Atomistry » Calcium » PDB 1lu1-1m8v » 1lv8
Atomistry »
  Calcium »
    PDB 1lu1-1m8v »
      1lv8 »

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

Go back to Calcium Binding Sites List in 1lv8
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

Go back to Calcium Binding Sites List in 1lv8
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

Go back to Calcium Binding Sites List in 1lv8
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

Go back to Calcium Binding Sites List in 1lv8
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

Go back to Calcium Binding Sites List in 1lv8
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

Go back to Calcium Binding Sites List in 1lv8
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: Sat Dec 12 03:05:54 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy