: Plant Nucleoside Hydrolase - PPNRH1 Enzyme

Enzymatic activity of Plant Nucleoside Hydrolase - PPNRH1 Enzyme

All present enzymatic activity of Plant Nucleoside Hydrolase - PPNRH1 Enzyme:
3.2.2.1;

Protein crystallography data

The structure of Plant Nucleoside Hydrolase - PPNRH1 Enzyme, PDB code: 4kpn 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) 38.68 / 3.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.850, 126.080, 253.640, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Plant Nucleoside Hydrolase - PPNRH1 Enzyme (pdb code 4kpn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Plant Nucleoside Hydrolase - PPNRH1 Enzyme, PDB code: 4kpn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4kpn

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Calcium binding site 1 out of 8 in the Plant Nucleoside Hydrolase - PPNRH1 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 - PPNRH1 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca400

b:62.2
occ:1.00
 OD1 A:ASP30 2.3 60.6 1.0
O A:LEU141 2.3 65.0 1.0
OD2 A:ASP258 2.6 87.1 1.0
OD1 A:ASP25 2.6 67.8 1.0
OD2 A:ASP30 2.9 62.7 1.0
CG A:ASP30 3.0 60.3 1.0
ND2 A:ASN54 3.3 73.0 1.0
CG A:ASP258 3.4 79.9 1.0
CG A:ASP25 3.4 67.9 1.0
OD1 A:ASP258 3.5 81.2 1.0
C A:LEU141 3.5 65.3 1.0
OD2 A:ASP25 3.6 74.1 1.0
OD1 A:ASP29 4.2 76.8 1.0
OD1 A:ASN184 4.2 76.8 1.0
CG A:ASN54 4.3 81.2 1.0
N A:GLY142 4.4 61.3 1.0
CB A:ASP30 4.4 56.6 1.0
CB A:LEU141 4.4 62.6 1.0
OD1 A:ASN54 4.5 79.6 1.0
O A:ASP25 4.5 61.3 1.0
CA A:GLY142 4.5 60.4 1.0
ND2 A:ASN184 4.5 82.3 1.0
CA A:LEU141 4.5 61.9 1.0
CD2 A:LEU167 4.5 67.8 1.0
CB A:ASP258 4.8 65.0 1.0
CB A:ASP25 4.8 59.7 1.0
CG A:ASN184 4.8 86.7 1.0
N A:ASP25 4.9 60.0 1.0
CG A:ASP29 4.9 76.2 1.0

Calcium binding site 2 out of 8 in 4kpn

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Calcium binding site 2 out of 8 in the Plant Nucleoside Hydrolase - PPNRH1 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 - PPNRH1 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca400

b:65.0
occ:1.00
 O B:LEU141 2.3 61.0 1.0
OD1 B:ASP30 2.3 63.6 1.0
OD1 B:ASP25 2.6 60.7 1.0
OD2 B:ASP258 2.6 80.2 1.0
OD2 B:ASP30 2.9 66.9 1.0
CG B:ASP30 3.0 63.1 1.0
ND2 B:ASN54 3.3 66.9 1.0
CG B:ASP258 3.4 76.3 1.0
CG B:ASP25 3.4 60.0 1.0
OD1 B:ASP258 3.5 78.7 1.0
C B:LEU141 3.5 61.4 1.0
OD2 B:ASP25 3.6 65.8 1.0
OD1 B:ASP29 4.2 79.7 1.0
CG B:ASN54 4.3 73.6 1.0
OD1 B:ASN184 4.3 67.5 1.0
N B:GLY142 4.4 58.0 1.0
CB B:LEU141 4.4 58.6 1.0
CB B:ASP30 4.4 55.9 1.0
CA B:GLY142 4.5 57.5 1.0
OD1 B:ASN54 4.5 68.5 1.0
O B:ASP25 4.5 54.8 1.0
CA B:LEU141 4.5 58.0 1.0
ND2 B:ASN184 4.5 63.3 1.0
CD2 B:LEU167 4.5 66.9 1.0
CB B:ASP25 4.8 51.7 1.0
CB B:ASP258 4.8 61.4 1.0
N B:ASP25 4.9 51.8 1.0
CG B:ASN184 4.9 73.3 1.0
CG B:ASP29 4.9 78.6 1.0

Calcium binding site 3 out of 8 in 4kpn

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Calcium binding site 3 out of 8 in the Plant Nucleoside Hydrolase - PPNRH1 Enzyme


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 - PPNRH1 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca400

b:62.5
occ:1.00
 O C:LEU141 2.3 64.4 1.0
OD1 C:ASP30 2.3 75.2 1.0
OD2 C:ASP258 2.5 83.1 1.0
OD1 C:ASP25 2.5 65.3 1.0
OD2 C:ASP30 2.9 78.4 1.0
CG C:ASP30 3.0 74.0 1.0
ND2 C:ASN54 3.3 60.2 1.0
CG C:ASP258 3.4 78.2 1.0
CG C:ASP25 3.4 65.9 1.0
OD1 C:ASP258 3.5 79.5 1.0
C C:LEU141 3.5 63.6 1.0
OD2 C:ASP25 3.6 72.6 1.0
OD1 C:ASP29 4.3 89.8 1.0
CG C:ASN54 4.3 70.2 1.0
OD1 C:ASN184 4.3 66.3 1.0
N C:GLY142 4.4 58.7 1.0
CB C:LEU141 4.4 58.9 1.0
CB C:ASP30 4.4 64.9 1.0
CA C:GLY142 4.5 58.1 1.0
O C:ASP25 4.5 61.1 1.0
CA C:LEU141 4.5 58.7 1.0
OD1 C:ASN54 4.5 68.9 1.0
CD2 C:LEU167 4.5 68.0 1.0
ND2 C:ASN184 4.5 68.5 1.0
CB C:ASP258 4.8 66.3 1.0
CB C:ASP25 4.8 58.3 1.0
N C:ASP25 4.8 58.0 1.0
CG C:ASN184 4.9 74.6 1.0
CG C:ASP29 4.9 88.3 1.0

Calcium binding site 4 out of 8 in 4kpn

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Calcium binding site 4 out of 8 in the Plant Nucleoside Hydrolase - PPNRH1 Enzyme


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 - PPNRH1 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca400

b:64.8
occ:1.00
 O D:LEU141 2.3 76.5 1.0
OD1 D:ASP30 2.4 76.6 1.0
OD1 D:ASP25 2.5 83.7 1.0
OD2 D:ASP258 2.6 89.2 1.0
OD2 D:ASP30 2.9 80.6 1.0
CG D:ASP30 3.0 76.4 1.0
ND2 D:ASN54 3.3 84.8 1.0
CG D:ASP258 3.4 84.2 1.0
CG D:ASP25 3.4 83.3 1.0
OD1 D:ASP258 3.5 84.7 1.0
C D:LEU141 3.5 76.8 1.0
OD2 D:ASP25 3.6 90.6 1.0
CG D:ASN54 4.3 94.0 1.0
OD1 D:ASP29 4.3 87.6 1.0
OD1 D:ASN184 4.3 87.4 1.0
N D:GLY142 4.4 72.2 1.0
CB D:LEU141 4.4 74.4 1.0
CB D:ASP30 4.5 68.6 1.0
O D:ASP25 4.5 74.4 1.0
OD1 D:ASN54 4.5 92.8 1.0
CA D:GLY142 4.5 71.2 1.0
CA D:LEU141 4.5 73.7 1.0
CD2 D:LEU167 4.5 75.3 1.0
ND2 D:ASN184 4.5 82.6 1.0
CB D:ASP25 4.8 72.1 1.0
CB D:ASP258 4.8 73.6 1.0
N D:ASP25 4.9 72.1 1.0
CG D:ASN184 4.9 91.5 1.0
CG D:ASP29 4.9 86.3 1.0

Calcium binding site 5 out of 8 in 4kpn

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Calcium binding site 5 out of 8 in the Plant Nucleoside Hydrolase - PPNRH1 Enzyme


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 - PPNRH1 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca400

b:77.7
occ:1.00
 OD1 E:ASP30 2.3 81.9 1.0
O E:LEU141 2.3 72.6 1.0
OD1 E:ASP25 2.6 86.7 1.0
OD2 E:ASP258 2.6 98.0 1.0
OD2 E:ASP30 2.9 82.0 1.0
CG E:ASP30 3.0 81.3 1.0
ND2 E:ASN54 3.3 84.7 1.0
CG E:ASP258 3.4 92.1 1.0
CG E:ASP25 3.4 85.8 1.0
OD1 E:ASP258 3.5 93.3 1.0
C E:LEU141 3.5 72.4 1.0
OD2 E:ASP25 3.6 90.9 1.0
CG E:ASN54 4.3 91.7 1.0
OD1 E:ASP29 4.3 98.9 1.0
OD1 E:ASN184 4.3 81.4 1.0
N E:GLY142 4.4 68.4 1.0
CB E:LEU141 4.4 69.2 1.0
CB E:ASP30 4.4 77.3 1.0
OD1 E:ASN54 4.5 85.9 1.0
O E:ASP25 4.5 78.7 1.0
CA E:GLY142 4.5 67.8 1.0
CA E:LEU141 4.5 68.2 1.0
ND2 E:ASN184 4.5 80.7 1.0
CD2 E:LEU167 4.6 75.8 1.0
CB E:ASP25 4.8 75.4 1.0
CB E:ASP258 4.8 80.4 1.0
N E:ASP25 4.9 74.5 1.0
CG E:ASN184 4.9 87.4 1.0
CG E:ASP29 4.9 98.0 1.0

Calcium binding site 6 out of 8 in 4kpn

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Calcium binding site 6 out of 8 in the Plant Nucleoside Hydrolase - PPNRH1 Enzyme


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 - PPNRH1 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca400

b:85.4
occ:1.00
 OD1 F:ASP30 2.3 0.2 1.0
O F:LEU141 2.3 96.8 1.0
OD1 F:ASP25 2.5 0.2 1.0
OD2 F:ASP258 2.6 0.7 1.0
OD2 F:ASP30 2.9 0.3 1.0
CG F:ASP30 3.0 0.5 1.0
ND2 F:ASN54 3.3 0.1 1.0
CG F:ASP258 3.4 0.5 1.0
CG F:ASP25 3.4 0.1 1.0
OD1 F:ASP258 3.5 0.2 1.0
C F:LEU141 3.5 97.5 1.0
OD2 F:ASP25 3.6 0.7 1.0
OD1 F:ASP29 4.3 0.8 1.0
CG F:ASN54 4.3 0.6 1.0
OD1 F:ASN184 4.3 99.7 1.0
N F:GLY142 4.4 93.6 1.0
CB F:ASP30 4.4 97.6 1.0
CB F:LEU141 4.4 95.0 1.0
O F:ASP25 4.5 97.1 1.0
OD1 F:ASN54 4.5 0.0 1.0
CA F:GLY142 4.5 92.2 1.0
CA F:LEU141 4.5 94.1 1.0
ND2 F:ASN184 4.6 97.9 1.0
CD2 F:LEU167 4.6 88.0 1.0
CB F:ASP25 4.8 95.0 1.0
CB F:ASP258 4.8 99.7 1.0
N F:ASP25 4.9 95.2 1.0
CG F:ASN184 4.9 0.6 1.0
CG F:ASP29 4.9 0.1 1.0

Calcium binding site 7 out of 8 in 4kpn

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Calcium binding site 7 out of 8 in the Plant Nucleoside Hydrolase - PPNRH1 Enzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Plant Nucleoside Hydrolase - PPNRH1 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca400

b:86.4
occ:1.00
 O G:LEU141 2.3 98.3 1.0
OD1 G:ASP30 2.4 0.5 1.0
OD1 G:ASP25 2.6 0.1 1.0
OD2 G:ASP258 2.6 0.9 1.0
OD2 G:ASP30 2.9 0.5 1.0
CG G:ASP30 3.0 0.4 1.0
ND2 G:ASN54 3.3 94.0 1.0
CG G:ASP258 3.4 0.6 1.0
CG G:ASP25 3.4 0.4 1.0
OD1 G:ASP258 3.5 0.5 1.0
C G:LEU141 3.5 97.6 1.0
OD2 G:ASP25 3.6 0.4 1.0
CG G:ASN54 4.3 0.0 1.0
OD1 G:ASP29 4.3 0.0 1.0
OD1 G:ASN184 4.3 0.4 1.0
N G:GLY142 4.4 93.2 1.0
CB G:LEU141 4.4 93.6 1.0
OD1 G:ASN54 4.5 99.8 1.0
CB G:ASP30 4.5 94.7 1.0
O G:ASP25 4.5 0.1 1.0
CA G:GLY142 4.5 92.9 1.0
CA G:LEU141 4.5 93.1 1.0
ND2 G:ASN184 4.5 0.4 1.0
CD2 G:LEU167 4.5 90.7 1.0
CB G:ASP25 4.8 99.4 1.0
CB G:ASP258 4.8 0.4 1.0
N G:ASP25 4.9 98.1 1.0
CG G:ASN184 4.9 0.1 1.0
CG G:ASP29 4.9 0.1 1.0

Calcium binding site 8 out of 8 in 4kpn

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Calcium binding site 8 out of 8 in the Plant Nucleoside Hydrolase - PPNRH1 Enzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Plant Nucleoside Hydrolase - PPNRH1 Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca400

b:0.8
occ:1.00
 O H:LEU141 2.3 0.2 1.0
OD1 H:ASP30 2.4 0.2 1.0
OD2 H:ASP258 2.6 0.6 1.0
OD1 H:ASP25 2.6 0.5 1.0
OD2 H:ASP30 2.9 0.4 1.0
CG H:ASP30 3.0 0.6 1.0
ND2 H:ASN54 3.3 0.2 1.0
CG H:ASP258 3.4 0.2 1.0
CG H:ASP25 3.4 0.2 1.0
OD1 H:ASP258 3.5 0.8 1.0
C H:LEU141 3.5 0.3 1.0
OD2 H:ASP25 3.6 0.1 1.0
CG H:ASN54 4.3 0.2 1.0
OD1 H:ASP29 4.3 0.7 1.0
OD1 H:ASN184 4.3 0.3 1.0
N H:GLY142 4.4 0.3 1.0
CB H:LEU141 4.4 0.1 1.0
CB H:ASP30 4.5 0.8 1.0
OD1 H:ASN54 4.5 0.7 1.0
O H:ASP25 4.5 0.4 1.0
CA H:GLY142 4.5 1.0 1.0
CA H:LEU141 4.5 0.2 1.0
ND2 H:ASN184 4.5 0.0 1.0
CD2 H:LEU167 4.5 0.0 1.0
CB H:ASP25 4.8 0.8 1.0
CB H:ASP258 4.8 0.5 1.0
N H:ASP25 4.9 0.8 1.0
CG H:ASN184 4.9 1.0 1.0
CG H:ASP29 4.9 0.9 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 23:38:05 2025

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