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Calcium in PDB 2py2: Structure of Herring Type II Antifreeze Protein

Protein crystallography data

The structure of Structure of Herring Type II Antifreeze Protein, PDB code: 2py2 was solved by Y.Liu, Z.Li, Q.Lin, J.Seetharaman, J.Sivaraman, C.-L.Hew, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.279, 146.415, 192.406, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Herring Type II Antifreeze Protein (pdb code 2py2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Herring Type II Antifreeze Protein, PDB code: 2py2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2py2

Go back to Calcium Binding Sites List in 2py2
Calcium binding site 1 out of 6 in the Structure of Herring Type II Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Herring Type II Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:23.4
occ:1.00
 O A:ASP114 2.4 11.7 1.0
OD1 A:ASP114 2.5 15.9 1.0
OD2 A:ASP94 2.5 20.1 1.0
OE1 A:GLN92 2.6 24.5 1.0
O A:HOH937 2.6 25.6 1.0
OD1 A:ASN113 2.8 28.5 1.0
OE1 A:GLU99 2.8 23.0 1.0
CG A:ASP114 3.4 14.5 1.0
CD A:GLN92 3.4 21.6 1.0
C A:ASP114 3.5 11.9 1.0
CG A:ASP94 3.5 22.3 1.0
N A:ASP114 3.6 12.1 1.0
NE2 A:GLN92 3.6 26.0 1.0
CD A:GLU99 3.7 24.1 1.0
CG A:ASN113 3.8 24.7 1.0
CA A:ASP114 4.0 12.8 1.0
CB A:ASP94 4.0 19.2 1.0
O A:HOH931 4.0 31.7 1.0
N A:ASP94 4.1 17.3 1.0
OD2 A:ASP114 4.2 14.5 1.0
CB A:ASP114 4.3 11.7 1.0
CG A:GLU99 4.3 21.8 1.0
NE2 E:HIS119 4.3 17.3 1.0
ND2 A:ASN113 4.3 27.0 1.0
C A:ASN113 4.4 13.4 1.0
O A:HOH993 4.4 31.3 1.0
OE2 A:GLU99 4.5 23.8 1.0
OD1 A:ASP94 4.6 23.7 1.0
N A:THR115 4.7 11.4 1.0
CA A:ASP94 4.7 18.7 1.0
CB A:GLU99 4.7 18.2 1.0
CA A:ASN113 4.8 14.0 1.0
CG A:GLN92 4.9 20.9 1.0
CB A:ASN113 4.9 18.8 1.0
CE1 E:HIS119 4.9 14.2 1.0
O A:GLU99 5.0 15.4 1.0

Calcium binding site 2 out of 6 in 2py2

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Calcium binding site 2 out of 6 in the Structure of Herring Type II Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Herring Type II Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:24.6
occ:1.00
 O B:ASP114 2.5 15.3 1.0
OD2 B:ASP94 2.5 24.7 1.0
OD1 B:ASP114 2.6 17.6 1.0
OD1 B:ASN113 2.6 25.5 1.0
OE1 B:GLN92 2.6 21.3 1.0
OE1 B:GLU99 2.7 28.4 1.0
O B:HOH978 2.9 43.1 1.0
CD B:GLN92 3.5 22.7 1.0
C B:ASP114 3.5 15.7 1.0
CG B:ASN113 3.5 23.7 1.0
N B:ASP114 3.5 14.0 1.0
CG B:ASP94 3.6 24.6 1.0
CG B:ASP114 3.6 18.1 1.0
NE2 B:GLN92 3.7 24.6 1.0
CD B:GLU99 3.8 29.8 1.0
CA B:ASP114 4.0 15.2 1.0
CB B:ASP94 4.1 20.9 1.0
ND2 B:ASN113 4.1 25.7 1.0
C B:ASN113 4.3 14.4 1.0
N B:ASP94 4.3 19.8 1.0
CB B:ASP114 4.4 16.7 1.0
CG B:GLU99 4.5 26.6 1.0
OD2 B:ASP114 4.5 18.5 1.0
O B:HOH956 4.5 35.2 1.0
OD1 B:ASP94 4.7 25.7 1.0
CA B:ASN113 4.7 14.5 1.0
CB B:ASN113 4.7 19.5 1.0
N B:THR115 4.7 15.4 1.0
OE2 B:GLU99 4.7 33.2 1.0
CB B:GLU99 4.8 19.9 1.0
CG B:GLN92 4.9 22.6 1.0
CA B:ASP94 4.9 21.0 1.0

Calcium binding site 3 out of 6 in 2py2

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Calcium binding site 3 out of 6 in the Structure of Herring Type II Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Herring Type II Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca903

b:20.2
occ:1.00
 O C:ASP114 2.4 12.8 1.0
OD1 C:ASP114 2.5 15.7 1.0
OE1 C:GLN92 2.5 22.4 1.0
OD2 C:ASP94 2.5 22.0 1.0
OD1 C:ASN113 2.6 21.6 1.0
OE1 C:GLU99 2.6 28.9 1.0
O C:HOH975 2.7 26.9 1.0
CD C:GLN92 3.3 23.4 1.0
CG C:ASN113 3.5 20.7 1.0
C C:ASP114 3.5 14.0 1.0
NE2 C:GLN92 3.5 24.4 1.0
CG C:ASP114 3.5 13.9 1.0
N C:ASP114 3.6 11.1 1.0
CG C:ASP94 3.6 24.4 1.0
CD C:GLU99 3.8 29.8 1.0
CA C:ASP114 4.0 11.6 1.0
ND2 C:ASN113 4.0 22.3 1.0
CB C:ASP94 4.1 20.8 1.0
C C:ASN113 4.2 12.6 1.0
N C:ASP94 4.3 18.3 1.0
CB C:ASP114 4.3 12.2 1.0
OD2 C:ASP114 4.4 14.4 1.0
CG C:GLU99 4.5 24.4 1.0
CA C:ASN113 4.6 13.0 1.0
CB C:ASN113 4.6 16.8 1.0
N C:THR115 4.7 11.6 1.0
OE2 C:GLU99 4.7 30.6 1.0
OD1 C:ASP94 4.7 27.0 1.0
CG C:GLN92 4.7 20.9 1.0
CB C:GLU99 4.8 20.3 1.0
CA C:ASP94 4.9 18.4 1.0
CA C:THR115 5.0 12.8 1.0

Calcium binding site 4 out of 6 in 2py2

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Calcium binding site 4 out of 6 in the Structure of Herring Type II Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Herring Type II Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca904

b:24.9
occ:1.00
 OD1 D:ASP114 2.5 15.9 1.0
O D:ASP114 2.5 14.2 1.0
OE1 D:GLN92 2.5 19.3 1.0
OD2 D:ASP94 2.6 28.3 1.0
OD1 D:ASN113 2.7 24.8 1.0
O D:HOH951 2.8 35.2 1.0
OE1 D:GLU99 2.8 31.6 1.0
CD D:GLN92 3.4 21.0 1.0
C D:ASP114 3.5 14.6 1.0
NE2 D:GLN92 3.5 20.9 1.0
CG D:ASP114 3.5 16.8 1.0
CD D:GLU99 3.6 29.7 1.0
N D:ASP114 3.6 12.8 1.0
CG D:ASP94 3.6 28.6 1.0
CG D:ASN113 3.6 21.5 1.0
CA D:ASP114 4.0 13.4 1.0
CB D:ASP94 4.0 24.8 1.0
CG D:GLU99 4.2 25.6 1.0
ND2 D:ASN113 4.2 24.3 1.0
N D:ASP94 4.2 19.8 1.0
C D:ASN113 4.3 14.2 1.0
CB D:ASP114 4.3 14.5 1.0
OE2 D:GLU99 4.4 32.5 1.0
OD2 D:ASP114 4.4 17.5 1.0
O D:HOH930 4.4 26.9 1.0
CA D:ASN113 4.7 13.6 1.0
N D:THR115 4.7 12.8 1.0
OD1 D:ASP94 4.7 31.8 1.0
CB D:ASN113 4.7 17.8 1.0
CB D:GLU99 4.7 22.0 1.0
CA D:ASP94 4.8 22.3 1.0
CG D:GLN92 4.8 17.1 1.0

Calcium binding site 5 out of 6 in 2py2

Go back to Calcium Binding Sites List in 2py2
Calcium binding site 5 out of 6 in the Structure of Herring Type II Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Herring Type II Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca905

b:25.5
occ:1.00
 O E:ASP114 2.4 11.6 1.0
OD1 E:ASP114 2.4 14.2 1.0
OD2 E:ASP94 2.5 20.6 1.0
OE1 E:GLN92 2.6 18.0 1.0
O E:HOH932 2.7 26.9 1.0
OE1 E:GLU99 2.8 21.9 1.0
OD1 E:ASN113 2.8 30.1 1.0
CD E:GLN92 3.4 20.8 1.0
CG E:ASP114 3.4 13.9 1.0
C E:ASP114 3.5 10.4 1.0
NE2 E:GLN92 3.5 21.6 1.0
N E:ASP114 3.5 10.2 1.0
CG E:ASP94 3.6 19.6 1.0
CD E:GLU99 3.6 22.9 1.0
CG E:ASN113 3.8 23.1 1.0
O E:HOH928 3.9 24.8 1.0
CA E:ASP114 3.9 9.7 1.0
CB E:ASP94 3.9 18.6 1.0
NE2 A:HIS119 4.2 16.2 1.0
CG E:GLU99 4.2 20.2 1.0
N E:ASP94 4.2 16.4 1.0
CB E:ASP114 4.2 10.5 1.0
OD2 E:ASP114 4.3 14.9 1.0
ND2 E:ASN113 4.3 26.4 1.0
O E:HOH952 4.4 28.3 1.0
C E:ASN113 4.4 12.0 1.0
OE2 E:GLU99 4.4 22.8 1.0
N E:THR115 4.6 12.2 1.0
OD1 E:ASP94 4.7 21.1 1.0
CB E:GLU99 4.7 17.9 1.0
CA E:ASP94 4.7 17.5 1.0
CE1 A:HIS119 4.7 11.8 1.0
CA E:ASN113 4.8 12.6 1.0
CG E:GLN92 4.8 18.9 1.0
CB E:ASN113 4.9 17.0 1.0
CA E:THR115 5.0 12.3 1.0

Calcium binding site 6 out of 6 in 2py2

Go back to Calcium Binding Sites List in 2py2
Calcium binding site 6 out of 6 in the Structure of Herring Type II Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Herring Type II Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca906

b:31.5
occ:1.00
 OE1 F:GLN92 2.4 30.1 1.0
O F:ASP114 2.6 13.8 1.0
OD2 F:ASP94 2.6 32.2 1.0
OD1 F:ASP114 2.6 16.6 1.0
OD1 F:ASN113 2.7 25.4 1.0
OE1 F:GLU99 2.7 33.1 1.0
O F:HOH907 2.9 35.4 1.0
CD F:GLN92 3.4 31.7 1.0
CG F:ASP94 3.5 29.8 1.0
C F:ASP114 3.6 13.4 1.0
CG F:ASP114 3.6 17.0 1.0
CG F:ASN113 3.7 24.1 1.0
N F:ASP114 3.7 13.9 1.0
CD F:GLU99 3.8 33.7 1.0
CB F:ASP94 3.9 23.9 1.0
NE2 F:GLN92 3.9 32.2 1.0
CA F:ASP114 4.1 13.1 1.0
ND2 F:ASN113 4.2 27.7 1.0
N F:ASP94 4.2 20.0 1.0
CG F:GLU99 4.3 29.3 1.0
CB F:ASP114 4.4 13.9 1.0
OD2 F:ASP114 4.5 17.8 1.0
C F:ASN113 4.5 14.2 1.0
CG F:GLN92 4.6 30.7 1.0
OD1 F:ASP94 4.6 31.3 1.0
CA F:ASP94 4.7 22.9 1.0
CB F:GLU99 4.7 24.8 1.0
N F:THR115 4.8 11.6 1.0
CB F:ASN113 4.8 19.3 1.0
OE2 F:GLU99 4.8 36.9 1.0
CA F:ASN113 4.8 14.9 1.0

Reference:

Y.Liu, Z.Li, Q.Lin, J.Kosinski, J.Seetharaman, J.M.Bujnicki, J.Sivaraman, C.L.Hew. Structure and Evolutionary Origin of Ca-Dependent Herring Type II Antifreeze Protein. Plos One V. 2 E548 2007.
ISSN: ESSN 1932-6203
PubMed: 17579720
DOI: 10.1371/JOURNAL.PONE.0000548
Page generated: Fri Jul 12 15:19:42 2024

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