Atomistry » Calcium » PDB 8izk-8jx8 » 8jjm
Atomistry »
  Calcium »
    PDB 8izk-8jx8 »
      8jjm »

Calcium in PDB 8jjm: X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63

Protein crystallography data

The structure of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63, PDB code: 8jjm was solved by Y.F.Sun, W.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.79 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.785, 55.495, 106.755, 90, 91.29, 90
R / Rfree (%) 16.1 / 19.2

Other elements in 8jjm:

The structure of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 (pdb code 8jjm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63, PDB code: 8jjm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8jjm

Go back to Calcium Binding Sites List in 8jjm
Calcium binding site 1 out of 6 in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:17.1
occ:1.00
 O A:TYR307 2.3 17.1 1.0
O A:GLY305 2.3 19.9 1.0
O A:HOH908 2.3 17.6 1.0
O A:TRP413 2.3 19.4 1.0
OD1 A:ASP414 2.4 19.1 1.0
OD1 A:ASP436 2.5 18.9 1.0
OD2 A:ASP436 2.6 18.0 1.0
CG A:ASP436 2.9 22.4 1.0
C A:TRP413 3.3 19.9 1.0
C A:GLY305 3.4 17.8 1.0
C A:TYR307 3.5 16.6 1.0
CG A:ASP414 3.5 24.3 1.0
CA A:ASP414 3.7 19.2 1.0
N A:TYR307 3.8 19.1 1.0
N A:ASP414 3.9 19.6 1.0
C A:SER306 4.0 20.1 1.0
CA A:TYR307 4.2 17.6 1.0
CB A:ASP414 4.2 19.8 1.0
N A:SER306 4.2 19.7 1.0
CG A:MET309 4.3 15.0 1.0
CA A:SER306 4.3 22.6 1.0
CA A:GLY305 4.3 17.8 1.0
CB A:ASP436 4.4 17.5 1.0
N A:ASP308 4.5 17.1 1.0
O A:SER306 4.5 17.8 1.0
CA A:TRP413 4.5 19.3 1.0
N A:MET309 4.5 15.6 1.0
OD2 A:ASP414 4.5 23.5 1.0
CB A:TRP413 4.6 20.4 1.0
O A:HOH1051 4.6 25.7 1.0
O A:HOH965 4.6 19.0 1.0
CA A:ASP308 4.7 16.6 1.0
O A:HOH695 4.7 34.7 1.0
CD1 A:TRP413 4.7 23.8 1.0
O A:HOH722 4.8 20.0 1.0
CB A:TYR307 4.8 15.7 1.0
CB A:MET309 5.0 16.3 1.0
N A:GLY437 5.0 22.1 1.0

Calcium binding site 2 out of 6 in 8jjm

Go back to Calcium Binding Sites List in 8jjm
Calcium binding site 2 out of 6 in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:14.5
occ:1.00
 OD1 A:ASP188 2.3 15.5 1.0
O A:ALA186 2.3 14.2 1.0
OD1 A:ASP207 2.4 13.7 1.0
O A:HOH825 2.4 15.5 1.0
O A:HOH625 2.4 18.9 1.0
OD2 A:ASP164 2.5 11.7 1.0
OD1 A:ASP164 2.5 15.4 1.0
CG A:ASP164 2.8 14.5 1.0
CG A:ASP207 3.1 15.0 1.0
CG A:ASP188 3.3 14.9 1.0
C A:ALA186 3.5 18.6 1.0
OD2 A:ASP207 3.7 14.7 1.0
N A:ASP188 3.8 13.8 1.0
OD2 A:ASP188 3.9 16.0 1.0
C A:TRP187 4.0 17.8 1.0
CB A:ASP207 4.1 13.5 1.0
N A:ALA186 4.1 21.1 1.0
CA A:ASP188 4.2 15.6 1.0
CA A:ASP207 4.2 13.6 1.0
CB A:ASP164 4.3 13.0 1.0
OD2 A:ASP209 4.3 34.2 1.0
CB A:ASP209 4.3 18.0 1.0
CB A:ASP188 4.4 14.2 1.0
CA A:TRP187 4.4 15.5 1.0
NA A:NA504 4.4 12.4 1.0
N A:TRP187 4.4 16.1 1.0
CA A:ALA186 4.4 17.5 1.0
O A:TRP187 4.5 18.8 1.0
N A:ASP209 4.6 15.8 1.0
CG A:ASP209 4.6 27.1 1.0
N A:MET208 4.7 12.6 1.0
C A:ASP207 4.7 15.4 1.0
O A:HOH901 4.8 24.2 1.0
OD2 A:ASP199 4.8 14.2 1.0

Calcium binding site 3 out of 6 in 8jjm

Go back to Calcium Binding Sites List in 8jjm
Calcium binding site 3 out of 6 in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:13.5
occ:1.00
 OD1 A:ASP199 2.3 12.8 1.0
O A:ASP199 2.3 13.5 1.0
OD1 A:ASP205 2.3 12.4 1.0
OD1 A:ASN108 2.4 12.7 1.0
O A:HIS240 2.4 13.8 1.0
O A:HOH814 2.4 13.8 1.0
CG A:ASP205 3.2 11.3 1.0
C A:ASP199 3.3 13.8 1.0
OD2 A:ASP205 3.3 15.6 1.0
CG A:ASP199 3.4 14.0 1.0
CG A:ASN108 3.5 11.1 1.0
C A:HIS240 3.5 13.8 1.0
CA A:ASP199 3.8 12.9 1.0
O A:HOH747 3.8 16.4 1.0
O A:ASN108 4.0 12.0 1.0
NA A:NA504 4.0 12.4 1.0
CB A:HIS240 4.1 13.2 1.0
ND2 A:ASN108 4.2 13.3 1.0
CB A:ASP199 4.2 12.2 1.0
OD2 A:ASP199 4.3 14.2 1.0
CA A:HIS240 4.3 13.4 1.0
N A:TYR200 4.4 11.8 1.0
O A:HOH802 4.4 14.3 1.0
N A:ILE241 4.5 13.6 1.0
CB A:ASP205 4.6 12.4 1.0
CB A:ASN108 4.6 11.7 1.0
CA A:ILE241 4.6 13.9 1.0
O A:LEU206 4.7 14.0 1.0
CA A:TYR200 4.7 12.1 1.0
CA A:ASN108 4.8 11.4 1.0
C A:ASN108 4.8 12.2 1.0
CG1 A:ILE241 4.9 12.2 1.0

Calcium binding site 4 out of 6 in 8jjm

Go back to Calcium Binding Sites List in 8jjm
Calcium binding site 4 out of 6 in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:28.3
occ:1.00
 O B:GLY305 2.3 30.5 1.0
O B:TYR307 2.3 27.8 1.0
OD1 B:ASP414 2.4 27.6 1.0
O B:TRP413 2.4 28.8 1.0
O B:HOH936 2.4 29.8 1.0
OD1 B:ASP436 2.5 25.2 1.0
OD2 B:ASP436 2.5 26.4 1.0
CG B:ASP436 2.9 28.4 1.0
C B:TRP413 3.4 26.7 1.0
C B:GLY305 3.4 26.5 1.0
C B:TYR307 3.5 27.0 1.0
CG B:ASP414 3.5 35.1 1.0
CA B:ASP414 3.8 27.2 1.0
N B:TYR307 3.8 31.1 1.0
N B:ASP414 4.0 26.0 1.0
C B:SER306 4.0 31.8 1.0
CB B:ASP414 4.1 26.3 1.0
CA B:TYR307 4.2 24.6 1.0
N B:SER306 4.2 28.7 1.0
CA B:GLY305 4.3 27.4 1.0
CA B:SER306 4.4 30.1 1.0
CB B:ASP436 4.4 30.5 1.0
N B:MET309 4.4 25.7 1.0
CG B:MET309 4.4 24.4 1.0
O B:SER306 4.5 30.0 1.0
N B:ASP308 4.5 28.9 1.0
OD2 B:ASP414 4.5 34.6 1.0
CA B:TRP413 4.6 29.0 1.0
CB B:TRP413 4.6 28.4 1.0
O B:HOH720 4.7 24.3 1.0
O B:HOH1028 4.7 36.9 1.0
CA B:ASP308 4.7 28.1 1.0
O B:HOH956 4.7 35.7 1.0
CB B:TYR307 4.8 26.5 1.0
CB B:MET309 4.9 25.6 1.0
CD1 B:TRP413 4.9 32.3 1.0
N B:GLY437 5.0 30.8 1.0
C B:ASP436 5.0 27.6 1.0

Calcium binding site 5 out of 6 in 8jjm

Go back to Calcium Binding Sites List in 8jjm
Calcium binding site 5 out of 6 in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:13.0
occ:1.00
 OD1 B:ASP199 2.3 14.1 1.0
OD1 B:ASP205 2.3 15.6 1.0
O B:HIS240 2.3 12.5 1.0
O B:ASP199 2.3 11.1 1.0
OD1 B:ASN108 2.3 13.4 1.0
O B:HOH848 2.4 14.2 1.0
CG B:ASP205 3.2 16.8 1.0
C B:ASP199 3.3 14.2 1.0
OD2 B:ASP205 3.3 17.2 1.0
CG B:ASP199 3.4 15.8 1.0
CG B:ASN108 3.5 12.9 1.0
C B:HIS240 3.5 13.5 1.0
O B:HOH690 3.8 15.7 1.0
CA B:ASP199 3.8 17.0 1.0
CB B:HIS240 4.0 12.3 1.0
O B:ASN108 4.0 13.1 1.0
NA B:NA504 4.1 13.7 1.0
ND2 B:ASN108 4.2 15.0 1.0
CB B:ASP199 4.2 13.8 1.0
OD2 B:ASP199 4.3 16.2 1.0
CA B:HIS240 4.3 12.3 1.0
O B:HOH675 4.3 14.8 1.0
N B:TYR200 4.4 13.7 1.0
N B:ILE241 4.5 12.2 1.0
CB B:ASP205 4.6 12.9 1.0
CB B:ASN108 4.6 13.0 1.0
CA B:ILE241 4.6 14.2 1.0
O B:LEU206 4.6 11.4 1.0
CA B:ASN108 4.7 12.8 1.0
C B:ASN108 4.8 12.7 1.0
CA B:TYR200 4.8 15.1 1.0
CG1 B:ILE241 4.8 14.4 1.0

Calcium binding site 6 out of 6 in 8jjm

Go back to Calcium Binding Sites List in 8jjm
Calcium binding site 6 out of 6 in the X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Crystal Structure of A Multifunctional Enzyme (AMY63) From Vibrio Alginolyticus 63 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:14.7
occ:1.00
 OD1 B:ASP207 2.3 14.3 1.0
OD1 B:ASP188 2.3 14.3 1.0
O B:HOH901 2.3 21.3 1.0
O B:ALA186 2.4 15.9 1.0
O B:HOH718 2.4 15.9 1.0
OD2 B:ASP164 2.4 14.5 1.0
OD1 B:ASP164 2.5 16.1 1.0
CG B:ASP164 2.8 17.5 1.0
CG B:ASP207 3.1 16.6 1.0
CG B:ASP188 3.4 17.4 1.0
C B:ALA186 3.6 17.7 1.0
OD2 B:ASP207 3.6 16.8 1.0
N B:ASP188 3.8 14.4 1.0
CB B:ASP207 4.0 14.6 1.0
OD2 B:ASP188 4.0 14.4 1.0
C B:TRP187 4.1 17.1 1.0
N B:ALA186 4.1 19.2 1.0
CA B:ASP188 4.2 13.8 1.0
CB B:ASP209 4.2 21.3 1.0
CA B:ASP207 4.2 13.8 1.0
CB B:ASP164 4.3 13.6 1.0
CB B:ASP188 4.4 14.0 1.0
CA B:ALA186 4.4 18.7 1.0
NA B:NA504 4.4 13.7 1.0
CA B:TRP187 4.5 17.6 1.0
N B:TRP187 4.5 18.9 1.0
O B:TRP187 4.5 16.7 1.0
O B:HOH657 4.6 31.8 1.0
N B:ASP209 4.6 16.3 1.0
N B:MET208 4.6 15.4 1.0
C B:ASP207 4.7 15.8 1.0
O B:HOH941 4.7 21.3 1.0
OD2 B:ASP199 4.9 16.2 1.0
CB B:ALA186 5.0 18.4 1.0

Reference:

Y.Sun, G.Liu, G.Liu, H.Tang, C.Sun, W.Zhang, L.Chen. The Novel Amylase Function of the Carboxyl Terminal Domain of AMY63. Biochem.Biophys.Res.Commun. V. 671 10 2023.
ISSN: ESSN 1090-2104
PubMed: 37290279
DOI: 10.1016/J.BBRC.2023.05.071
Page generated: Fri Jul 19 09:58:59 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy