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Calcium in PDB 2zoc: Crystal Structure of Recombinant Human Annexin IV

Protein crystallography data

The structure of Crystal Structure of Recombinant Human Annexin IV, PDB code: 2zoc was solved by M.Konno, Y.Kaneko-Kanzaki, N.Fushinobu-Okushi, K.Mochizuki, E.Uchikaw, A.Satoh, K.Aikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.223, 55.132, 127.147, 90.00, 91.45, 90.00
R / Rfree (%) 21.6 / 25.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Recombinant Human Annexin IV (pdb code 2zoc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Recombinant Human Annexin IV, PDB code: 2zoc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2zoc

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Calcium binding site 1 out of 8 in the Crystal Structure of Recombinant Human Annexin IV


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 Recombinant Human Annexin IV within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:16.3
occ:1.00
 O A:MET99 2.2 12.7 1.0
OD1 A:ASP143 2.3 12.8 1.0
O A:GLY103 2.4 15.1 1.0
O A:GLY101 2.4 15.7 1.0
OD2 A:ASP143 2.6 16.5 1.0
CG A:ASP143 2.8 14.3 1.0
C A:MET99 3.4 14.0 1.0
C A:GLY103 3.6 16.4 1.0
C A:GLY101 3.7 15.9 1.0
CA A:MET99 4.1 13.3 1.0
N A:GLY101 4.1 15.2 1.0
N A:GLY103 4.1 17.1 1.0
C A:ALA102 4.2 17.7 1.0
CB A:ASP143 4.3 16.1 1.0
C A:LYS100 4.3 15.1 1.0
CA A:GLY103 4.3 16.3 1.0
N A:LYS100 4.4 13.7 1.0
O A:ALA102 4.4 18.7 1.0
CA A:GLY101 4.5 14.6 1.0
N A:THR104 4.5 14.8 1.0
CA A:LYS100 4.6 15.5 1.0
CB A:THR104 4.6 17.6 1.0
N A:ALA102 4.6 16.4 1.0
CA A:THR104 4.6 15.6 1.0
CA A:ALA102 4.7 17.7 1.0
O A:LYS100 4.7 16.0 1.0
CB A:MET99 4.7 13.0 1.0
CG2 A:THR104 4.8 17.8 1.0
CA A:ASP143 4.9 15.8 1.0

Calcium binding site 2 out of 8 in 2zoc

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Calcium binding site 2 out of 8 in the Crystal Structure of Recombinant Human Annexin IV


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 Recombinant Human Annexin IV within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:14.9
occ:1.00
 O A:GLY182 2.1 16.5 1.0
O A:LYS185 2.3 16.9 1.0
O A:GLY187 2.3 16.5 1.0
OE2 A:GLU227 2.4 10.9 1.0
OE1 A:GLU227 2.5 14.3 1.0
CD A:GLU227 2.8 11.2 1.0
C A:GLY182 3.1 16.2 1.0
C A:LYS185 3.4 17.4 1.0
C A:GLY187 3.5 13.9 1.0
N A:GLY187 3.7 13.4 1.0
CA A:GLY182 3.8 13.9 1.0
N A:GLU183 4.0 15.1 1.0
N A:LYS185 4.1 18.1 1.0
OG1 A:THR188 4.1 11.3 1.0
CA A:LYS185 4.2 17.5 1.0
CA A:GLY187 4.2 14.5 1.0
CG A:GLU227 4.3 10.6 1.0
O A:GLU183 4.3 14.5 1.0
C A:TRP186 4.3 13.3 1.0
CA A:GLU183 4.3 16.1 1.0
CB A:LYS185 4.4 18.9 1.0
C A:GLU183 4.4 16.9 1.0
N A:TRP186 4.4 15.6 1.0
N A:THR188 4.5 14.6 1.0
O A:HOH541 4.6 23.7 1.0
CA A:TRP186 4.6 14.3 1.0
CA A:THR188 4.7 14.2 1.0
N A:GLY182 4.9 15.2 1.0
O A:ALA181 4.9 13.0 1.0
O A:HOH626 4.9 24.7 1.0
CB A:THR188 5.0 13.8 1.0

Calcium binding site 3 out of 8 in 2zoc

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Calcium binding site 3 out of 8 in the Crystal Structure of Recombinant Human Annexin IV


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 Recombinant Human Annexin IV within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:21.6
occ:1.00
 O A:LYS225 2.2 12.2 1.0
O A:THR228 2.3 12.5 1.0
OE1 A:GLU233 2.4 14.5 1.0
CD A:GLU233 3.3 18.0 1.0
C A:LYS225 3.3 14.5 1.0
C A:THR228 3.5 14.1 1.0
OE2 A:GLU233 3.7 15.1 1.0
CA A:SER229 3.9 14.9 1.0
CA A:LYS225 3.9 13.4 1.0
CB A:SER229 4.1 17.2 1.0
N A:SER229 4.2 14.3 1.0
N A:SER226 4.4 13.3 1.0
CG A:GLU233 4.5 15.5 1.0
N A:THR228 4.6 15.1 1.0
O A:HOH637 4.6 25.4 1.0
CA A:THR228 4.6 13.6 1.0
O A:ILE224 4.6 13.5 1.0
CB A:LYS225 4.7 14.5 1.0
CA A:SER226 4.7 15.1 1.0
C A:SER226 4.9 14.6 1.0

Calcium binding site 4 out of 8 in 2zoc

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Calcium binding site 4 out of 8 in the Crystal Structure of Recombinant Human Annexin IV


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 Recombinant Human Annexin IV within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:10.3
occ:1.00
 O A:MET258 2.2 10.9 1.0
OD2 A:ASP302 2.3 12.2 1.0
O A:GLY262 2.4 10.4 1.0
O A:GLY260 2.5 12.2 1.0
OD1 A:ASP302 2.6 9.7 1.0
CG A:ASP302 2.8 11.4 1.0
C A:MET258 3.3 11.2 1.0
C A:GLY262 3.5 10.0 1.0
C A:GLY260 3.7 14.9 1.0
N A:GLY262 3.8 12.0 1.0
CA A:MET258 4.0 10.6 1.0
CA A:GLY262 4.1 12.4 1.0
N A:GLY260 4.2 14.8 1.0
OG1 A:THR263 4.2 8.9 1.0
C A:LEU261 4.2 13.8 1.0
CB A:ASP302 4.2 14.3 1.0
C A:LYS259 4.4 15.2 1.0
N A:LYS259 4.4 13.0 1.0
O A:HOH562 4.5 21.7 1.0
CB A:MET258 4.5 10.2 1.0
N A:THR263 4.5 11.0 1.0
CA A:GLY260 4.6 14.2 1.0
N A:LEU261 4.6 13.6 1.0
CA A:LEU261 4.7 12.7 1.0
CA A:LYS259 4.7 13.9 1.0
CA A:THR263 4.8 11.2 1.0
O A:LEU261 4.8 13.3 1.0
O A:HOH635 4.9 30.7 1.0
CA A:ASP302 4.9 15.7 1.0
O A:LYS259 5.0 15.0 1.0

Calcium binding site 5 out of 8 in 2zoc

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Calcium binding site 5 out of 8 in the Crystal Structure of Recombinant Human Annexin IV


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 Recombinant Human Annexin IV within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:20.6
occ:1.00
 O B:MET99 2.2 15.4 1.0
O B:GLY101 2.3 16.3 1.0
OD1 B:ASP143 2.4 18.6 1.0
O B:GLY103 2.5 16.8 1.0
OD2 B:ASP143 2.6 18.7 1.0
CG B:ASP143 2.8 18.1 1.0
C B:MET99 3.3 18.1 1.0
C B:GLY101 3.5 17.8 1.0
C B:GLY103 3.7 17.3 1.0
CA B:MET99 3.9 16.9 1.0
N B:GLY103 3.9 17.1 1.0
C B:ALA102 4.1 17.4 1.0
N B:GLY101 4.2 19.8 1.0
C B:LYS100 4.3 20.2 1.0
CB B:ASP143 4.3 20.8 1.0
OG1 B:THR104 4.3 18.1 1.0
CA B:ALA102 4.3 16.4 1.0
N B:ALA102 4.4 15.9 1.0
N B:LYS100 4.4 18.9 1.0
CA B:GLY103 4.4 17.4 1.0
CA B:GLY101 4.5 17.2 1.0
CB B:MET99 4.5 14.4 1.0
O B:ALA102 4.6 16.7 1.0
O B:LYS100 4.6 21.7 1.0
CA B:LYS100 4.7 20.6 1.0
N B:THR104 4.7 17.2 1.0
CA B:THR104 4.8 14.8 1.0
CA B:ASP143 4.9 19.7 1.0

Calcium binding site 6 out of 8 in 2zoc

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Calcium binding site 6 out of 8 in the Crystal Structure of Recombinant Human Annexin IV


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 Recombinant Human Annexin IV within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca506

b:18.4
occ:1.00
 O B:GLY182 2.2 22.0 1.0
O B:LYS185 2.2 25.2 1.0
OE1 B:GLU227 2.3 17.2 1.0
O B:GLY187 2.4 21.5 1.0
OE2 B:GLU227 2.8 15.6 1.0
CD B:GLU227 2.9 16.7 1.0
C B:GLY182 3.1 25.6 1.0
C B:LYS185 3.5 24.0 1.0
C B:GLY187 3.6 22.4 1.0
N B:GLY187 3.7 22.0 1.0
CA B:GLY182 3.7 24.1 1.0
OG1 B:THR188 4.0 19.7 1.0
N B:GLU183 4.0 23.9 1.0
CA B:GLY187 4.2 21.5 1.0
N B:LYS185 4.2 25.3 1.0
CA B:LYS185 4.3 24.5 1.0
C B:TRP186 4.3 22.3 1.0
O B:GLU183 4.3 24.3 1.0
CA B:GLU183 4.4 25.5 1.0
CG B:GLU227 4.4 18.3 1.0
N B:TRP186 4.4 23.2 1.0
C B:GLU183 4.4 25.7 1.0
CA B:TRP186 4.5 22.2 1.0
N B:THR188 4.7 21.5 1.0
CB B:LYS185 4.7 24.2 1.0
CA B:THR188 4.9 21.9 1.0
N B:GLY182 4.9 25.8 1.0

Calcium binding site 7 out of 8 in 2zoc

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Calcium binding site 7 out of 8 in the Crystal Structure of Recombinant Human Annexin IV


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 Recombinant Human Annexin IV within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca507

b:28.9
occ:1.00
 O B:THR228 2.2 23.1 1.0
O B:LYS225 2.2 23.5 1.0
OE1 B:GLU233 2.4 20.8 1.0
C B:THR228 3.4 23.0 1.0
C B:LYS225 3.4 22.6 1.0
CD B:GLU233 3.5 20.7 1.0
CA B:SER229 3.7 22.5 1.0
CB B:SER229 3.8 22.0 1.0
N B:SER229 4.0 22.5 1.0
OE2 B:GLU233 4.1 19.9 1.0
CA B:LYS225 4.1 21.7 1.0
N B:SER226 4.5 23.0 1.0
CG B:GLU233 4.6 19.3 1.0
CA B:THR228 4.6 24.0 1.0
N B:THR228 4.6 23.9 1.0
CA B:SER226 4.7 23.1 1.0
O B:ILE224 4.8 20.7 1.0
C B:SER226 4.8 23.1 1.0
CB B:LYS225 4.8 20.7 1.0
CB B:GLU233 5.0 18.4 1.0
O B:SER226 5.0 23.8 1.0

Calcium binding site 8 out of 8 in 2zoc

Go back to Calcium Binding Sites List in 2zoc
Calcium binding site 8 out of 8 in the Crystal Structure of Recombinant Human Annexin IV


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 Recombinant Human Annexin IV within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca508

b:18.5
occ:1.00
 O B:GLY262 2.3 15.7 1.0
OD2 B:ASP302 2.3 16.8 1.0
O B:MET258 2.3 15.6 1.0
O B:GLY260 2.4 24.0 1.0
OD1 B:ASP302 2.5 15.9 1.0
CG B:ASP302 2.7 16.3 1.0
C B:GLY262 3.4 17.1 1.0
C B:MET258 3.5 16.0 1.0
C B:GLY260 3.6 23.4 1.0
N B:GLY262 3.7 21.1 1.0
CA B:MET258 4.1 16.5 1.0
CA B:GLY262 4.1 20.2 1.0
C B:LEU261 4.2 23.1 1.0
OG1 B:THR263 4.2 16.4 1.0
CB B:ASP302 4.2 17.4 1.0
N B:GLY260 4.3 21.6 1.0
O B:HOH546 4.3 21.4 1.0
C B:LYS259 4.4 20.7 1.0
CA B:LEU261 4.4 22.5 1.0
N B:LEU261 4.5 24.1 1.0
N B:THR263 4.5 18.0 1.0
O B:HOH580 4.5 38.1 1.0
CA B:GLY260 4.5 22.7 1.0
N B:LYS259 4.6 18.3 1.0
O B:LYS259 4.6 20.7 1.0
CB B:MET258 4.7 16.4 1.0
CA B:THR263 4.8 16.2 1.0
CA B:LYS259 4.8 19.8 1.0
O B:LEU261 4.9 23.1 1.0
CA B:ASP302 4.9 16.5 1.0

Reference:

M.Konno, Y.Kaneko-Kanzaki, N.Fushinobu-Okushi, K.Mochizuki, E.Uchikawa, A.Satoh, K.Aikawa. The Comparison of the Loop Structure of Membrane Binding Sites Between Human and Bovine Annexin IV To Be Published.
Page generated: Fri Jul 12 20:08:17 2024

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