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Calcium in PDB 1lvu: Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit

Enzymatic activity of Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit

All present enzymatic activity of Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit:
2.4.2.1;

Protein crystallography data

The structure of Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit, PDB code: 1lvu was solved by A.Bzowska, G.Koellner, B.Wielgus-Kutrowska, A.Stroh, G.Raszewski, A.Holy, T.Steiner, J.Frank, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.014, 132.625, 177.528, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit (pdb code 1lvu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit, PDB code: 1lvu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1lvu

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Calcium binding site 1 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


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 Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8001

b:17.0
occ:1.00
 OE2 A:GLU58 2.2 14.8 1.0
O A:HOH8094 2.3 19.5 1.0
O A:SER51 2.4 14.2 1.0
O A:HOH8018 2.4 12.4 1.0
OE2 D:GLU58 2.4 12.6 1.0
O A:HOH8022 2.5 14.5 1.0
OE1 D:GLU58 2.5 14.9 1.0
CD D:GLU58 2.8 14.3 1.0
C A:SER51 3.3 14.4 1.0
CD A:GLU58 3.4 15.4 1.0
CA A:SER51 3.8 13.8 1.0
CA D:CA8002 4.0 15.2 1.0
CG A:GLU58 4.0 17.1 1.0
O D:HOH8266 4.3 36.2 1.0
CG D:GLU58 4.3 15.3 1.0
CB D:SER51 4.3 14.1 1.0
OE1 A:GLU58 4.4 16.8 1.0
O A:ILE53 4.5 16.6 1.0
N A:GLU52 4.5 15.2 1.0
CB A:SER51 4.5 14.0 1.0
O A:TYR50 4.6 13.6 1.0
O D:SER51 4.6 16.1 1.0
O A:PHE56 4.6 17.0 1.0
O D:HOH8154 4.7 22.4 1.0
CA A:GLU52 4.9 17.9 1.0
CA D:SER51 4.9 14.6 1.0
N A:SER51 5.0 13.8 1.0

Calcium binding site 2 out of 10 in 1lvu

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Calcium binding site 2 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


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 Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8009

b:23.9
occ:1.00
 O A:HOH8082 2.4 19.5 1.0
OE1 A:GLU8 2.4 22.2 1.0
O E:HOH8274 2.5 33.6 1.0
OE1 E:GLU1008 2.5 15.4 1.0
O E:HOH8032 2.5 17.5 1.0
O A:HOH8091 2.5 30.9 1.0
CD A:GLU8 3.4 21.9 1.0
CD E:GLU1008 3.5 18.9 1.0
CG A:GLU8 3.7 19.6 1.0
CG E:GLU1008 3.8 16.1 1.0
NH1 A:ARG154 4.4 11.4 1.0
NH1 E:ARG1154 4.4 14.8 1.0
NE2 A:GLN11 4.4 21.9 1.0
OE2 A:GLU8 4.5 24.0 1.0
OE1 E:GLN1011 4.5 21.6 1.0
OE2 E:GLU1008 4.6 17.9 1.0
O A:HOH8101 4.6 24.2 1.0
O A:HOH8237 4.6 35.8 1.0
O E:HOH8086 4.7 27.3 1.0
O A:HOH8124 5.0 53.7 1.0

Calcium binding site 3 out of 10 in 1lvu

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Calcium binding site 3 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


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 Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca8004

b:14.1
occ:1.00
 OE1 B:GLU1058 2.1 13.5 1.0
O B:SER1051 2.3 15.6 1.0
O B:HOH8071 2.4 20.1 1.0
O B:HOH8022 2.4 8.1 1.0
OE1 F:GLU2058 2.5 14.4 1.0
O B:HOH8052 2.5 15.5 1.0
OE2 F:GLU2058 2.5 14.2 1.0
CD F:GLU2058 2.8 12.3 1.0
CD B:GLU1058 3.3 12.9 1.0
C B:SER1051 3.3 15.2 1.0
CA B:SER1051 3.8 13.1 1.0
CG B:GLU1058 3.9 14.1 1.0
CA F:CA8003 3.9 12.8 1.0
CG F:GLU2058 4.3 12.5 1.0
OE2 B:GLU1058 4.3 16.4 1.0
CB F:SER2051 4.4 13.1 1.0
N B:GLU1052 4.5 14.9 1.0
CB B:SER1051 4.5 14.1 1.0
O B:ILE1053 4.6 12.3 1.0
O B:TYR1050 4.6 10.2 1.0
O F:SER2051 4.6 14.5 1.0
O B:PHE1056 4.7 14.8 1.0
O F:HOH1632 4.8 37.8 1.0
O B:HOH8073 4.8 17.1 1.0
O B:HOH8153 4.9 36.0 1.0
CA B:GLU1052 4.9 16.9 1.0
CA F:SER2051 5.0 13.0 1.0
N B:SER1051 5.0 13.0 1.0

Calcium binding site 4 out of 10 in 1lvu

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Calcium binding site 4 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


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 Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca8007

b:24.9
occ:1.00
 O B:HOH8244 2.4 27.0 1.0
OD1 B:ASP1215 2.5 15.2 1.0
O B:HOH8043 2.5 18.0 1.0
O B:HOH8337 2.5 42.8 1.0
OD2 B:ASP1215 2.6 13.1 1.0
CG B:ASP1215 2.8 12.6 1.0
NH1 B:ARG1210 4.3 19.3 1.0
CB B:ASP1215 4.3 12.2 1.0
OD1 B:ASN1121 4.4 21.0 1.0
CA B:GLY1190 4.5 16.6 1.0
O B:GLU1189 4.6 18.8 1.0
O B:GLY1213 4.8 14.7 1.0
N B:THR1191 4.8 15.3 1.0
O B:HOH8171 4.9 28.3 1.0

Calcium binding site 5 out of 10 in 1lvu

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Calcium binding site 5 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca8010

b:16.8
occ:1.00
 O B:HOH8131 2.3 25.7 1.0
OE1 D:GLU8 2.3 9.9 1.0
O B:HOH8037 2.4 15.3 1.0
O D:HOH8033 2.4 11.9 1.0
OE1 B:GLU1008 2.4 14.8 1.0
O D:HOH8131 2.4 18.1 1.0
CD D:GLU8 3.4 13.0 1.0
CD B:GLU1008 3.4 14.6 1.0
CG D:GLU8 3.8 12.3 1.0
CG B:GLU1008 3.8 13.7 1.0
NH1 D:ARG154 4.3 11.3 1.0
NH1 B:ARG1154 4.3 9.6 1.0
OE1 D:GLN11 4.5 17.8 1.0
OE2 D:GLU8 4.5 16.1 1.0
OE1 B:GLN1011 4.5 17.9 1.0
OE2 B:GLU1008 4.5 13.4 1.0
O D:HOH8094 4.6 22.9 1.0
O B:HOH8200 4.6 24.2 1.0
O B:HOH8103 4.7 28.5 1.0
O D:HOH8118 4.9 27.8 1.0
O B:HOH8122 4.9 33.3 1.0

Calcium binding site 6 out of 10 in 1lvu

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Calcium binding site 6 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca8005

b:16.7
occ:1.00
 OE2 C:GLU2058 2.2 16.4 1.0
O C:HOH355 2.3 21.9 1.0
O C:SER2051 2.3 17.1 1.0
O E:HOH8072 2.4 21.2 1.0
O C:HOH117 2.5 10.0 1.0
OE1 E:GLU1058 2.5 13.2 1.0
OE2 E:GLU1058 2.6 15.5 1.0
CD E:GLU1058 2.9 13.8 1.0
C C:SER2051 3.3 17.2 1.0
CD C:GLU2058 3.4 17.2 1.0
CA C:SER2051 3.7 17.8 1.0
CG C:GLU2058 3.9 18.1 1.0
CA E:CA8006 4.0 19.7 1.0
CG E:GLU1058 4.4 17.4 1.0
OE1 C:GLU2058 4.4 15.8 1.0
CB C:SER2051 4.4 19.2 1.0
CB E:SER1051 4.4 18.1 1.0
N C:GLU2052 4.5 17.7 1.0
O C:ILE2053 4.5 18.0 1.0
O C:TYR2050 4.5 16.2 1.0
O E:HOH8211 4.5 44.7 1.0
O C:PHE2056 4.6 18.6 1.0
O E:SER1051 4.6 15.3 1.0
O E:HOH8153 4.7 33.5 1.0
O E:HOH8042 4.7 16.6 1.0
O C:HOH950 4.7 34.2 1.0
O C:HOH1409 4.8 37.0 1.0
N C:SER2051 4.9 15.7 1.0
CA C:GLU2052 4.9 19.1 1.0
CA E:SER1051 5.0 16.6 1.0

Calcium binding site 7 out of 10 in 1lvu

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Calcium binding site 7 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca8002

b:15.2
occ:1.00
 OE1 D:GLU58 2.1 14.9 1.0
O D:HOH8058 2.2 15.9 1.0
O D:SER51 2.4 16.1 1.0
O D:HOH8154 2.4 22.4 1.0
O D:HOH8044 2.4 18.7 1.0
OE1 A:GLU58 2.4 16.8 1.0
OE2 A:GLU58 2.5 14.8 1.0
CD A:GLU58 2.8 15.4 1.0
CD D:GLU58 3.3 14.3 1.0
C D:SER51 3.3 14.9 1.0
CA D:SER51 3.7 14.6 1.0
CG D:GLU58 3.8 15.3 1.0
CA A:CA8001 4.0 17.0 1.0
CG A:GLU58 4.3 17.1 1.0
OE2 D:GLU58 4.3 12.6 1.0
O A:HOH8249 4.4 37.6 1.0
O D:HOH8272 4.4 43.6 1.0
CB A:SER51 4.4 14.0 1.0
O D:ILE53 4.5 13.0 1.0
N D:GLU52 4.5 14.4 1.0
O A:HOH8094 4.5 19.5 1.0
CB D:SER51 4.5 14.1 1.0
O D:TYR50 4.5 10.4 1.0
O D:PHE56 4.5 16.0 1.0
O A:HOH8074 4.7 26.4 1.0
O A:SER51 4.7 14.2 1.0
O D:HOH8160 4.8 30.4 1.0
CA D:GLU52 4.9 15.6 1.0
N D:SER51 4.9 13.3 1.0
O A:HOH8116 5.0 41.4 1.0
CA A:SER51 5.0 13.8 1.0

Calcium binding site 8 out of 10 in 1lvu

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Calcium binding site 8 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca8006

b:19.7
occ:1.00
 OE2 E:GLU1058 2.1 15.5 1.0
O E:HOH8090 2.2 23.5 1.0
O E:SER1051 2.3 15.3 1.0
O E:HOH8042 2.4 16.6 1.0
O E:HOH8059 2.4 15.4 1.0
OE2 C:GLU2058 2.5 16.4 1.0
OE1 C:GLU2058 2.5 15.8 1.0
CD C:GLU2058 2.8 17.2 1.0
CD E:GLU1058 3.3 13.8 1.0
C E:SER1051 3.3 16.8 1.0
CA E:SER1051 3.8 16.6 1.0
CG E:GLU1058 3.9 17.4 1.0
O E:HOH8192 3.9 46.4 1.0
CA C:CA8005 4.0 16.7 1.0
OE1 E:GLU1058 4.3 13.2 1.0
CG C:GLU2058 4.3 18.1 1.0
CB C:SER2051 4.5 19.2 1.0
O E:ILE1053 4.5 15.4 1.0
N E:GLU1052 4.5 16.8 1.0
O E:TYR1050 4.5 17.3 1.0
CB E:SER1051 4.5 18.1 1.0
O E:PHE1056 4.5 16.5 1.0
O C:SER2051 4.7 17.1 1.0
O E:HOH8211 4.8 44.7 1.0
O E:HOH8072 4.8 21.2 1.0
CA E:GLU1052 4.9 18.1 1.0
N E:SER1051 4.9 16.4 1.0
O C:HOH453 5.0 27.9 1.0

Calcium binding site 9 out of 10 in 1lvu

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Calcium binding site 9 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca8003

b:12.8
occ:1.00
 O F:HOH306 2.2 16.1 1.0
OE2 F:GLU2058 2.3 14.2 1.0
O F:SER2051 2.3 14.5 1.0
O B:HOH8073 2.4 17.1 1.0
O F:HOH204 2.5 10.9 1.0
OE2 B:GLU1058 2.5 16.4 1.0
OE1 B:GLU1058 2.5 13.5 1.0
CD B:GLU1058 2.8 12.9 1.0
C F:SER2051 3.3 13.2 1.0
CD F:GLU2058 3.5 12.3 1.0
CA F:SER2051 3.7 13.0 1.0
CA B:CA8004 3.9 14.1 1.0
CG F:GLU2058 4.0 12.5 1.0
CG B:GLU1058 4.3 14.1 1.0
O B:HOH8153 4.4 36.0 1.0
O F:ILE2053 4.4 15.0 1.0
N F:GLU2052 4.4 13.4 1.0
CB B:SER1051 4.5 14.1 1.0
OE1 F:GLU2058 4.5 14.4 1.0
CB F:SER2051 4.5 13.1 1.0
O F:PHE2056 4.6 13.4 1.0
O F:TYR2050 4.6 9.8 1.0
O B:HOH8071 4.6 20.1 1.0
O B:HOH8140 4.7 29.8 1.0
O B:SER1051 4.7 15.6 1.0
O B:HOH8134 4.8 26.7 1.0
CA F:GLU2052 4.8 14.1 1.0
N F:SER2051 4.9 10.7 1.0

Calcium binding site 10 out of 10 in 1lvu

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Calcium binding site 10 out of 10 in the Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase in A New Space Group with Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca8008

b:24.4
occ:1.00
 OD1 F:ASP2215 2.1 10.6 1.0
O F:HOH582 2.3 22.4 1.0
OD2 F:ASP2215 2.4 7.9 1.0
CG F:ASP2215 2.6 10.2 1.0
O F:HOH76 2.6 20.3 1.0
O F:HOH588 3.4 36.8 1.0
ND2 F:ASN2121 3.7 16.0 1.0
NH1 F:ARG2210 3.9 14.1 1.0
CB F:ASP2215 4.1 9.8 1.0
NH2 F:ARG2210 4.4 13.8 1.0
O F:HOH1014 4.5 25.0 1.0
CZ F:ARG2210 4.6 14.3 1.0
O F:GLY2213 4.7 15.4 1.0
O F:HOH292 4.7 21.8 1.0
O F:GLU2189 4.7 20.4 1.0
CA F:GLY2190 4.8 15.2 1.0
CG F:ASN2121 4.9 16.5 1.0
CA F:ASP2215 4.9 11.8 1.0

Reference:

A.Bzowska, G.Koellner, B.Wielgus-Kutrowska, A.Stroh, G.Raszewski, A.Holy, T.Steiner, J.Frank. Crystal Structure of Calf Spleen Purine Nucleoside Phosphorylase with Two Full Trimers in the Asymmetric Unit: Important Implications For the Mechanism of Catalysis J.Mol.Biol. V. 342 1015 2004.
ISSN: ISSN 0022-2836
PubMed: 15342253
DOI: 10.1016/J.JMB.2004.07.017
Page generated: Thu Jul 11 12:07:08 2024

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