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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

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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

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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

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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

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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

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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

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