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Calcium in PDB 4r84: Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound

Enzymatic activity of Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound

All present enzymatic activity of Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound:
2.4.99.1;

Protein crystallography data

The structure of Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound, PDB code: 4r84 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) 39.75 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.340, 81.450, 111.210, 99.02, 91.59, 101.20
R / Rfree (%) 17.2 / 20.3

Other elements in 4r84:

The structure of Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound (pdb code 4r84). 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 with Cmp-3F(A)NEU5AC Bound, PDB code: 4r84:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4r84

Go back to Calcium Binding Sites List in 4r84
Calcium binding site 1 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound


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 with Cmp-3F(A)NEU5AC Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:27.8
occ:1.00
 O A:HOH657 2.3 28.1 1.0
O A:LEU350 2.4 29.7 1.0
OD2 A:ASP395 2.4 24.4 1.0
O A:SER348 2.4 26.9 1.0
OD1 A:ASN352 2.4 23.9 1.0
O A:TYR345 2.5 24.6 1.0
O A:HOH619 2.6 23.2 1.0
CG A:ASN352 3.4 21.3 1.0
C A:SER348 3.5 32.5 1.0
C A:LEU350 3.5 30.9 1.0
CG A:ASP395 3.5 32.3 1.0
C A:TYR345 3.6 27.6 1.0
ND2 A:ASN352 3.6 23.2 1.0
N A:LEU350 3.9 28.3 1.0
CB A:ASP395 4.0 26.3 1.0
N A:SER348 4.2 31.0 1.0
CA A:LEU350 4.2 27.6 1.0
CA A:SER348 4.2 32.6 1.0
C A:PRO349 4.2 29.7 1.0
CB A:SER348 4.3 32.4 1.0
CA A:TYR345 4.4 24.2 1.0
N A:PRO349 4.5 34.9 1.0
C A:PRO351 4.5 25.8 1.0
O A:PRO351 4.6 24.4 1.0
N A:PRO351 4.6 28.6 1.0
CA A:PRO349 4.6 31.5 1.0
N A:SER346 4.6 26.1 1.0
OD1 A:ASP395 4.6 27.7 1.0
OG A:SER348 4.6 35.0 1.0
CB A:LEU350 4.7 26.9 1.0
O A:PRO349 4.7 36.6 1.0
CA A:SER346 4.7 27.6 1.0
CB A:ASN352 4.7 19.7 1.0
CA A:PRO351 4.8 26.4 1.0
O A:GLN344 4.8 23.5 1.0
N A:ASN352 4.8 23.8 1.0
O A:HOH648 4.9 26.9 1.0
C A:SER346 5.0 24.8 1.0

Calcium binding site 2 out of 4 in 4r84

Go back to Calcium Binding Sites List in 4r84
Calcium binding site 2 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound


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 with Cmp-3F(A)NEU5AC Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:21.6
occ:1.00
 OD2 B:ASP395 2.2 21.0 1.0
O B:SER348 2.3 22.6 1.0
OD1 B:ASN352 2.4 18.2 1.0
O B:HOH614 2.4 22.9 1.0
O B:TYR345 2.5 22.5 1.0
O B:LEU350 2.5 24.3 1.0
O B:HOH616 2.6 23.0 1.0
CG B:ASN352 3.3 21.8 1.0
C B:SER348 3.4 23.9 1.0
CG B:ASP395 3.4 22.0 1.0
C B:TYR345 3.6 25.6 1.0
C B:LEU350 3.6 25.3 1.0
ND2 B:ASN352 3.7 22.3 1.0
N B:LEU350 3.9 22.1 1.0
CB B:ASP395 3.9 24.4 1.0
N B:SER348 4.1 25.9 1.0
CA B:SER348 4.2 23.6 1.0
C B:PRO349 4.2 25.3 1.0
CA B:LEU350 4.3 24.6 1.0
CB B:SER348 4.3 25.5 1.0
N B:PRO349 4.3 23.5 1.0
CA B:TYR345 4.4 21.1 1.0
OD1 B:ASP395 4.4 22.6 1.0
CA B:PRO349 4.5 22.7 1.0
O B:PRO351 4.5 21.5 1.0
OG B:SER348 4.6 23.6 1.0
C B:PRO351 4.6 24.5 1.0
N B:SER346 4.6 27.7 1.0
CB B:ASN352 4.7 19.0 1.0
N B:PRO351 4.7 28.0 1.0
O B:HOH880 4.7 45.1 1.0
O B:GLN344 4.7 22.8 1.0
CB B:LEU350 4.7 20.7 1.0
O B:HOH788 4.8 39.5 1.0
CA B:SER346 4.8 22.7 1.0
O B:PRO349 4.8 27.5 1.0
O D:HOH607 4.8 22.4 1.0
N B:ASN352 4.9 20.2 1.0
CA B:PRO351 4.9 24.2 1.0
C B:SER346 5.0 23.8 1.0
CA B:ASN352 5.0 22.1 1.0

Calcium binding site 3 out of 4 in 4r84

Go back to Calcium Binding Sites List in 4r84
Calcium binding site 3 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound


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 with Cmp-3F(A)NEU5AC Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:24.0
occ:1.00
 OD2 C:ASP395 2.3 22.4 1.0
O C:SER348 2.3 23.5 1.0
OD1 C:ASN352 2.4 19.4 1.0
O C:LEU350 2.4 24.1 1.0
O C:TYR345 2.5 23.2 1.0
O C:HOH611 2.5 22.7 1.0
O C:HOH610 2.6 22.6 1.0
CG C:ASN352 3.3 22.6 1.0
C C:SER348 3.4 22.9 1.0
CG C:ASP395 3.5 23.7 1.0
C C:LEU350 3.6 25.0 1.0
C C:TYR345 3.6 23.2 1.0
ND2 C:ASN352 3.7 21.4 1.0
N C:LEU350 3.9 20.7 1.0
CB C:ASP395 4.0 22.9 1.0
C C:PRO349 4.2 25.3 1.0
CA C:SER348 4.2 22.7 1.0
N C:SER348 4.2 24.2 1.0
CA C:LEU350 4.2 22.9 1.0
CB C:SER348 4.3 23.4 1.0
N C:PRO349 4.3 24.0 1.0
CA C:TYR345 4.4 20.7 1.0
CA C:PRO349 4.4 21.5 1.0
OG C:SER348 4.5 22.6 1.0
OD1 C:ASP395 4.5 24.3 1.0
C C:PRO351 4.5 24.3 1.0
O C:PRO351 4.6 22.8 1.0
N C:SER346 4.6 22.1 1.0
CB C:LEU350 4.7 20.5 1.0
CB C:ASN352 4.7 18.5 1.0
N C:PRO351 4.7 24.3 1.0
O C:GLN344 4.7 21.5 1.0
CA C:SER346 4.7 20.3 0.5
O C:PRO349 4.7 25.9 1.0
N C:ASN352 4.8 18.9 1.0
CA C:SER346 4.8 20.8 0.5
CA C:PRO351 4.8 24.1 1.0
CA C:ASN352 5.0 19.9 1.0
C C:SER346 5.0 27.9 1.0

Calcium binding site 4 out of 4 in 4r84

Go back to Calcium Binding Sites List in 4r84
Calcium binding site 4 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound


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 with Cmp-3F(A)NEU5AC Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:37.7
occ:1.00
 OD2 D:ASP395 2.3 41.9 1.0
O D:TYR345 2.3 37.0 1.0
O D:SER348 2.3 48.2 1.0
OD1 D:ASN352 2.5 29.3 1.0
O D:HOH709 2.5 34.7 1.0
O D:LEU350 2.6 44.5 1.0
CG D:ASN352 3.4 38.7 1.0
C D:SER348 3.4 59.1 1.0
C D:TYR345 3.5 33.8 1.0
CG D:ASP395 3.5 49.2 1.0
ND2 D:ASN352 3.7 38.2 1.0
C D:LEU350 3.8 43.0 1.0
N D:SER348 4.0 55.1 1.0
CA D:SER348 4.1 53.2 1.0
N D:LEU350 4.2 33.7 1.0
CB D:ASP395 4.2 47.6 1.0
CB D:SER348 4.2 45.6 1.0
CA D:TYR345 4.3 34.3 1.0
C D:PRO349 4.5 43.8 1.0
N D:SER346 4.5 42.8 1.0
N D:PRO349 4.5 56.5 1.0
OD1 D:ASP395 4.5 44.4 1.0
CA D:LEU350 4.5 41.6 1.0
OG D:SER348 4.6 47.2 1.0
CA D:SER346 4.6 42.8 1.0
O D:GLN344 4.6 43.5 1.0
CA D:PRO349 4.7 55.8 1.0
C D:PRO351 4.7 37.7 1.0
N D:GLN347 4.8 48.3 1.0
C D:SER346 4.8 49.8 1.0
CB D:ASN352 4.8 28.1 1.0
O D:PRO351 4.8 35.4 1.0
N D:PRO351 4.8 37.5 1.0
CA D:PRO351 5.0 36.8 1.0
N D:ASN352 5.0 30.2 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 01:51:48 2025

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