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Calcium in PDB 1v6c: Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11

Protein crystallography data

The structure of Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11, PDB code: 1v6c was solved by D.Dong, T.Ihara, H.Motoshima, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.62 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.942, 138.476, 64.772, 90.00, 97.48, 90.00
R / Rfree (%) 19.6 / 21.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 (pdb code 1v6c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11, PDB code: 1v6c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1v6c

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Calcium binding site 1 out of 7 in the Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11


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 Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:11.2
occ:1.00
 O A:GLU80 2.2 13.0 1.0
O A:ILE76 2.3 10.2 1.0
OE1 A:GLU2 2.4 12.3 1.0
O A:VAL82 2.4 13.1 1.0
OD1 A:ASP39 2.4 14.1 1.0
OD1 A:ASN78 2.4 11.8 1.0
OD2 A:ASP39 2.5 11.7 1.0
CG A:ASP39 2.8 12.6 1.0
CG A:ASN78 3.4 13.5 1.0
C A:GLU80 3.4 14.5 1.0
CD A:GLU2 3.5 14.5 1.0
C A:ILE76 3.5 10.2 1.0
C A:VAL82 3.5 12.5 1.0
N A:VAL82 3.6 10.7 1.0
ND2 A:ASN78 3.9 12.3 1.0
N A:ASN78 3.9 12.2 1.0
CG A:GLU2 4.0 14.7 1.0
C A:GLY81 4.1 11.1 1.0
CA A:VAL82 4.1 12.0 1.0
N A:GLU80 4.2 17.6 1.0
CA A:GLY81 4.3 11.2 1.0
CB A:ASP39 4.3 12.3 1.0
N A:GLY81 4.3 13.0 1.0
CA A:ALA77 4.4 10.9 1.0
N A:ALA77 4.4 10.2 1.0
CA A:GLU80 4.4 16.2 1.0
CG A:GLU80 4.5 20.7 1.0
C A:ALA77 4.5 12.0 1.0
CA A:ILE76 4.5 11.1 1.0
OE2 A:GLU2 4.5 14.6 1.0
N A:ILE76 4.6 11.6 1.0
CB A:ASN78 4.6 12.5 1.0
N A:VAL83 4.7 11.4 1.0
CA A:ASN78 4.7 13.4 1.0
CG1 A:VAL83 4.7 12.8 1.0
C A:ASN78 4.9 14.6 1.0
O A:GLY81 4.9 10.1 1.0
CB A:GLU2 4.9 16.7 1.0
N A:ASN79 4.9 15.8 1.0
CA A:ASP39 4.9 12.9 1.0
CA A:VAL83 5.0 11.5 1.0

Calcium binding site 2 out of 7 in 1v6c

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Calcium binding site 2 out of 7 in the Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11


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 Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:15.8
occ:1.00
 O A:LEU405 2.3 18.9 1.0
O A:GLY409 2.3 18.9 1.0
O A:VAL407 2.3 21.6 1.0
OD1 A:ASP404 2.3 18.6 1.0
OD1 A:ASP411 2.3 15.4 1.0
O A:HOH511 2.3 13.5 1.0
C A:LEU405 3.5 19.1 1.0
C A:GLY409 3.5 20.0 1.0
CG A:ASP404 3.5 21.5 1.0
C A:VAL407 3.5 21.8 1.0
CG A:ASP411 3.6 15.8 1.0
N A:LEU405 3.8 17.0 1.0
N A:GLY409 3.9 20.6 1.0
OD2 A:ASP404 4.0 22.4 1.0
OG1 A:THR414 4.1 14.6 1.0
C A:ALA408 4.1 21.5 1.0
N A:VAL407 4.2 21.2 1.0
O A:GLY415 4.2 14.1 1.0
C A:SER406 4.2 21.9 1.0
CA A:LEU405 4.2 17.7 1.0
CA A:GLY409 4.3 20.8 1.0
N A:ASP411 4.3 16.2 1.0
CB A:ASP411 4.3 13.5 1.0
O A:SER406 4.4 22.0 1.0
CA A:VAL407 4.4 21.5 1.0
N A:ARG410 4.4 19.5 1.0
N A:ALA408 4.4 21.7 1.0
OD2 A:ASP411 4.5 13.7 1.0
N A:SER406 4.5 19.9 1.0
CA A:ALA408 4.5 21.7 1.0
CG1 A:VAL407 4.5 22.8 1.0
CB A:SER406 4.5 22.4 1.0
C A:ASP404 4.5 18.0 1.0
C A:ARG410 4.6 18.4 1.0
CA A:ARG410 4.6 19.4 1.0
O A:ALA408 4.6 21.1 1.0
CA A:SER406 4.6 22.0 1.0
CB A:ASP404 4.7 19.7 1.0
CA A:ASP404 4.7 17.6 1.0
CA A:ASP411 5.0 14.4 1.0

Calcium binding site 3 out of 7 in 1v6c

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Calcium binding site 3 out of 7 in the Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11


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 Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:22.3
occ:1.00
 O A:VAL174 2.2 10.9 1.0
O A:TYR171 2.3 9.9 1.0
O A:HOH512 2.4 13.3 1.0
O A:ALA169 2.4 8.9 1.0
OE1 A:GLN195 2.4 12.4 1.0
C A:VAL174 3.4 11.7 1.0
C A:TYR171 3.4 11.2 1.0
C A:ALA169 3.6 9.9 1.0
CD A:GLN195 3.6 15.1 1.0
O A:HOH703 3.7 25.2 1.0
N A:TYR171 3.8 10.7 1.0
C A:SER170 3.8 10.6 1.0
CA A:SER170 4.0 9.2 1.0
N A:SER176 4.0 10.3 1.0
N A:VAL174 4.1 11.3 1.0
CA A:VAL174 4.1 11.1 1.0
N A:ASP172 4.2 12.1 1.0
CA A:ASP172 4.2 14.0 1.0
N A:SER170 4.2 10.8 1.0
CB A:SER176 4.3 9.1 1.0
CA A:TYR171 4.3 10.7 1.0
CB A:VAL174 4.3 10.8 1.0
O A:SER170 4.3 11.5 1.0
CB A:GLN195 4.4 13.3 1.0
N A:MET175 4.4 10.6 1.0
NH1 A:ARG395 4.4 14.8 1.0
CG A:GLN195 4.4 13.4 1.0
C A:ASP172 4.5 13.8 1.0
O A:GLN195 4.5 11.8 1.0
C A:MET175 4.5 11.5 1.0
OE1 A:GLU197 4.5 18.6 1.0
CA A:MET175 4.5 10.8 1.0
NE2 A:GLN195 4.6 13.5 1.0
O A:ASP172 4.7 13.3 1.0
CA A:ALA169 4.7 8.5 1.0
CA A:SER176 4.7 10.5 1.0
O A:PRO168 4.8 10.6 1.0

Calcium binding site 4 out of 7 in 1v6c

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Calcium binding site 4 out of 7 in the Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11


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 Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca506

b:10.1
occ:1.00
 O B:GLU80 2.3 12.0 1.0
O B:ILE76 2.3 7.5 1.0
OE1 B:GLU2 2.3 12.2 1.0
OD1 B:ASP39 2.3 11.9 1.0
O B:VAL82 2.4 8.9 1.0
OD1 B:ASN78 2.4 11.3 1.0
CG B:ASP39 3.0 13.6 1.0
OD2 B:ASP39 3.1 14.3 1.0
CG B:ASN78 3.3 13.7 1.0
CD B:GLU2 3.4 14.5 1.0
C B:VAL82 3.5 9.8 1.0
C B:ILE76 3.5 8.5 1.0
C B:GLU80 3.5 13.9 1.0
N B:VAL82 3.6 10.7 1.0
N B:ASN78 3.8 12.4 1.0
ND2 B:ASN78 3.8 13.3 1.0
CG B:GLU2 3.9 13.5 1.0
CA B:VAL82 4.1 8.8 1.0
C B:GLY81 4.1 11.6 1.0
N B:GLU80 4.2 15.4 1.0
CA B:ALA77 4.3 10.9 1.0
N B:ALA77 4.3 10.3 1.0
CA B:GLY81 4.4 12.1 1.0
CB B:ASP39 4.4 12.0 1.0
N B:GLY81 4.4 12.2 1.0
CA B:GLU80 4.4 15.3 1.0
C B:ALA77 4.5 12.3 1.0
OE2 B:GLU2 4.5 14.3 1.0
CA B:ILE76 4.5 8.6 1.0
CB B:ASN78 4.5 13.1 1.0
N B:ILE76 4.5 8.4 1.0
CA B:ASN78 4.6 13.2 1.0
N B:VAL83 4.6 8.5 1.0
CG1 B:VAL83 4.6 13.9 1.0
CG B:GLU80 4.7 25.0 1.0
C B:ASN78 4.8 14.6 1.0
N B:ASN79 4.8 14.8 1.0
O B:GLY81 4.9 10.0 1.0
CA B:ASP39 4.9 11.0 1.0
CA B:VAL83 4.9 9.9 1.0

Calcium binding site 5 out of 7 in 1v6c

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Calcium binding site 5 out of 7 in the Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11


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 Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca507

b:14.0
occ:1.00
 O B:GLY409 2.2 18.8 1.0
O B:LEU405 2.3 15.1 1.0
OD1 B:ASP411 2.3 13.4 1.0
OD1 B:ASP404 2.3 14.7 1.0
O B:VAL407 2.3 21.3 1.0
O B:HOH512 2.4 11.1 1.0
C B:GLY409 3.4 18.2 1.0
C B:LEU405 3.4 14.5 1.0
CG B:ASP404 3.5 17.2 1.0
CG B:ASP411 3.5 13.3 1.0
C B:VAL407 3.5 23.0 1.0
N B:LEU405 3.8 12.2 1.0
N B:GLY409 3.9 20.7 1.0
OD2 B:ASP404 4.0 20.6 1.0
OG1 B:THR414 4.1 10.4 1.0
C B:ALA408 4.1 22.3 1.0
N B:VAL407 4.1 22.6 1.0
O B:GLY415 4.2 11.8 1.0
C B:SER406 4.2 21.4 1.0
CA B:LEU405 4.2 13.3 1.0
CA B:GLY409 4.2 19.1 1.0
N B:ASP411 4.3 14.4 1.0
CB B:ASP411 4.4 13.3 1.0
OD2 B:ASP411 4.4 13.2 1.0
N B:ARG410 4.4 17.5 1.0
CA B:VAL407 4.4 22.4 1.0
N B:ALA408 4.4 22.4 1.0
N B:SER406 4.5 17.0 1.0
CA B:ALA408 4.5 23.1 1.0
CB B:SER406 4.5 21.6 1.0
O B:SER406 4.5 22.3 1.0
CA B:ARG410 4.5 17.3 1.0
CG2 B:VAL407 4.5 23.6 1.0
C B:ARG410 4.5 16.4 1.0
C B:ASP404 4.5 12.4 1.0
O B:ALA408 4.5 22.2 1.0
CA B:SER406 4.6 20.3 1.0
CB B:ASP404 4.7 15.0 1.0
CA B:ASP404 4.7 12.6 1.0

Calcium binding site 6 out of 7 in 1v6c

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Calcium binding site 6 out of 7 in the Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11


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 Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca508

b:20.7
occ:1.00
 O B:VAL174 2.3 6.4 1.0
OE1 B:GLN195 2.3 8.6 1.0
O B:ALA169 2.3 7.4 1.0
O B:HOH513 2.4 10.4 1.0
O B:TYR171 2.4 8.7 1.0
C B:TYR171 3.4 9.4 1.0
C B:VAL174 3.4 7.8 1.0
C B:ALA169 3.5 8.8 1.0
CD B:GLN195 3.5 11.0 1.0
N B:TYR171 3.7 9.3 1.0
C B:SER170 3.8 8.6 1.0
CA B:SER170 3.9 7.5 1.0
N B:SER176 4.1 6.9 1.0
N B:VAL174 4.2 6.8 1.0
N B:SER170 4.2 6.6 1.0
N B:ASP172 4.2 9.0 1.0
CA B:VAL174 4.2 7.9 1.0
CB B:SER176 4.2 8.1 1.0
CA B:ASP172 4.3 10.7 1.0
CA B:TYR171 4.3 8.5 1.0
CB B:GLN195 4.3 10.8 1.0
O B:SER170 4.3 9.3 1.0
CG B:GLN195 4.3 10.2 1.0
CB B:VAL174 4.4 9.2 1.0
O B:GLN195 4.4 9.4 1.0
NH1 B:ARG395 4.4 9.3 1.0
N B:MET175 4.5 7.3 1.0
C B:ASP172 4.5 10.1 1.0
NE2 B:GLN195 4.5 10.4 1.0
OE1 B:GLU197 4.5 13.9 1.0
C B:MET175 4.5 7.5 1.0
CA B:MET175 4.6 7.5 1.0
CA B:ALA169 4.7 7.0 1.0
O B:ASP172 4.7 8.9 1.0
CA B:SER176 4.7 7.7 1.0
O B:PRO168 4.8 9.2 1.0
CA B:GLN195 5.0 10.1 1.0

Calcium binding site 7 out of 7 in 1v6c

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Calcium binding site 7 out of 7 in the Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11


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 Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca509

b:8.8
occ:0.50
 O B:HOH548 2.3 12.9 1.0
O B:HOH594 2.4 16.7 1.0
O B:GLU388 4.0 9.0 1.0
O B:HOH688 4.1 14.6 1.0
O B:HOH524 4.3 10.2 1.0
O B:PRO387 4.3 10.0 1.0
C B:GLU388 4.5 8.9 1.0
OE1 B:GLU388 4.5 23.0 1.0
O B:CYS389 4.6 8.6 1.0
CA B:GLU388 4.7 10.3 1.0

Reference:

D.Dong, T.Ihara, H.Motoshima, K.Watanabe. Crystal Structure of Psychrophilic Subtilisin-Like Protease APA1 From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 To Be Published.
Page generated: Thu Jul 11 23:55:12 2024

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