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Calcium in PDB 5ngy: Crystal Structure of Leuconostoc Citreum Nrrl B-1299 Dextransucrase Dsr-M

Protein crystallography data

The structure of Crystal Structure of Leuconostoc Citreum Nrrl B-1299 Dextransucrase Dsr-M, PDB code: 5ngy was solved by M.Claverie, G.Cioci, M.Remaud-Simeon, C.Moulis, S.Tranier, M.Vuillemin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.869, 128.810, 234.518, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.6

Other elements in 5ngy:

The structure of Crystal Structure of Leuconostoc Citreum Nrrl B-1299 Dextransucrase Dsr-M also contains other interesting chemical elements:

Praseodymium (Pr) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Leuconostoc Citreum Nrrl B-1299 Dextransucrase Dsr-M (pdb code 5ngy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Leuconostoc Citreum Nrrl B-1299 Dextransucrase Dsr-M, PDB code: 5ngy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5ngy

Go back to Calcium Binding Sites List in 5ngy
Calcium binding site 1 out of 2 in the Crystal Structure of Leuconostoc Citreum Nrrl B-1299 Dextransucrase Dsr-M


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 Leuconostoc Citreum Nrrl B-1299 Dextransucrase Dsr-M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1501

b:41.1
occ:1.00
OE2 A:GLU627 2.2 51.1 1.0
OD1 A:ASP1182 2.3 51.0 1.0
O A:ASN681 2.4 45.2 1.0
OD2 A:ASP633 2.4 54.0 1.0
O A:GLU627 2.7 48.4 1.0
OD1 A:ASP633 2.7 56.6 1.0
CG A:ASP633 2.9 55.1 1.0
CD A:GLU627 3.3 50.5 1.0
C A:ASN681 3.6 45.5 1.0
CG A:ASP1182 3.6 50.4 1.0
C A:GLU627 3.7 49.1 1.0
CG A:GLU627 3.8 49.8 1.0
O A:VAL634 4.1 50.2 1.0
CA A:VAL682 4.1 46.4 1.0
CG1 A:VAL682 4.2 46.7 1.0
CA A:GLU627 4.2 48.8 1.0
O A:ASP1182 4.2 52.2 1.0
N A:VAL682 4.3 46.1 1.0
OD2 A:ASP1182 4.3 49.2 1.0
OE1 A:GLU627 4.4 49.9 1.0
CB A:ASP633 4.4 54.0 1.0
CB A:ASP1182 4.6 50.9 1.0
CB A:GLU627 4.6 49.4 1.0
ND2 A:ASN1274 4.6 51.6 1.0
CA A:ASN681 4.7 45.2 1.0
CA A:ASP1182 4.7 50.9 1.0
CB A:ASN681 4.7 45.4 1.0
CB A:VAL682 4.7 46.4 1.0
N A:LEU628 4.8 50.4 1.0
C A:ASP1182 4.9 51.9 1.0
ND2 A:ASN636 4.9 47.3 1.0

Calcium binding site 2 out of 2 in 5ngy

Go back to Calcium Binding Sites List in 5ngy
Calcium binding site 2 out of 2 in the Crystal Structure of Leuconostoc Citreum Nrrl B-1299 Dextransucrase Dsr-M


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 Leuconostoc Citreum Nrrl B-1299 Dextransucrase Dsr-M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1501

b:45.0
occ:1.00
OE2 B:GLU627 2.2 55.9 1.0
O B:ASN681 2.3 48.8 1.0
OD1 B:ASP1182 2.3 61.7 1.0
OD2 B:ASP633 2.5 48.3 1.0
O B:GLU627 2.5 54.5 1.0
OD1 B:ASP633 2.7 49.2 1.0
CG B:ASP633 2.9 48.9 1.0
CD B:GLU627 3.3 57.0 1.0
C B:ASN681 3.5 49.7 1.0
C B:GLU627 3.5 55.0 1.0
CG B:ASP1182 3.6 61.8 1.0
CG B:GLU627 3.7 56.0 1.0
CA B:GLU627 4.0 55.1 1.0
CA B:VAL682 4.2 49.8 1.0
O B:VAL634 4.2 53.1 1.0
CG1 B:VAL682 4.3 51.0 1.0
OD2 B:ASP1182 4.3 63.5 1.0
N B:VAL682 4.3 49.6 1.0
O B:ASP1182 4.4 58.5 1.0
OE1 B:GLU627 4.4 59.1 1.0
CB B:ASP633 4.4 49.5 1.0
CB B:GLU627 4.5 55.2 1.0
CA B:ASN681 4.6 50.4 1.0
CB B:ASP1182 4.6 60.3 1.0
CB B:ASN681 4.6 49.6 1.0
N B:LEU628 4.6 55.0 1.0
ND2 B:ASN1274 4.7 53.3 1.0
CA B:ASP1182 4.8 58.7 1.0
CB B:VAL682 4.8 50.4 1.0
C B:ASP1182 5.0 57.3 1.0

Reference:

M.Claverie, G.Cioci, M.Vuillemin, N.Monties, P.Roblin, G.Lippens, M.Remaud-Simeon, C.Moulis. Investigations on the Determinants Responsible For Low Molar Mass Dextran Formation By Dsr-M Dextransucrase Acs Catalysis 2017.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.7B02182
Page generated: Wed Oct 28 09:21:28 2020

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