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Calcium in PDB 7eby: Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C

Protein crystallography data

The structure of Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C, PDB code: 7eby was solved by M.Yamasaki, Y.Sumida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.63 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 83.586, 92.117, 162.111, 94.79, 96.31, 104.9
R / Rfree (%) 20.4 / 25.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C (pdb code 7eby). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C, PDB code: 7eby:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7eby

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Calcium binding site 1 out of 6 in the Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C


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 D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:18.7
occ:1.00
 OE2 A:GLU169 2.3 19.8 1.0
OD1 A:ASN165 2.3 20.4 1.0
OD1 A:ASP357 2.4 22.1 1.0
O A:GLY487 2.4 18.9 1.0
OD2 A:ASP354 2.5 18.0 1.0
O A:GLU356 2.5 20.9 1.0
OD1 A:ASP354 2.6 15.6 1.0
CG A:ASP354 2.9 15.9 1.0
CD A:GLU169 3.4 19.8 1.0
CG A:ASN165 3.4 19.1 1.0
C A:GLY487 3.4 18.4 1.0
CG A:ASP357 3.6 18.2 1.0
C A:GLU356 3.6 18.1 1.0
CA A:GLY487 3.8 22.0 1.0
CG A:GLU169 3.9 18.4 1.0
NH2 A:ARG482 3.9 15.5 1.0
ND2 A:ASN165 4.0 16.4 1.0
O A:HOH1204 4.0 21.4 1.0
CA A:ASP357 4.0 16.3 1.0
N A:ASP357 4.2 17.5 1.0
CB A:ASP354 4.4 11.1 1.0
CB A:ASP357 4.4 20.8 1.0
CZ A:ARG482 4.4 18.8 1.0
N A:ASN165 4.4 13.1 1.0
OE1 A:GLU169 4.4 22.0 1.0
NE A:ARG482 4.5 17.8 1.0
OD2 A:ASP357 4.5 14.9 1.0
N A:LEU488 4.6 20.4 1.0
N A:GLU356 4.7 17.3 1.0
CB A:ASN165 4.7 21.4 1.0
CA A:GLU356 4.7 13.8 1.0
O A:HOH1071 4.8 14.2 1.0
C A:ASN165 4.8 18.4 1.0
O A:ASN165 4.9 18.7 1.0
CA A:ASN165 4.9 18.8 1.0

Calcium binding site 2 out of 6 in 7eby

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Calcium binding site 2 out of 6 in the Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C


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 D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:15.7
occ:1.00
 OD1 B:ASN165 2.3 14.4 1.0
OE2 B:GLU169 2.3 15.9 1.0
OD1 B:ASP357 2.4 19.5 1.0
O B:GLU356 2.4 17.7 1.0
OD2 B:ASP354 2.6 19.1 1.0
OD1 B:ASP354 2.6 18.6 1.0
O B:GLY487 2.6 18.4 1.0
CG B:ASP354 2.9 19.3 1.0
CG B:ASN165 3.4 16.6 1.0
CD B:GLU169 3.4 13.8 1.0
C B:GLU356 3.5 19.6 1.0
C B:GLY487 3.6 16.4 1.0
CG B:ASP357 3.6 18.2 1.0
ND2 B:ASN165 3.8 16.9 1.0
O B:HOH1052 3.8 16.5 1.0
CG B:GLU169 3.9 19.2 1.0
CA B:GLY487 3.9 18.0 1.0
CA B:ASP357 4.0 14.9 1.0
NH2 B:ARG482 4.0 16.3 1.0
N B:ASP357 4.1 15.1 1.0
CB B:ASP357 4.4 16.9 1.0
CB B:ASP354 4.4 14.0 1.0
OE1 B:GLU169 4.5 21.3 1.0
N B:ASN165 4.5 13.7 1.0
CZ B:ARG482 4.5 21.1 1.0
NE B:ARG482 4.5 15.2 1.0
OD2 B:ASP357 4.5 18.7 1.0
N B:GLU356 4.7 19.9 1.0
CB B:ASN165 4.7 19.3 1.0
CA B:GLU356 4.7 15.0 1.0
O B:HOH1017 4.7 19.7 1.0
O B:ASN165 4.8 16.0 1.0
N B:LEU488 4.8 15.2 1.0
C B:ASN165 4.8 17.0 1.0
CA B:ASN165 4.9 15.1 1.0

Calcium binding site 3 out of 6 in 7eby

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Calcium binding site 3 out of 6 in the Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C


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 D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca908

b:14.3
occ:1.00
 OD2 C:ASP354 2.2 14.5 1.0
OD1 C:ASP357 2.2 17.8 1.0
OE2 C:GLU169 2.3 15.0 1.0
OD1 C:ASN165 2.3 10.8 1.0
O C:GLU356 2.4 14.7 1.0
OD1 C:ASP354 2.6 14.7 1.0
O C:GLY487 2.6 11.6 1.0
CG C:ASP354 2.7 12.8 1.0
CD C:GLU169 3.4 16.0 1.0
CG C:ASN165 3.4 17.6 1.0
CG C:ASP357 3.5 17.6 1.0
C C:GLU356 3.5 13.6 1.0
C C:GLY487 3.6 17.6 1.0
O C:HOH1051 3.8 21.5 1.0
NH2 C:ARG482 3.8 15.9 1.0
CA C:GLY487 3.9 14.2 1.0
CA C:ASP357 3.9 14.7 1.0
ND2 C:ASN165 3.9 13.0 1.0
CG C:GLU169 4.0 18.1 1.0
N C:ASP357 4.1 12.6 1.0
CB C:ASP357 4.2 12.7 1.0
CB C:ASP354 4.3 15.8 1.0
CZ C:ARG482 4.4 15.7 1.0
OD2 C:ASP357 4.4 16.9 1.0
OE1 C:GLU169 4.4 16.6 1.0
N C:ASN165 4.4 12.1 1.0
NE C:ARG482 4.4 17.3 1.0
N C:GLU356 4.6 10.5 1.0
CA C:GLU356 4.6 16.1 1.0
CB C:ASN165 4.7 15.6 1.0
N C:LEU488 4.8 16.8 1.0
C C:ASN165 4.8 17.5 1.0
O C:ASN165 4.9 16.1 1.0
CA C:ASN165 4.9 12.9 1.0

Calcium binding site 4 out of 6 in 7eby

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Calcium binding site 4 out of 6 in the Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C


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 D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca909

b:19.0
occ:1.00
 OD1 D:ASN165 2.3 13.7 1.0
OD2 D:ASP354 2.4 21.8 1.0
OE2 D:GLU169 2.4 15.3 1.0
O D:GLU356 2.4 13.3 1.0
OD1 D:ASP357 2.5 21.6 1.0
OD1 D:ASP354 2.5 17.7 1.0
O D:GLY487 2.6 17.4 1.0
CG D:ASP354 2.8 16.9 1.0
CG D:ASN165 3.3 19.1 1.0
CD D:GLU169 3.5 18.2 1.0
C D:GLU356 3.5 14.6 1.0
C D:GLY487 3.6 18.1 1.0
CG D:ASP357 3.7 14.7 1.0
ND2 D:ASN165 3.8 15.6 1.0
CA D:GLY487 3.8 15.7 1.0
O D:HOH1089 3.9 19.7 1.0
NH2 D:ARG482 3.9 16.2 1.0
CG D:GLU169 4.0 17.2 1.0
CA D:ASP357 4.0 15.7 1.0
N D:ASP357 4.2 14.2 1.0
CB D:ASP354 4.3 14.1 1.0
N D:ASN165 4.4 13.1 1.0
CZ D:ARG482 4.4 17.6 1.0
NE D:ARG482 4.4 12.1 1.0
CB D:ASP357 4.5 13.9 1.0
OE1 D:GLU169 4.5 19.7 1.0
N D:GLU356 4.6 12.8 1.0
OD2 D:ASP357 4.6 24.3 1.0
CB D:ASN165 4.6 16.0 1.0
CA D:GLU356 4.7 16.5 1.0
N D:LEU488 4.8 13.9 1.0
O D:HOH1126 4.8 21.4 1.0
O D:ASN165 4.8 16.9 1.0
CA D:ASN165 4.8 17.3 1.0
C D:ASN165 4.9 18.1 1.0

Calcium binding site 5 out of 6 in 7eby

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Calcium binding site 5 out of 6 in the Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C


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 D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca906

b:18.1
occ:1.00
 OE2 E:GLU169 2.4 16.9 1.0
OD2 E:ASP354 2.4 22.2 1.0
O E:GLU356 2.4 18.6 1.0
OD1 E:ASP357 2.4 19.0 1.0
OD1 E:ASN165 2.4 20.3 1.0
O E:GLY487 2.6 19.1 1.0
OD1 E:ASP354 2.6 13.5 1.0
CG E:ASP354 2.8 16.6 1.0
CG E:ASN165 3.5 17.8 1.0
CD E:GLU169 3.5 19.4 1.0
C E:GLU356 3.5 18.2 1.0
C E:GLY487 3.5 19.6 1.0
CG E:ASP357 3.6 17.5 1.0
O E:HOH1120 3.7 20.2 1.0
CA E:GLY487 3.8 19.5 1.0
ND2 E:ASN165 3.9 13.5 1.0
NH2 E:ARG482 3.9 13.4 1.0
CA E:ASP357 4.0 19.0 1.0
CG E:GLU169 4.0 14.7 1.0
N E:ASP357 4.1 16.8 1.0
CB E:ASP354 4.3 12.7 1.0
CB E:ASP357 4.4 13.9 1.0
CZ E:ARG482 4.4 17.0 1.0
NE E:ARG482 4.4 20.9 1.0
N E:ASN165 4.5 17.9 1.0
OE1 E:GLU169 4.5 15.7 1.0
OD2 E:ASP357 4.5 17.1 1.0
N E:GLU356 4.6 11.8 1.0
CA E:GLU356 4.6 15.2 1.0
CB E:ASN165 4.7 17.5 1.0
N E:LEU488 4.8 20.7 1.0
O E:HOH1094 4.8 23.0 1.0
O E:ASN165 4.9 17.6 1.0
C E:ASN165 4.9 17.4 1.0
CA E:ASN165 5.0 16.9 1.0

Calcium binding site 6 out of 6 in 7eby

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Calcium binding site 6 out of 6 in the Crystal Structure of D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C


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 D-Succinylase (Dsa) From Cupriavidus Sp. P4-10-C within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca909

b:13.9
occ:1.00
 OD1 F:ASP357 2.3 13.8 1.0
OE2 F:GLU169 2.3 18.3 1.0
OD1 F:ASN165 2.3 15.4 1.0
O F:GLU356 2.4 13.9 1.0
OD1 F:ASP354 2.5 16.3 1.0
OD2 F:ASP354 2.5 16.2 1.0
O F:GLY487 2.6 15.4 1.0
CG F:ASP354 2.8 16.6 1.0
CG F:ASN165 3.4 15.3 1.0
CD F:GLU169 3.4 16.2 1.0
C F:GLU356 3.4 11.5 1.0
CG F:ASP357 3.5 16.3 1.0
C F:GLY487 3.6 13.7 1.0
CA F:GLY487 3.8 15.2 1.0
NH2 F:ARG482 3.9 17.7 1.0
CA F:ASP357 3.9 12.2 1.0
O F:HOH1059 3.9 16.9 1.0
ND2 F:ASN165 3.9 14.8 1.0
CG F:GLU169 4.0 15.3 1.0
N F:ASP357 4.0 16.8 1.0
CB F:ASP357 4.2 10.8 1.0
CB F:ASP354 4.3 14.3 1.0
OD2 F:ASP357 4.4 17.3 1.0
N F:ASN165 4.4 12.6 1.0
CZ F:ARG482 4.4 12.7 1.0
OE1 F:GLU169 4.4 13.6 1.0
NE F:ARG482 4.5 15.1 1.0
N F:GLU356 4.6 9.2 1.0
CA F:GLU356 4.6 15.3 1.0
CB F:ASN165 4.7 13.8 1.0
N F:LEU488 4.8 13.3 1.0
O F:HOH1030 4.8 14.4 1.0
C F:ASN165 4.8 16.6 1.0
CA F:ASN165 4.9 13.6 1.0
O F:ASN165 4.9 14.4 1.0

Reference:

Y.Sumida, M.Yamasaki, Y.Nishiya, S.Kumagai, T.Yamada, M.Azuma. Protein Engineering of D-Succinylase From Cupriavidus Sp. For D-Amino Acid Synthesis and the Structural Implications. Adv.Synth.Catal. V. 363 4770 2021.
ISSN: ESSN 1615-4169
DOI: 10.1002/ADSC.202100587
Page generated: Wed Jul 9 21:50:31 2025

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