Calcium in PDB 6d2c: Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48

Protein crystallography data

The structure of Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48, PDB code: 6d2c was solved by T.Ulaganathan, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.24 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.488, 102.117, 103.708, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 (pdb code 6d2c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48, PDB code: 6d2c:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6d2c

Go back to Calcium Binding Sites List in 6d2c
Calcium binding site 1 out of 2 in the Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:21.7
occ:1.00
O A:SER81 2.2 19.9 1.0
OD1 A:ASN61 2.3 21.4 1.0
O A:ALA84 2.3 23.7 1.0
OD1 A:ASN85 2.4 22.7 1.0
O A:GLY59 2.5 23.5 1.0
OD2 A:ASP79 2.5 23.2 1.0
OD1 A:ASP79 2.5 21.0 1.0
CG A:ASP79 2.8 22.0 1.0
CG A:ASN61 3.2 23.7 1.0
C A:ALA84 3.3 24.1 1.0
C A:SER81 3.5 20.6 1.0
C A:GLY59 3.5 26.0 1.0
CG A:ASN85 3.6 20.7 1.0
CA A:ASN85 3.8 19.8 1.0
N A:ASN85 3.8 21.6 1.0
CA A:GLY59 4.0 18.6 1.0
CB A:ASN61 4.0 23.4 1.0
N A:ASN61 4.0 21.5 1.0
ND2 A:ASN61 4.1 20.1 1.0
CB A:ASN85 4.2 24.4 1.0
CA A:CYS82 4.3 21.2 1.0
N A:ALA84 4.3 22.3 1.0
N A:SER81 4.3 20.5 1.0
CB A:ASP79 4.3 18.7 1.0
N A:CYS82 4.4 20.9 1.0
CA A:SER81 4.4 22.7 1.0
CA A:ALA84 4.4 21.9 1.0
CE1 A:HIS107 4.5 22.8 1.0
N A:THR60 4.6 21.3 1.0
ND2 A:ASN85 4.6 22.3 1.0
CD1 A:ILE118 4.7 22.2 1.0
C A:CYS82 4.7 25.7 1.0
CA A:ASN61 4.7 22.7 1.0
CB A:SER81 4.7 19.8 1.0
NE2 A:HIS107 4.9 25.5 1.0
CA A:THR60 4.9 22.5 1.0
O A:HOH620 5.0 24.4 1.0
N A:TYR83 5.0 22.5 1.0

Calcium binding site 2 out of 2 in 6d2c

Go back to Calcium Binding Sites List in 6d2c
Calcium binding site 2 out of 2 in the Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:24.5
occ:1.00
O B:SER81 2.3 20.9 1.0
OD1 B:ASN61 2.3 21.0 1.0
O B:ALA84 2.3 24.7 1.0
OD2 B:ASP79 2.4 24.5 1.0
OD1 B:ASN85 2.5 23.4 1.0
OD1 B:ASP79 2.5 22.7 1.0
O B:GLY59 2.5 23.2 1.0
CG B:ASP79 2.8 25.2 1.0
CG B:ASN61 3.2 23.7 1.0
C B:ALA84 3.3 23.6 1.0
C B:SER81 3.5 22.8 1.0
C B:GLY59 3.5 24.2 1.0
CG B:ASN85 3.6 28.4 1.0
CA B:ASN85 3.8 24.4 1.0
N B:ASN85 3.9 22.6 1.0
CB B:ASN61 4.0 27.9 1.0
CA B:GLY59 4.0 23.6 1.0
N B:ASN61 4.1 26.6 1.0
ND2 B:ASN61 4.1 25.1 1.0
CA B:CYS82 4.3 25.4 1.0
CB B:ASP79 4.3 20.2 1.0
CB B:ASN85 4.3 25.9 1.0
N B:ALA84 4.3 22.9 1.0
N B:SER81 4.4 21.7 1.0
N B:CYS82 4.4 22.1 1.0
CA B:ALA84 4.4 24.3 1.0
CA B:SER81 4.5 24.8 1.0
CE1 B:HIS107 4.5 23.6 1.0
N B:THR60 4.6 23.1 1.0
ND2 B:ASN85 4.6 26.4 1.0
C B:CYS82 4.7 29.4 1.0
CA B:ASN61 4.7 25.7 1.0
CD1 B:ILE118 4.7 20.7 1.0
CB B:SER81 4.8 23.0 1.0
N B:TYR83 4.9 25.6 1.0
CA B:THR60 4.9 24.3 1.0
O B:HOH601 5.0 23.9 1.0

Reference:

T.Ulaganathan, E.Banin, W.Helbert, M.Cygler. Structural and Functional Characterization of PL28 Family Ulvan Lyase NLR48 Fromnonlabens Ulvanivorans. J. Biol. Chem. V. 293 11564 2018.
ISSN: ESSN 1083-351X
PubMed: 29875159
DOI: 10.1074/JBC.RA118.003659
Page generated: Sat Dec 12 06:02:11 2020

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