Calcium in PDB 6d3u: Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48

Protein crystallography data

The structure of Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48, PDB code: 6d3u 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) 46.05 / 2.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.464, 102.664, 103.034, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 (pdb code 6d3u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48, PDB code: 6d3u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6d3u

Go back to Calcium Binding Sites List in 6d3u
Calcium binding site 1 out of 2 in the Complex 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 Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:42.3
occ:1.00
O A:ALA84 2.2 40.8 1.0
OD1 A:ASN61 2.2 40.2 1.0
O A:SER81 2.3 41.5 1.0
OD1 A:ASN85 2.4 41.1 1.0
OD2 A:ASP79 2.4 38.4 1.0
OD1 A:ASP79 2.6 41.2 1.0
O A:GLY59 2.7 47.0 1.0
CG A:ASP79 2.9 42.1 1.0
CG A:ASN61 3.3 40.3 1.0
C A:ALA84 3.3 42.2 1.0
C A:SER81 3.5 46.6 1.0
CG A:ASN85 3.6 43.4 1.0
C A:GLY59 3.6 44.8 1.0
CA A:ASN85 3.8 43.2 1.0
N A:ASN85 3.9 40.7 1.0
CA A:GLY59 4.0 44.8 1.0
CB A:ASN61 4.1 40.0 1.0
ND2 A:ASN61 4.1 39.5 1.0
N A:ASN61 4.2 43.0 1.0
CB A:ASN85 4.3 44.1 1.0
CA A:CYS82 4.3 46.4 1.0
N A:SER81 4.3 39.3 1.0
N A:CYS82 4.4 43.7 1.0
N A:ALA84 4.4 43.4 1.0
CB A:ASP79 4.4 40.9 1.0
CA A:SER81 4.4 38.3 1.0
CA A:ALA84 4.5 41.8 1.0
CE1 A:HIS107 4.6 37.2 1.0
ND2 A:ASN85 4.6 45.8 1.0
CD1 A:ILE118 4.6 36.7 1.0
N A:THR60 4.7 43.7 1.0
C A:CYS82 4.7 49.5 1.0
CA A:ASN61 4.8 43.7 1.0
CB A:SER81 4.8 39.1 1.0
O A:HOH539 4.9 40.6 1.0
N A:TYR83 5.0 44.3 1.0
NE2 A:HIS107 5.0 45.0 1.0

Calcium binding site 2 out of 2 in 6d3u

Go back to Calcium Binding Sites List in 6d3u
Calcium binding site 2 out of 2 in the Complex 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 Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:44.9
occ:1.00
OD1 B:ASN61 2.2 44.4 1.0
O B:ALA84 2.3 40.0 1.0
O B:SER81 2.3 43.6 1.0
OD1 B:ASN85 2.4 47.8 1.0
OD2 B:ASP79 2.5 38.8 1.0
OD1 B:ASP79 2.6 39.2 1.0
O B:GLY59 2.7 45.6 1.0
CG B:ASP79 2.8 42.9 1.0
CG B:ASN61 3.2 47.7 1.0
C B:ALA84 3.3 45.5 1.0
C B:SER81 3.5 51.0 1.0
CG B:ASN85 3.6 47.3 1.0
C B:GLY59 3.6 43.9 1.0
CA B:ASN85 3.8 42.3 1.0
N B:ASN85 3.9 41.7 1.0
CB B:ASN61 4.0 45.6 1.0
CA B:GLY59 4.0 45.7 1.0
N B:ASN61 4.1 45.7 1.0
ND2 B:ASN61 4.2 41.6 1.0
CA B:CYS82 4.2 50.8 1.0
CB B:ASN85 4.3 44.1 1.0
N B:CYS82 4.3 43.7 1.0
CB B:ASP79 4.4 41.0 1.0
N B:SER81 4.4 46.9 1.0
N B:ALA84 4.5 43.5 1.0
CA B:SER81 4.5 42.9 1.0
CA B:ALA84 4.5 46.3 1.0
CE1 B:HIS107 4.5 44.6 1.0
ND2 B:ASN85 4.6 45.1 1.0
N B:THR60 4.7 42.6 1.0
C B:CYS82 4.7 56.0 1.0
CA B:ASN61 4.7 47.5 1.0
CD1 B:ILE118 4.8 35.1 1.0
CB B:SER81 5.0 45.6 1.0
O B:HOH554 5.0 44.9 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 06:02:16 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy