Calcium in PDB 5nur: Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry

The structure of Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry, PDB code: 5nur was solved by J.Abellon-Ruiz, S.S.Kaptan, A.Basle, B.Claudi, D.Bumann, U.Kleinekathofer, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.40 / 3.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	190.550, 179.660, 133.390, 90.00, 116.55, 90.00
R / Rfree (%)	21.9 / 25.9

The binding sites of Calcium atom in the Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry (pdb code 5nur). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry, PDB code: 5nur:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:0.9 occ:1.00 OD1 C:ASN252 2.1 1.0 1.0 O4 C:KDO404 2.4 0.8 1.0 O5 C:KDO404 2.5 0.1 1.0 CG C:ASN252 2.5 0.8 1.0 ND2 C:ASN252 2.5 0.4 1.0 O C:ASN207 2.6 0.6 1.0 C4 C:KDO404 3.3 1.0 1.0 OD1 C:ASN236 3.4 0.3 1.0 C5 C:KDO404 3.4 0.0 1.0 C C:ASN207 3.6 0.3 1.0 CB C:ASN252 3.7 0.9 1.0 C3 C:KDO404 3.7 0.7 1.0 N C:ASN207 3.7 0.4 1.0 CA C:ASN252 3.9 0.4 1.0 CG C:ASN236 4.0 0.4 1.0 O1A C:KDO404 4.1 0.3 1.0 O C:ASN252 4.1 0.5 1.0 CA C:ASN207 4.2 0.5 1.0 ND2 C:ASN236 4.2 0.6 1.0 C C:ASN252 4.5 0.0 1.0 N C:GLY208 4.6 0.8 1.0 CB C:ASN207 4.6 0.9 1.0 C6 C:KDO404 4.8 0.7 1.0 C2 C:KDO404 4.8 0.1 1.0 C C:GLY206 4.8 0.3 1.0 CA C:GLY208 4.9 0.8 1.0 C1 C:KDO404 4.9 0.3 1.0 O6 C:KDO404 5.0 0.6 1.0 CA C:GLY206 5.0 0.4 1.0

Calcium binding site 2 out of 3 in the Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:0.5 occ:1.00 C1 A:KDO406 2.2 0.7 1.0 O1A A:KDO406 2.3 0.1 1.0 OD1 A:ASN252 2.3 0.6 1.0 O1B A:KDO406 2.4 0.5 1.0 O A:ASN207 2.8 0.9 1.0 OD1 A:ASN236 2.8 0.9 1.0 O6 A:KDO406 3.1 0.5 1.0 C2 A:KDO406 3.2 0.4 1.0 CG A:ASN252 3.2 0.5 1.0 CG A:ASN236 3.3 98.4 1.0 ND2 A:ASN236 3.3 97.6 1.0 CB A:ASN252 3.6 0.5 1.0 O4 A:KDO406 3.6 0.7 1.0 C A:ASN207 3.8 0.3 1.0 CA A:ASN252 3.8 0.6 1.0 N A:ASN207 3.9 0.7 1.0 C3 A:KDO406 4.0 0.9 1.0 O A:ASN252 4.2 0.3 1.0 O8 A:KDO406 4.2 0.6 1.0 C4 A:KDO406 4.2 0.3 1.0 CA A:ASN207 4.3 0.6 1.0 C6 A:KDO406 4.4 0.8 1.0 ND2 A:ASN252 4.4 0.1 1.0 C A:ASN252 4.5 0.8 1.0 CB A:ASN207 4.5 0.4 1.0 CB A:ASN236 4.6 92.0 1.0 C5 A:KDO406 4.7 0.7 1.0 N A:GLY208 4.8 0.5 1.0 O5 A:KDO406 4.9 0.0 1.0 C A:GLY206 4.9 0.3 1.0 O4 A:KDO405 5.0 0.8 1.0 C7 A:KDO406 5.0 0.0 1.0

Calcium binding site 3 out of 3 in the Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca405 b:0.6 occ:1.00 O4 E:KDO403 2.2 0.3 1.0 OD1 E:ASN252 2.4 0.6 1.0 O E:ASN207 2.6 0.7 1.0 C4 E:KDO403 3.0 0.8 1.0 ND2 E:ASN236 3.1 0.9 1.0 CG E:ASN252 3.5 0.1 1.0 C5 E:KDO403 3.5 0.3 1.0 OD1 E:ASN236 3.5 0.7 1.0 O5 E:KDO403 3.7 0.3 1.0 CG E:ASN236 3.8 0.5 1.0 C E:ASN207 3.8 0.8 1.0 ND2 E:ASN252 3.8 0.3 1.0 CA E:GLY208 4.3 0.7 1.0 C3 E:KDO403 4.3 0.6 1.0 N E:GLY208 4.5 0.3 1.0 CB E:ASN252 4.8 0.2 1.0 CA E:ASN207 4.9 0.3 1.0 O E:ASN252 4.9 95.6 1.0 N E:ASN207 5.0 1.0 1.0

J.Abellon-Ruiz, S.S.Kaptan, A.Basle, B.Claudi, D.Bumann, U.Kleinekathofer, B.Van Den Berg. Structural Basis For Maintenance of Bacterial Outer Membrane Lipid Asymmetry. Nat Microbiol V. 2 1616 2017.
ISSN: ESSN 2058-5276
PubMed: 29038444
DOI: 10.1038/S41564-017-0046-X