Calcium in PDB 3vhq: Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin

Enzymatic activity of Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin

All present enzymatic activity of Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin:
3.4.21.62;

Protein crystallography data

The structure of Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin, PDB code: 3vhq was solved by R.Uehara, Y.Takeuchi, S.Tanaka, H.Matsumura, 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) 36.08 / 2.15
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 73.434, 92.780, 124.279, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin (pdb code 3vhq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin, PDB code: 3vhq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3vhq

Go back to Calcium Binding Sites List in 3vhq
Calcium binding site 1 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca399

b:31.0
occ:1.00
O A:VAL108 2.2 30.0 1.0
O A:ALA227 2.3 29.9 1.0
OE1 A:GLU229 2.3 24.1 1.0
OE1 A:GLN110 2.3 26.6 1.0
O A:HOH420 2.4 25.6 1.0
OE2 A:GLU229 2.5 27.6 1.0
O A:HOH413 2.6 29.5 1.0
CD A:GLU229 2.7 28.5 1.0
CD A:GLN110 3.4 32.1 1.0
C A:VAL108 3.4 28.8 1.0
C A:ALA227 3.6 29.6 1.0
NE2 A:GLN110 3.9 30.6 1.0
N A:GLN110 4.1 25.6 1.0
CG2 A:VAL108 4.1 28.3 1.0
CG A:GLU229 4.2 22.4 1.0
N A:ILE109 4.3 27.5 1.0
CA A:VAL108 4.3 29.2 1.0
N A:ALA227 4.3 28.9 1.0
C A:ASP226 4.4 29.3 1.0
CA A:ILE109 4.4 26.5 1.0
CA A:ALA227 4.5 28.5 1.0
N A:ALA228 4.5 27.5 1.0
CA A:ALA228 4.5 27.0 1.0
C A:ILE109 4.5 27.1 1.0
O A:ASP225 4.6 28.1 1.0
C A:ALA228 4.6 25.3 1.0
O A:ASP226 4.7 29.7 1.0
CG A:GLN110 4.7 24.5 1.0
CA A:ASP226 4.8 29.4 1.0
CB A:GLN110 4.8 25.7 1.0
N A:GLU229 4.8 24.6 1.0
O A:HOH564 4.8 46.8 1.0
N A:GLY221 4.8 27.5 1.0
CB A:VAL108 4.8 29.1 1.0
CA A:GLN110 5.0 25.6 1.0
O A:ASP222 5.0 31.4 1.0

Calcium binding site 2 out of 5 in 3vhq

Go back to Calcium Binding Sites List in 3vhq
Calcium binding site 2 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca400

b:33.0
occ:1.00
OD1 A:ASP208 2.2 31.1 1.0
OD2 A:ASP226 2.2 30.3 1.0
O A:VAL210 2.2 27.8 1.0
O A:HOH406 2.2 25.8 1.0
O A:LEU205 2.3 31.5 1.0
O A:HOH578 2.5 32.9 1.0
CG A:ASP208 3.1 33.2 1.0
CG A:ASP226 3.1 27.2 1.0
OD2 A:ASP208 3.4 33.1 1.0
C A:VAL210 3.4 28.7 1.0
C A:LEU205 3.4 30.9 1.0
OD1 A:ASP226 3.4 29.4 1.0
N A:VAL210 3.8 30.6 1.0
N A:ASP226 4.0 28.8 1.0
CA A:VAL210 4.1 29.4 1.0
N A:GLY206 4.3 31.2 1.0
O A:ALA211 4.3 27.5 1.0
CA A:GLY206 4.3 30.0 1.0
CA A:LEU205 4.4 29.3 1.0
N A:ALA227 4.4 28.9 1.0
CB A:ASP226 4.4 27.1 1.0
N A:GLY209 4.4 29.9 1.0
N A:ALA211 4.4 29.5 1.0
CB A:ASP208 4.4 30.5 1.0
OD1 A:ASP225 4.5 26.8 1.0
C A:ASP226 4.5 29.3 1.0
O A:ILE204 4.5 26.7 1.0
CA A:ASP226 4.5 29.4 1.0
N A:ASP208 4.5 30.3 1.0
C A:GLY206 4.5 29.3 1.0
CA A:ALA211 4.5 28.5 1.0
C A:ALA211 4.6 28.4 1.0
C A:ASP208 4.6 30.0 1.0
CB A:VAL210 4.7 31.3 1.0
O A:GLY206 4.7 29.6 1.0
CA A:ASP208 4.8 30.0 1.0
C A:GLY209 4.8 29.1 1.0
CB A:ASP225 4.9 27.6 1.0

Calcium binding site 3 out of 5 in 3vhq

Go back to Calcium Binding Sites List in 3vhq
Calcium binding site 3 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:32.8
occ:1.00
OD1 A:ASP222 2.2 29.2 1.0
O A:ILE218 2.3 28.6 1.0
OD1 A:ASP212 2.4 32.3 1.0
OD2 A:ASP225 2.4 32.2 1.0
OD2 A:ASP214 2.4 38.4 1.0
OD1 A:ASP216 2.5 31.4 1.0
CG A:ASP216 3.3 32.6 1.0
CG A:ASP222 3.4 30.3 1.0
C A:ILE218 3.5 30.0 1.0
CG A:ASP212 3.5 33.0 1.0
CG A:ASP214 3.5 35.6 1.0
CG A:ASP225 3.6 30.9 1.0
OD2 A:ASP216 3.6 30.3 1.0
OD1 A:ASP214 3.9 38.0 1.0
CA A:CA403 4.0 52.6 1.0
N A:ILE218 4.0 31.1 1.0
CB A:ASP222 4.1 27.9 1.0
CA A:ILE218 4.2 29.8 1.0
OD1 A:ASP225 4.2 26.8 1.0
OD2 A:ASP212 4.2 31.5 1.0
CA A:ASP212 4.3 31.9 1.0
N A:ASP216 4.3 34.7 1.0
CB A:ILE218 4.3 30.1 1.0
OD2 A:ASP222 4.4 29.8 1.0
CB A:ASP212 4.4 31.4 1.0
N A:ASP214 4.5 36.3 1.0
CB A:ASP216 4.5 34.3 1.0
N A:ILE219 4.5 30.1 1.0
C A:ASP212 4.6 32.8 1.0
N A:LYS213 4.6 34.8 1.0
CB A:ASP225 4.6 27.6 1.0
N A:GLY215 4.7 37.2 1.0
N A:GLY217 4.8 32.9 1.0
CB A:ASP214 4.8 35.7 1.0
CA A:ASP216 4.8 34.5 1.0
CA A:ILE219 4.9 29.9 1.0
CA A:ASP214 5.0 37.6 1.0

Calcium binding site 4 out of 5 in 3vhq

Go back to Calcium Binding Sites List in 3vhq
Calcium binding site 4 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:31.9
occ:1.00
O A:VAL170 2.2 28.9 1.0
OE1 A:GLN84 2.3 33.8 1.0
O A:ILE168 2.4 38.2 1.0
OD1 A:ASN166 2.4 30.8 1.0
O A:LEU164 2.5 33.6 1.0
OD1 A:ASP124 2.6 29.7 1.0
OD2 A:ASP124 2.7 33.0 1.0
CG A:ASP124 3.0 31.7 1.0
CD A:GLN84 3.3 34.9 1.0
C A:VAL170 3.3 29.2 1.0
CG A:ASN166 3.4 35.1 1.0
C A:ILE168 3.6 36.9 1.0
C A:LEU164 3.6 32.2 1.0
N A:VAL170 3.6 30.9 1.0
CG A:GLN84 3.7 37.6 1.0
ND2 A:ASN166 4.0 38.8 1.0
N A:ASN166 4.0 33.3 1.0
CA A:VAL170 4.1 30.0 1.0
C A:GLY169 4.1 32.2 1.0
CG1 A:ILE168 4.3 34.9 1.0
N A:VAL171 4.3 29.6 1.0
CA A:GLY169 4.4 33.4 1.0
N A:ILE168 4.4 39.5 1.0
CA A:LEU164 4.4 32.7 1.0
N A:GLY169 4.4 35.2 1.0
CB A:GLN84 4.5 39.5 1.0
N A:LEU164 4.5 31.6 1.0
NE2 A:GLN84 4.5 28.1 1.0
CA A:VAL171 4.5 28.9 1.0
N A:ASN165 4.5 31.3 1.0
CB A:ASP124 4.5 31.4 1.0
CA A:ILE168 4.5 37.9 1.0
CA A:ASN165 4.5 31.7 1.0
CB A:ASN166 4.6 34.0 1.0
CB A:LEU164 4.6 32.6 1.0
CA A:ASN166 4.7 35.2 1.0
C A:ASN165 4.7 32.0 1.0
C A:ASN166 4.7 36.7 1.0
O A:ASN166 4.8 37.6 1.0
CB A:VAL171 4.8 29.1 1.0
O A:GLY169 4.9 31.1 1.0
C A:ALA163 4.9 29.7 1.0

Calcium binding site 5 out of 5 in 3vhq

Go back to Calcium Binding Sites List in 3vhq
Calcium binding site 5 out of 5 in the Crystal Structure of the CA6 Site Mutant of Pro-Sa-Subtilisin


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 the CA6 Site Mutant of Pro-Sa-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:52.6
occ:1.00
OD2 A:ASP216 2.4 30.3 1.0
OD1 A:ASP214 2.4 38.0 1.0
OD1 A:ASP222 2.6 29.2 1.0
OD2 A:ASP224 2.7 40.2 1.0
OD2 A:ASP222 2.7 29.8 1.0
CG A:ASP222 3.0 30.3 1.0
CG A:ASP214 3.4 35.6 1.0
CG A:ASP216 3.4 32.6 1.0
CG A:ASP224 3.6 36.6 1.0
CB A:ASP224 3.7 32.7 1.0
OD2 A:ASP214 3.7 38.4 1.0
O A:HOH500 3.9 47.0 1.0
CA A:CA401 4.0 32.8 1.0
OD1 A:ASP216 4.0 31.4 1.0
CB A:ASP222 4.4 27.9 1.0
CB A:ASP216 4.5 34.3 1.0
CB A:ASP214 4.7 35.7 1.0
OD1 A:ASP224 4.7 39.8 1.0
N A:ASP224 4.8 32.3 1.0
CA A:ASP224 4.8 31.8 1.0
CD1 A:ILE218 5.0 27.7 1.0

Reference:

R.Uehara, Y.Takeuchi, S.I.Tanaka, K.Takano, Y.Koga, S.Kanaya. Requirement of Ca(2+) Ions For the Hyperthermostability of Tk-Subtilisin From Thermococcus Kodakarensis Biochemistry V. 51 5369 2012.
ISSN: ISSN 0006-2960
PubMed: 22686281
DOI: 10.1021/BI300427U
Page generated: Sat Dec 12 04:34:11 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy