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Calcium in PDB 1lv8: 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: 1lv8 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) 19.85 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.140, 134.235, 177.148, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 25.8

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 1lv8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 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: 1lv8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1lv8

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Calcium binding site 1 out of 6 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:Ca7002

b:31.9
occ:1.00
 O D:HOH7085 2.0 32.0 1.0
OE2 A:GLU58 2.2 27.7 1.0
OE1 D:GLU58 2.4 28.9 1.0
O A:SER51 2.4 38.0 1.0
OE2 D:GLU58 2.5 21.9 1.0
O A:HOH7069 2.5 36.7 1.0
O A:HOH7052 2.7 25.3 1.0
CD D:GLU58 2.7 33.4 1.0
CD A:GLU58 3.4 34.8 1.0
C A:SER51 3.4 30.4 1.0
CA D:CA7001 3.8 35.3 1.0
CA A:SER51 3.8 31.8 1.0
CG A:GLU58 4.0 30.9 1.0
CG D:GLU58 4.2 36.3 1.0
OE1 A:GLU58 4.4 38.3 1.0
CB D:SER51 4.4 31.1 1.0
O A:HOH7119 4.5 46.5 1.0
O D:SER51 4.5 33.5 1.0
N A:GLU52 4.5 32.9 1.0
CB A:SER51 4.6 33.9 1.0
O A:PHE56 4.6 38.7 1.0
O A:TYR50 4.6 26.1 1.0
O D:HOH7100 4.7 35.7 1.0
O A:ILE53 4.8 30.1 1.0
O A:HOH7080 4.9 42.7 1.0
CA A:GLU52 4.9 39.0 1.0
N A:SER51 5.0 30.1 1.0

Calcium binding site 2 out of 6 in 1lv8

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Calcium binding site 2 out of 6 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
B:Ca7005

b:28.4
occ:1.00
 OE1 B:GLU1058 2.2 22.5 1.0
O F:HOH376 2.3 22.7 1.0
O B:HOH363 2.3 30.4 1.0
O B:SER1051 2.4 36.4 1.0
O F:HOH588 2.4 29.6 1.0
OE1 F:GLU2058 2.5 19.3 1.0
OE2 F:GLU2058 2.5 28.5 1.0
CD F:GLU2058 2.8 28.2 1.0
CD B:GLU1058 3.3 33.9 1.0
C B:SER1051 3.4 32.9 1.0
CG B:GLU1058 3.7 35.0 1.0
CA B:SER1051 3.8 25.9 1.0
CA F:CA7006 3.9 26.0 1.0
CG F:GLU2058 4.3 26.1 1.0
OE2 B:GLU1058 4.4 35.7 1.0
CB F:SER2051 4.5 20.8 1.0
N B:GLU1052 4.5 28.9 1.0
O F:HOH368 4.6 33.4 1.0
O B:TYR1050 4.6 24.9 1.0
CB B:SER1051 4.6 35.2 1.0
O B:PHE1056 4.6 37.3 1.0
O B:ILE1053 4.7 26.4 1.0
O F:SER2051 4.7 41.9 1.0
CA B:GLU1052 4.9 27.7 1.0
CA F:SER2051 5.0 34.2 1.0
N B:SER1051 5.0 18.2 1.0

Calcium binding site 3 out of 6 in 1lv8

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Calcium binding site 3 out of 6 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
C:Ca7004

b:31.0
occ:1.00
 OE2 C:GLU2058 2.0 24.8 1.0
O C:HOH262 2.3 28.4 1.0
O C:SER2051 2.4 46.1 1.0
O C:HOH718 2.4 35.6 1.0
OE2 E:GLU1058 2.4 26.7 1.0
O C:HOH305 2.5 32.3 1.0
OE1 E:GLU1058 2.5 37.1 1.0
CD E:GLU1058 2.8 43.4 1.0
CD C:GLU2058 3.1 30.5 1.0
C C:SER2051 3.4 39.6 1.0
CG C:GLU2058 3.7 36.4 1.0
CA C:SER2051 3.8 38.4 1.0
CA E:CA7003 3.9 32.0 1.0
OE1 C:GLU2058 4.2 29.7 1.0
O C:ILE2053 4.3 37.1 1.0
CG E:GLU1058 4.3 35.9 1.0
O C:TYR2050 4.5 29.6 1.0
N C:GLU2052 4.5 39.4 1.0
O C:PHE2056 4.5 27.4 1.0
CB C:SER2051 4.6 38.9 1.0
O E:SER1051 4.7 31.9 1.0
CB E:SER1051 4.7 44.3 1.0
CA C:GLU2052 4.9 35.7 1.0
N C:SER2051 4.9 30.4 1.0
O E:HOH693 5.0 32.3 1.0

Calcium binding site 4 out of 6 in 1lv8

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Calcium binding site 4 out of 6 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
D:Ca7001

b:35.3
occ:1.00
 OE2 D:GLU58 2.1 21.9 1.0
O D:SER51 2.3 33.5 1.0
OE2 A:GLU58 2.3 27.7 1.0
O D:HOH7034 2.4 24.6 1.0
OE1 A:GLU58 2.4 38.3 1.0
O D:HOH7032 2.5 26.0 1.0
O D:HOH7100 2.5 35.7 1.0
CD A:GLU58 2.7 34.8 1.0
C D:SER51 3.3 37.9 1.0
CD D:GLU58 3.3 33.4 1.0
CA D:SER51 3.8 36.5 1.0
CA A:CA7002 3.8 31.9 1.0
CG D:GLU58 4.0 36.3 1.0
CG A:GLU58 4.2 30.9 1.0
OE1 D:GLU58 4.3 28.9 1.0
CB A:SER51 4.4 33.9 1.0
N D:GLU52 4.4 34.5 1.0
O A:SER51 4.5 38.0 1.0
CB D:SER51 4.5 31.1 1.0
O D:PHE56 4.5 36.8 1.0
O A:HOH7069 4.6 36.7 1.0
O D:ILE53 4.6 31.7 1.0
O D:TYR50 4.7 38.7 1.0
CA D:GLU52 4.8 35.4 1.0
CA A:SER51 4.9 31.8 1.0
N D:SER51 5.0 33.9 1.0

Calcium binding site 5 out of 6 in 1lv8

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Calcium binding site 5 out of 6 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
E:Ca7003

b:32.0
occ:1.00
 OE2 E:GLU1058 2.2 26.7 1.0
O E:HOH439 2.2 29.7 1.0
OE1 C:GLU2058 2.4 29.7 1.0
O E:SER1051 2.4 31.9 1.0
O E:HOH155 2.5 29.7 1.0
OE2 C:GLU2058 2.5 24.8 1.0
O E:HOH693 2.6 32.3 1.0
CD C:GLU2058 2.8 30.5 1.0
CD E:GLU1058 3.3 43.4 1.0
C E:SER1051 3.4 29.6 1.0
CG E:GLU1058 3.8 35.9 1.0
CA E:SER1051 3.9 36.5 1.0
CA C:CA7004 3.9 31.0 1.0
CG C:GLU2058 4.3 36.4 1.0
OE1 E:GLU1058 4.4 37.1 1.0
O E:ILE1053 4.4 36.1 1.0
CB C:SER2051 4.5 38.9 1.0
N E:GLU1052 4.5 37.7 1.0
O E:PHE1056 4.6 32.1 1.0
O E:TYR1050 4.6 36.8 1.0
CB E:SER1051 4.7 44.3 1.0
O C:SER2051 4.7 46.1 1.0
O C:HOH718 4.7 35.6 1.0
O E:HOH86 4.7 40.1 1.0
CA E:GLU1052 4.9 34.2 1.0
CA C:SER2051 5.0 38.4 1.0

Calcium binding site 6 out of 6 in 1lv8

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Calcium binding site 6 out of 6 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
F:Ca7006

b:26.0
occ:1.00
 OE1 F:GLU2058 2.2 19.3 1.0
O F:SER2051 2.2 41.9 1.0
O F:HOH368 2.2 33.4 1.0
OE1 B:GLU1058 2.4 22.5 1.0
O F:HOH287 2.4 28.1 1.0
O F:HOH207 2.4 25.3 1.0
OE2 B:GLU1058 2.6 35.7 1.0
CD B:GLU1058 2.8 33.9 1.0
C F:SER2051 3.3 36.1 1.0
CD F:GLU2058 3.4 28.2 1.0
CA F:SER2051 3.8 34.2 1.0
CA B:CA7005 3.9 28.4 1.0
CG F:GLU2058 3.9 26.1 1.0
CG B:GLU1058 4.3 35.0 1.0
OE2 F:GLU2058 4.4 28.5 1.0
N F:GLU2052 4.4 37.3 1.0
O F:ILE2053 4.5 29.5 1.0
O F:TYR2050 4.5 29.3 1.0
CB B:SER1051 4.5 35.2 1.0
O B:SER1051 4.6 36.4 1.0
CB F:SER2051 4.6 20.8 1.0
O F:PHE2056 4.6 36.6 1.0
O F:HOH588 4.7 29.6 1.0
CA F:GLU2052 4.8 33.2 1.0
N F:SER2051 5.0 26.2 1.0
N F:ILE2053 5.0 25.3 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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