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Calcium in PDB 4r83: Crystal Structure of Sialyltransferase From Photobacterium Damsela

Enzymatic activity of Crystal Structure of Sialyltransferase From Photobacterium Damsela

All present enzymatic activity of Crystal Structure of Sialyltransferase From Photobacterium Damsela:
2.4.99.1;

Protein crystallography data

The structure of Crystal Structure of Sialyltransferase From Photobacterium Damsela, PDB code: 4r83 was solved by A.J.Fisher, X.Chen, Y.Li, N.Huynh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.84 / 1.93
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.670, 81.340, 111.840, 98.60, 92.76, 100.85
R / Rfree (%) 17.9 / 21.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Sialyltransferase From Photobacterium Damsela (pdb code 4r83). 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 Sialyltransferase From Photobacterium Damsela, PDB code: 4r83:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4r83

Go back to Calcium Binding Sites List in 4r83
Calcium binding site 1 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela


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 Sialyltransferase From Photobacterium Damsela within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:52.1
occ:1.00
 O A:HOH683 2.0 40.6 1.0
OD2 A:ASP395 2.2 70.8 1.0
OD1 A:ASN352 2.4 45.4 1.0
O A:SER348 2.5 60.7 1.0
O A:LEU350 2.5 57.4 1.0
O A:TYR345 2.5 56.3 1.0
O A:HOH692 2.6 41.7 1.0
CG A:ASP395 3.3 60.9 1.0
CG A:ASN352 3.5 45.6 1.0
C A:SER348 3.5 62.4 1.0
C A:TYR345 3.6 53.9 1.0
C A:LEU350 3.7 60.6 1.0
CB A:ASP395 3.8 51.1 1.0
ND2 A:ASN352 4.0 46.5 1.0
N A:LEU350 4.0 62.6 1.0
N A:SER348 4.1 53.5 1.0
CA A:SER348 4.1 65.3 1.0
CB A:SER348 4.2 68.0 1.0
CA A:TYR345 4.3 48.1 1.0
CA A:LEU350 4.3 59.0 1.0
C A:PRO349 4.4 61.4 1.0
OD1 A:ASP395 4.4 48.8 1.0
OG A:SER348 4.4 63.6 1.0
N A:PRO349 4.5 62.5 1.0
N A:SER346 4.6 56.9 1.0
O A:GLN344 4.6 54.8 1.0
C A:PRO351 4.6 52.0 1.0
O A:PRO351 4.6 46.3 1.0
O A:HOH863 4.6 56.3 1.0
CA A:PRO349 4.7 60.8 1.0
CB A:ASN352 4.7 44.5 1.0
CA A:SER346 4.8 59.1 1.0
N A:PRO351 4.8 55.7 1.0
CB A:LEU350 4.8 52.8 1.0
C A:SER346 4.9 57.2 1.0
N A:ASN352 4.9 50.7 1.0
N A:GLN347 4.9 53.0 1.0
CA A:PRO351 4.9 55.0 1.0
O A:PRO349 5.0 59.4 1.0
CA A:ASN352 5.0 39.2 1.0
CE1 A:PHE397 5.0 54.0 1.0

Calcium binding site 2 out of 4 in 4r83

Go back to Calcium Binding Sites List in 4r83
Calcium binding site 2 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela


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 Sialyltransferase From Photobacterium Damsela within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:34.3
occ:1.00
 O B:LEU350 2.3 36.8 1.0
OD2 B:ASP395 2.3 30.7 1.0
OD1 B:ASN352 2.4 33.7 1.0
O B:TYR345 2.4 38.7 1.0
O B:SER348 2.4 40.5 1.0
O B:HOH613 2.4 31.3 1.0
O B:HOH606 2.5 29.0 1.0
CG B:ASN352 3.3 35.5 1.0
CG B:ASP395 3.4 32.9 1.0
C B:SER348 3.5 40.7 1.0
C B:LEU350 3.5 32.3 1.0
C B:TYR345 3.5 37.7 1.0
ND2 B:ASN352 3.5 32.0 1.0
N B:LEU350 3.8 42.8 1.0
CB B:ASP395 3.9 29.9 1.0
C B:PRO349 4.1 43.7 1.0
CA B:LEU350 4.2 33.5 1.0
N B:SER348 4.3 36.7 1.0
CA B:SER348 4.3 42.1 1.0
CA B:TYR345 4.3 33.4 1.0
N B:PRO349 4.4 42.0 1.0
CB B:SER348 4.4 38.7 1.0
CA B:PRO349 4.4 46.2 1.0
N B:SER346 4.5 38.2 1.0
C B:PRO351 4.5 35.0 1.0
OD1 B:ASP395 4.5 30.2 1.0
O B:PRO351 4.5 30.7 1.0
N B:PRO351 4.6 45.0 1.0
O B:PRO349 4.6 42.2 1.0
OG B:SER348 4.6 35.7 1.0
CA B:SER346 4.7 41.8 1.0
CB B:ASN352 4.7 28.5 1.0
CB B:LEU350 4.7 33.2 1.0
O B:GLN344 4.7 33.8 1.0
O D:HOH617 4.8 31.6 1.0
CA B:PRO351 4.8 38.7 1.0
N B:ASN352 4.8 35.7 1.0
C B:SER346 4.9 39.2 1.0
CA B:ASN352 5.0 28.4 1.0

Calcium binding site 3 out of 4 in 4r83

Go back to Calcium Binding Sites List in 4r83
Calcium binding site 3 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela


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 Sialyltransferase From Photobacterium Damsela within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:32.4
occ:1.00
 OD2 C:ASP395 2.2 31.5 1.0
OD1 C:ASN352 2.4 28.5 1.0
O C:TYR345 2.4 32.6 1.0
O C:LEU350 2.4 31.3 1.0
O C:SER348 2.4 31.4 1.0
O C:HOH650 2.5 35.2 1.0
O C:HOH602 2.6 24.7 1.0
CG C:ASN352 3.3 36.3 1.0
CG C:ASP395 3.3 33.3 1.0
C C:SER348 3.4 36.9 1.0
C C:TYR345 3.5 33.7 1.0
C C:LEU350 3.6 38.1 1.0
ND2 C:ASN352 3.7 30.6 1.0
N C:LEU350 3.9 40.8 1.0
CB C:ASP395 3.9 28.9 1.0
C C:PRO349 4.2 41.3 1.0
CA C:LEU350 4.3 41.0 1.0
N C:SER348 4.3 32.4 1.0
CA C:SER348 4.3 33.9 1.0
CA C:TYR345 4.3 27.2 1.0
N C:PRO349 4.4 33.2 1.0
CB C:SER348 4.4 34.8 1.0
OD1 C:ASP395 4.4 29.5 1.0
CA C:PRO349 4.5 38.9 1.0
C C:PRO351 4.5 34.5 1.0
N C:SER346 4.5 38.0 1.0
O C:PRO351 4.5 31.9 1.0
OG C:SER348 4.6 35.2 1.0
N C:PRO351 4.6 34.2 1.0
CA C:SER346 4.7 37.2 1.0
CB C:ASN352 4.7 32.8 1.0
O C:GLN344 4.7 32.3 1.0
CB C:LEU350 4.8 42.4 1.0
N C:ASN352 4.8 27.7 1.0
O C:PRO349 4.8 36.1 1.0
CA C:PRO351 4.8 34.4 1.0
C C:SER346 4.9 37.9 1.0
CA C:ASN352 4.9 27.7 1.0

Calcium binding site 4 out of 4 in 4r83

Go back to Calcium Binding Sites List in 4r83
Calcium binding site 4 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela


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 Sialyltransferase From Photobacterium Damsela within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:81.0
occ:1.00
 OD2 D:ASP395 2.3 80.8 1.0
OD1 D:ASN352 2.4 67.9 1.0
O D:SER348 2.4 92.3 1.0
O D:TYR345 2.4 93.1 1.0
O D:LEU350 2.6 80.0 1.0
CG D:ASN352 3.4 67.5 1.0
CG D:ASP395 3.4 85.1 1.0
C D:SER348 3.5 88.4 1.0
C D:TYR345 3.5 80.2 1.0
ND2 D:ASN352 3.7 68.8 1.0
C D:LEU350 3.8 78.9 1.0
CB D:ASP395 3.9 81.4 1.0
N D:SER348 4.0 93.5 1.0
N D:LEU350 4.0 69.6 1.0
CA D:SER348 4.2 87.8 1.0
CA D:TYR345 4.3 77.9 1.0
CA D:LEU350 4.4 73.1 1.0
CB D:SER348 4.4 88.0 1.0
C D:PRO349 4.4 82.7 1.0
N D:SER346 4.5 76.5 1.0
OD1 D:ASP395 4.5 86.6 1.0
N D:PRO349 4.6 87.0 1.0
O D:GLN344 4.7 73.0 1.0
C D:PRO351 4.7 69.0 1.0
O D:PRO351 4.7 68.7 1.0
CA D:SER346 4.7 80.2 1.0
CE1 D:PHE397 4.7 74.9 1.0
CB D:ASN352 4.7 60.0 1.0
CA D:PRO349 4.7 82.7 1.0
OG D:SER348 4.7 93.7 1.0
N D:GLN347 4.8 77.8 1.0
CB D:LEU350 4.8 75.5 1.0
C D:SER346 4.8 78.9 1.0
N D:PRO351 4.8 74.8 1.0
CZ D:PHE397 4.9 77.9 1.0
N D:ASN352 4.9 67.6 1.0

Reference:

N.Huynh, Y.Li, H.Yu, S.Huang, K.Lau, X.Chen, A.J.Fisher. Crystal Structures of Sialyltransferase From Photobacterium Damselae Febs Lett. 2014.
ISSN: ISSN 0014-5793
DOI: 10.1016/J.FEBSLET.2014.11.003
Page generated: Wed Jul 9 01:51:30 2025

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