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Calcium in PDB 6jq9: Crystal Structure of A Lyase From Alteromonas Sp.

Protein crystallography data

The structure of Crystal Structure of A Lyase From Alteromonas Sp., PDB code: 6jq9 was solved by H.M.Qin, Q.Q.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.89 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.048, 121.768, 124.304, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 28.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Lyase From Alteromonas Sp. (pdb code 6jq9). 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 A Lyase From Alteromonas Sp., PDB code: 6jq9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6jq9

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Calcium binding site 1 out of 4 in the Crystal Structure of A Lyase From Alteromonas Sp.


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 A Lyase From Alteromonas Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:15.2
occ:1.00
 O A:LYS224 2.2 17.3 1.0
OD2 A:ASP212 2.3 17.6 1.0
OD2 A:ASP222 2.3 18.1 1.0
O A:HOH935 2.4 13.6 1.0
O A:HOH919 2.5 21.0 1.0
OD1 A:ASP222 2.6 19.3 1.0
O A:HOH709 2.8 11.9 1.0
CG A:ASP222 2.8 19.8 1.0
CG A:ASP212 3.3 18.6 1.0
C A:LYS224 3.4 17.0 1.0
CB A:ASP212 3.6 18.3 1.0
CB A:LYS224 4.1 15.8 1.0
O A:HOH737 4.2 19.0 1.0
CA A:LYS224 4.2 16.1 1.0
CB A:ASP222 4.3 20.3 1.0
OE1 A:GLN218 4.3 35.3 1.0
N A:LYS224 4.3 16.9 1.0
O A:ASP184 4.4 19.0 1.0
OD1 A:ASP212 4.5 20.8 1.0
N A:HIS225 4.5 17.4 1.0
O A:HOH1085 4.6 20.2 1.0
N A:GLN218 4.6 21.4 1.0
CA A:SER217 4.7 22.8 1.0
CG A:GLN218 4.8 27.1 1.0
OD1 A:ASP185 4.8 16.8 1.0
CA A:HIS225 4.8 19.4 1.0
O A:LEU216 4.9 20.7 1.0
CD A:GLN218 4.9 28.7 1.0

Calcium binding site 2 out of 4 in 6jq9

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Calcium binding site 2 out of 4 in the Crystal Structure of A Lyase From Alteromonas Sp.


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 A Lyase From Alteromonas Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:14.3
occ:1.00
 O A:HOH766 2.3 7.3 1.0
O A:HOH824 2.3 18.5 1.0
O A:PHE328 2.3 15.7 1.0
O A:HOH920 2.4 11.4 1.0
O A:ASN323 2.4 19.3 1.0
OD2 A:ASP326 2.4 21.2 1.0
O A:HOH913 2.5 19.9 1.0
CG A:ASP326 3.4 17.6 1.0
C A:PHE328 3.5 19.5 1.0
C A:ASN323 3.6 18.2 1.0
OD1 A:ASP326 3.8 15.4 1.0
CA A:ASN324 4.2 17.1 1.0
CB A:PHE328 4.2 18.0 1.0
CA A:PHE328 4.3 18.3 1.0
O A:LYS329 4.3 17.8 1.0
O A:ASP326 4.4 22.3 1.0
N A:ASN324 4.4 17.5 1.0
O A:SER321 4.4 13.8 1.0
O A:HOH860 4.4 12.4 1.0
N A:PHE328 4.4 20.2 1.0
C A:LYS329 4.5 18.6 1.0
OD1 A:ASN324 4.5 21.8 1.0
N A:LYS329 4.5 17.8 1.0
O A:TYR330 4.5 16.4 1.0
OD1 A:ASN381 4.6 19.6 1.0
CA A:LYS329 4.6 21.1 1.0
CB A:ASP326 4.7 19.1 1.0
N A:ASP326 4.7 18.8 1.0
CA A:ASN323 4.7 19.2 1.0
C A:ASP326 4.8 20.1 1.0
C A:ASN324 4.8 18.3 1.0
CB A:ASN323 4.9 20.0 1.0
CA A:ASP326 5.0 20.3 1.0
N A:TYR330 5.0 17.3 1.0
N A:ASN323 5.0 19.0 1.0
O A:HOH877 5.0 16.3 1.0

Calcium binding site 3 out of 4 in 6jq9

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Calcium binding site 3 out of 4 in the Crystal Structure of A Lyase From Alteromonas Sp.


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 A Lyase From Alteromonas Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:11.8
occ:1.00
 O B:HOH942 2.0 17.6 1.0
O B:ASN323 2.2 17.8 1.0
O B:HOH747 2.2 12.6 1.0
OD1 B:ASP326 2.3 18.6 1.0
O B:PHE328 2.3 17.9 1.0
O B:HOH726 2.5 20.9 1.0
O B:HOH832 2.5 22.7 1.0
CG B:ASP326 3.4 20.7 1.0
C B:ASN323 3.4 17.7 1.0
C B:PHE328 3.5 16.0 1.0
OD2 B:ASP326 3.8 18.0 1.0
CA B:ASN324 4.0 15.1 1.0
N B:ASN324 4.1 15.9 1.0
O B:SER321 4.3 13.9 1.0
CA B:PHE328 4.3 17.1 1.0
OD1 B:ASN381 4.4 17.2 1.0
O B:LYS329 4.4 16.2 1.0
O B:ASP326 4.4 19.6 1.0
CB B:PHE328 4.4 16.1 1.0
OD1 B:ASN324 4.4 21.8 1.0
N B:PHE328 4.5 17.4 1.0
C B:LYS329 4.5 15.9 1.0
C B:ASN324 4.5 16.1 1.0
N B:LYS329 4.5 17.9 1.0
O B:HOH840 4.5 16.6 1.0
CA B:ASN323 4.6 17.9 1.0
N B:ASP326 4.6 17.8 1.0
CB B:ASP326 4.7 19.3 1.0
CA B:LYS329 4.7 16.9 1.0
C B:ASP326 4.7 20.2 1.0
O B:TYR330 4.8 14.9 1.0
N B:ASP325 4.8 18.0 1.0
N B:ASN323 4.9 19.8 1.0
CB B:ASN323 4.9 18.6 1.0
CA B:ASP326 4.9 18.5 1.0
O B:HOH875 5.0 20.8 1.0

Calcium binding site 4 out of 4 in 6jq9

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Calcium binding site 4 out of 4 in the Crystal Structure of A Lyase From Alteromonas Sp.


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 A Lyase From Alteromonas Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:17.9
occ:1.00
 OD2 B:ASP222 2.4 19.2 1.0
O B:LYS224 2.4 17.1 1.0
O B:HOH1008 2.5 25.8 1.0
O B:HOH771 2.6 26.1 1.0
OD1 B:ASP222 2.6 22.4 1.0
CG B:ASP222 2.8 23.6 1.0
OD2 B:ASP212 2.9 18.3 1.0
CG B:ASP212 3.4 15.6 1.0
C B:LYS224 3.6 16.9 1.0
CB B:ASP212 3.6 19.1 1.0
O B:HOH733 4.1 13.4 1.0
CB B:LYS224 4.1 17.8 1.0
CA B:LYS224 4.3 18.0 1.0
CB B:ASP222 4.3 25.3 1.0
OD1 B:ASP212 4.4 19.6 1.0
N B:LYS224 4.4 19.7 1.0
O B:ASP184 4.4 23.7 1.0
OE1 B:GLN218 4.4 27.7 1.0
OD1 B:ASP185 4.6 22.9 1.0
N B:HIS225 4.6 16.8 1.0
O B:LEU216 4.7 25.7 1.0
CA B:SER217 4.7 24.4 1.0
N B:GLN218 4.8 24.2 1.0
CA B:HIS225 4.9 19.3 1.0
CD B:GLN218 5.0 27.9 1.0

Reference:

H.M.Qin, Q.Q.Guo. Crystal Structure of A Lyase From Alteromonas Sp. To Be Published.
Page generated: Wed Jul 9 15:18:20 2025

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