Atomistry » Calcium » PDB 1v3e-1vfm » 1v6c
Atomistry »
  Calcium »
    PDB 1v3e-1vfm »
      1v6c »

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

Go back to Calcium Binding Sites List in 1v6c
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

Go back to Calcium Binding Sites List in 1v6c
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

Go back to Calcium Binding Sites List in 1v6c
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

Go back to Calcium Binding Sites List in 1v6c
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

Go back to Calcium Binding Sites List in 1v6c
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

Go back to Calcium Binding Sites List in 1v6c
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

Go back to Calcium Binding Sites List in 1v6c
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy