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Calcium in PDB 4r37: Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac

Enzymatic activity of Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac

All present enzymatic activity of Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac:
2.3.1.129;

Protein crystallography data

The structure of Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac, PDB code: 4r37 was solved by A.J.Fisher, X.Chen, A.Ngo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.00 / 1.90
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 149.403, 149.403, 149.403, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 18.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac (pdb code 4r37). 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 Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac, PDB code: 4r37:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4r37

Go back to Calcium Binding Sites List in 4r37
Calcium binding site 1 out of 4 in the Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:11.2
occ:0.33
 OD1 A:ASN89 2.3 12.0 1.0
O A:HOH1124 2.3 16.9 1.0
O A:HOH1229 2.5 29.8 0.3
CG A:ASN89 3.3 12.0 1.0
ND2 A:ASN89 3.7 12.3 1.0
CA A:GLY59 4.2 13.0 1.0
O A:HOH1310 4.4 36.4 1.0
O A:GLY59 4.4 13.0 1.0
CB A:ASN89 4.6 11.5 1.0
C A:GLY59 4.8 12.8 1.0

Calcium binding site 2 out of 4 in 4r37

Go back to Calcium Binding Sites List in 4r37
Calcium binding site 2 out of 4 in the Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:47.0
occ:1.00
 O B:HOH538 2.5 35.1 1.0
O A:HOH1321 2.5 37.9 1.0
O A:HOH1372 3.5 46.0 1.0
OE1 A:GLU250 4.3 19.6 0.5
O A:HOH1210 4.5 27.9 1.0
O A:HOH1281 4.6 33.8 1.0
ND2 B:ASN221 4.8 32.3 1.0
O B:HOH414 5.0 18.0 1.0
CD A:GLU250 5.0 21.2 0.5

Calcium binding site 3 out of 4 in 4r37

Go back to Calcium Binding Sites List in 4r37
Calcium binding site 3 out of 4 in the Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:29.3
occ:1.00
 O B:HOH457 2.2 26.9 1.0
O B:HOH525 2.3 33.9 1.0
O B:HOH430 2.3 21.5 1.0
O A:HOH1188 2.3 25.7 1.0
O A:HOH1254 2.5 31.6 1.0
O A:HOH1168 2.5 23.4 1.0
O B:HOH456 2.6 26.9 1.0
O B:HOH557 4.1 36.6 1.0
O B:HOH483 4.3 29.3 1.0
ND2 A:ASN106 4.4 16.1 1.0
OD2 B:ASP244 4.4 21.8 1.0
OD1 A:ASN106 4.4 13.8 1.0
O A:HOH1109 4.5 13.1 1.0
O A:HOH1185 4.6 25.1 1.0
OD1 B:ASP244 4.6 21.4 1.0
O B:HOH470 4.7 27.9 1.0
CG A:ASN106 4.9 15.1 1.0
OE1 B:GLU240 4.9 31.5 1.0
CG B:ASP244 4.9 22.9 1.0

Calcium binding site 4 out of 4 in 4r37

Go back to Calcium Binding Sites List in 4r37
Calcium binding site 4 out of 4 in the Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of Lpxa, A Udp-N-Acetylglucosamine Acyltransferase From Bacteroides Fragilis 9343 with Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:18.0
occ:0.33
 OD1 B:ASN89 2.3 14.8 1.0
O B:HOH424 2.4 20.8 1.0
O B:HOH547 2.5 35.9 0.3
CG B:ASN89 3.3 15.7 1.0
ND2 B:ASN89 3.7 16.8 1.0
CA B:GLY59 4.2 18.4 1.0
O B:GLY59 4.3 16.5 1.0
O B:HOH535 4.5 34.9 1.0
CB B:ASN89 4.6 17.5 1.0
C B:GLY59 4.8 18.1 1.0

Reference:

A.Ngo, K.T.Fong, D.L.Cox, X.Chen, A.J.Fisher. Structures of Bacteroides Fragilis Uridine 5'-Diphosphate-N-Acetylglucosamine (Udp-Glcnac) Acyltransferase (Bflpxa). Acta Crystallogr.,Sect.D V. 71 1068 2015.
ISSN: ISSN 0907-4449
PubMed: 25945572
DOI: 10.1107/S1399004715003326
Page generated: Wed Jul 9 01:49:14 2025

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