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Calcium in PDB 3afg: Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis

Enzymatic activity of Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis

All present enzymatic activity of Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis:
3.4.21.62;

Protein crystallography data

The structure of Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis, PDB code: 3afg was solved by T.Foophow, S.Tanaka, C.Angkawidjaja, Y.Koga, K.Takano, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.17 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.009, 123.996, 141.037, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis (pdb code 3afg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis, PDB code: 3afg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3afg

Go back to Calcium Binding Sites List in 3afg
Calcium binding site 1 out of 4 in the Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis


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 Pron-Tk-Sp From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca540

b:15.0
occ:1.00
 OD1 A:ASP460 2.2 14.6 1.0
O A:HOH542 2.2 11.2 1.0
OE2 A:GLU484 2.3 13.9 1.0
O A:LEU461 2.3 9.8 1.0
OD1 A:ASP462 2.3 11.7 1.0
O A:THR478 2.4 13.2 1.0
C A:LEU461 3.3 11.3 1.0
CD A:GLU484 3.4 13.3 1.0
CG A:ASP460 3.4 15.2 1.0
CG A:ASP462 3.5 14.6 1.0
C A:THR478 3.6 12.5 1.0
NZ A:LYS4 3.6 16.3 1.0
N A:LEU461 3.9 11.4 1.0
N A:THR478 3.9 12.6 1.0
N A:ASP462 4.0 11.9 1.0
OD2 A:ASP460 4.0 10.8 1.0
C A:TYR477 4.1 13.1 1.0
CA A:ASP462 4.1 13.6 1.0
CG A:GLU484 4.1 11.2 1.0
C A:ASP460 4.2 11.6 1.0
CA A:LEU461 4.2 12.0 1.0
OE1 A:GLU484 4.3 14.5 1.0
CA A:TYR477 4.3 14.8 1.0
OD2 A:ASP462 4.3 15.4 1.0
CA A:THR478 4.3 11.5 1.0
O A:HOH543 4.4 8.4 1.0
CG2 A:THR478 4.4 8.7 1.0
CB A:ASP462 4.4 14.7 1.0
O A:TYR477 4.4 12.4 1.0
CA A:ASP460 4.5 11.7 1.0
CB A:ASP460 4.5 13.4 1.0
CH2 A:TRP454 4.5 10.7 1.0
N A:ALA479 4.6 10.7 1.0
O A:HOH544 4.7 14.7 1.0
CZ2 A:TRP454 4.8 8.3 1.0
O A:ASP460 4.8 11.6 1.0
CA A:ALA479 4.8 12.2 1.0
O A:SER476 4.9 15.5 1.0

Calcium binding site 2 out of 4 in 3afg

Go back to Calcium Binding Sites List in 3afg
Calcium binding site 2 out of 4 in the Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis


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 Pron-Tk-Sp From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca541

b:18.9
occ:1.00
 O A:PRO397 2.3 12.5 1.0
O A:TYR475 2.3 14.7 1.0
O A:ILE400 2.4 8.6 1.0
O A:HOH618 2.5 32.9 1.0
O A:HOH598 2.5 11.0 1.0
OD1 A:ASP474 2.5 11.8 1.0
O A:HOH725 2.9 26.6 1.0
C A:PRO397 3.4 12.9 1.0
C A:TYR475 3.5 14.8 1.0
CG A:ASP474 3.5 13.2 1.0
C A:ILE400 3.6 11.4 1.0
OD2 A:ASP474 3.8 11.2 1.0
N A:TYR475 4.0 14.6 1.0
CA A:PRO397 4.2 13.8 1.0
N A:ILE400 4.2 12.4 1.0
CA A:SER476 4.3 14.7 1.0
N A:ASP398 4.4 11.3 1.0
N A:SER476 4.4 14.2 1.0
O A:LYS485 4.4 13.6 1.0
CA A:ILE400 4.4 10.6 1.0
CA A:TYR475 4.4 16.1 1.0
O A:HOH629 4.4 22.8 1.0
CA A:ASP398 4.5 12.8 1.0
CD1 A:TYR475 4.5 35.2 1.0
N A:ALA401 4.6 9.7 1.0
CE1 A:TYR475 4.6 35.5 1.0
CB A:ILE400 4.6 9.9 1.0
CB A:SER476 4.6 12.9 1.0
CB A:PRO397 4.7 12.8 1.0
O A:HOH595 4.8 17.0 1.0
C A:ASP398 4.8 12.9 1.0
CG A:TYR475 4.8 23.9 1.0
CB A:ASP474 4.8 13.0 1.0
N A:GLU399 4.9 14.3 1.0
C A:ASP474 5.0 15.9 1.0

Calcium binding site 3 out of 4 in 3afg

Go back to Calcium Binding Sites List in 3afg
Calcium binding site 3 out of 4 in the Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis


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 Pron-Tk-Sp From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca540

b:24.3
occ:1.00
 OE2 B:GLU484 2.2 22.4 1.0
OD1 B:ASP460 2.3 29.2 1.0
O B:HOH638 2.3 16.2 1.0
O B:LEU461 2.3 31.2 1.0
OD1 B:ASP462 2.3 36.0 1.0
O B:THR478 2.4 26.0 1.0
C B:LEU461 3.2 31.0 1.0
CD B:GLU484 3.4 21.8 1.0
CG B:ASP460 3.4 31.9 1.0
CG B:ASP462 3.5 33.3 1.0
C B:THR478 3.6 26.0 1.0
N B:LEU461 3.8 30.4 1.0
N B:ASP462 4.0 29.3 1.0
OD2 B:ASP460 4.0 32.3 1.0
CG B:GLU484 4.1 21.7 1.0
NZ B:LYS4 4.1 39.4 1.0
N B:THR478 4.1 28.1 1.0
CA B:ASP462 4.1 28.8 1.0
CA B:LEU461 4.2 29.5 1.0
C B:TYR477 4.2 29.2 1.0
C B:ASP460 4.2 31.6 1.0
CG2 B:THR478 4.3 21.5 1.0
OE1 B:GLU484 4.3 22.1 1.0
OD2 B:ASP462 4.4 30.6 1.0
CA B:TYR477 4.4 30.4 1.0
CA B:THR478 4.4 26.2 1.0
CA B:ASP460 4.4 30.9 1.0
CB B:ASP462 4.4 28.4 1.0
CH2 B:TRP454 4.5 27.8 1.0
CB B:ASP460 4.5 28.9 1.0
O B:HOH722 4.5 18.3 1.0
O B:HOH615 4.5 18.1 1.0
O B:TYR477 4.6 29.7 1.0
N B:ALA479 4.6 26.6 1.0
CA B:ALA479 4.7 25.1 1.0
CZ2 B:TRP454 4.8 26.4 1.0
C B:ALA479 4.9 24.8 1.0
O B:ASP460 4.9 32.0 1.0

Calcium binding site 4 out of 4 in 3afg

Go back to Calcium Binding Sites List in 3afg
Calcium binding site 4 out of 4 in the Crystal Structure of Pron-Tk-Sp From Thermococcus Kodakaraensis


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 Pron-Tk-Sp From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca541

b:36.8
occ:1.00
 O B:PRO397 2.3 25.0 1.0
O B:TYR475 2.3 25.9 1.0
O B:ILE400 2.3 22.4 1.0
O B:HOH642 2.6 19.9 1.0
OD1 B:ASP474 2.8 26.0 1.0
O B:HOH622 3.1 53.3 1.0
C B:PRO397 3.4 26.2 1.0
C B:TYR475 3.5 27.3 1.0
C B:ILE400 3.5 23.2 1.0
CG B:ASP474 3.7 31.8 1.0
OD2 B:ASP474 4.0 29.4 1.0
N B:TYR475 4.0 27.3 1.0
N B:ILE400 4.1 26.3 1.0
CA B:PRO397 4.1 25.8 1.0
CA B:ILE400 4.3 23.8 1.0
N B:SER476 4.3 27.9 1.0
N B:ASP398 4.4 28.0 1.0
CA B:SER476 4.4 26.4 1.0
CA B:TYR475 4.4 28.2 1.0
N B:ALA401 4.4 22.7 1.0
CA B:ASP398 4.5 30.3 1.0
O B:LYS485 4.5 21.7 1.0
CB B:ILE400 4.6 25.1 1.0
CB B:PRO397 4.6 24.1 1.0
O B:HOH569 4.7 24.1 1.0
CB B:SER476 4.8 26.6 1.0
N B:GLU399 4.8 31.6 1.0
C B:ASP398 4.8 31.4 1.0
CD1 B:TYR475 4.9 40.8 1.0
CG B:TYR475 5.0 33.5 1.0

Reference:

T.Foophow, S.Tanaka, C.Angkawidjaja, Y.Koga, K.Takano, S.Kanaya. Crystal Structure of A Subtilisin Homologue, Tk-Sp, From Thermococcus Kodakaraensis: Requirement of A C-Terminal Beta-Jelly Roll Domain For Hyperstability. J.Mol.Biol. V. 400 865 2010.
ISSN: ISSN 0022-2836
PubMed: 20595040
DOI: 10.1016/J.JMB.2010.05.064
Page generated: Tue Jul 8 10:46:06 2025

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