Calcium in PDB 6q77: Structure of Fucosylated D-Antimicrobial Peptide SB12 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.002 Angstrom Resolution

Protein crystallography data

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB12 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.002 Angstrom Resolution, PDB code: 6q77 was solved by S.Baeriswyl, A.Stocker, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.95 / 2.00
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 51.518, 51.518, 97.905, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 26.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB12 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.002 Angstrom Resolution (pdb code 6q77). 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 Fucosylated D-Antimicrobial Peptide SB12 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.002 Angstrom Resolution, PDB code: 6q77:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6q77

Go back to Calcium Binding Sites List in 6q77
Calcium binding site 1 out of 2 in the Structure of Fucosylated D-Antimicrobial Peptide SB12 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.002 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Fucosylated D-Antimicrobial Peptide SB12 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.002 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:55.1
occ:1.00
OD1 A:ASP99 2.3 61.2 1.0
OE1 A:GLU95 2.4 46.5 1.0
OD1 A:ASP101 2.4 50.9 1.0
O4 B:ZDC1 2.5 52.4 1.0
OE2 A:GLU95 2.5 50.8 1.0
OD1 A:ASP104 2.5 49.4 1.0
O3 B:ZDC1 2.5 39.1 1.0
OD2 A:ASP104 2.6 64.4 1.0
CD A:GLU95 2.8 54.7 1.0
CG A:ASP104 2.9 63.0 1.0
CG A:ASP99 3.3 72.0 1.0
C4 B:ZDC1 3.3 47.2 1.0
C3 B:ZDC1 3.4 47.7 1.0
CG A:ASP101 3.5 60.4 1.0
OD2 A:ASP99 3.5 65.1 1.0
CA A:CA203 3.7 53.5 1.0
OD2 A:ASP101 4.0 50.6 1.0
N A:ASP101 4.1 51.5 1.0
CG A:GLU95 4.2 46.5 1.0
N A:TYR102 4.3 54.7 1.0
CB A:ASP104 4.4 48.6 1.0
N A:ASN100 4.4 48.7 1.0
OD1 A:ASP96 4.5 59.0 1.0
N A:ASP96 4.5 49.3 1.0
CA A:GLU95 4.6 51.1 1.0
CB A:ASP101 4.6 58.6 1.0
N A:GLY97 4.6 60.0 1.0
CB A:ASP99 4.7 80.1 1.0
C5 B:ZDC1 4.7 54.0 1.0
CA A:ASP101 4.7 59.4 1.0
C2 B:ZDC1 4.8 52.6 1.0
CB A:GLU95 4.8 51.1 1.0
N A:ASP99 4.8 66.9 1.0
C A:ASP99 4.9 59.1 1.0
N A:ASP104 4.9 49.4 1.0
OD1 A:ASN103 4.9 51.1 1.0
O2 B:ZDC1 4.9 65.3 1.0
C A:ASP101 4.9 52.8 1.0
CG A:ASP96 5.0 58.9 1.0
CA A:ASN100 5.0 54.5 1.0

Calcium binding site 2 out of 2 in 6q77

Go back to Calcium Binding Sites List in 6q77
Calcium binding site 2 out of 2 in the Structure of Fucosylated D-Antimicrobial Peptide SB12 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.002 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Fucosylated D-Antimicrobial Peptide SB12 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.002 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:53.5
occ:1.00
O A:ASN21 2.4 54.0 1.0
OD1 A:ASN103 2.5 51.1 1.0
OD2 A:ASP101 2.5 50.6 1.0
O2 B:ZDC1 2.5 65.3 1.0
O3 B:ZDC1 2.5 39.1 1.0
OD2 A:ASP104 2.6 64.4 1.0
OD1 A:ASP101 3.1 50.9 1.0
CG A:ASP101 3.2 60.4 1.0
C3 B:ZDC1 3.3 47.7 1.0
C2 B:ZDC1 3.4 52.6 1.0
C A:ASN21 3.5 55.8 1.0
CG A:ASN103 3.6 55.7 1.0
C4 B:ZDC1 3.7 47.2 1.0
CA A:CA202 3.7 55.1 1.0
CG A:ASP104 3.8 63.0 1.0
CB A:ASN21 4.1 50.8 1.0
ND2 A:ASN103 4.1 58.0 1.0
CA A:ASP104 4.1 50.4 1.0
N A:ASP104 4.1 49.4 1.0
CA A:SER22 4.2 61.7 1.0
N A:SER22 4.3 60.0 1.0
O4 B:ZDC1 4.4 52.4 1.0
OD2 A:ASP99 4.4 65.1 1.0
C A:ASN103 4.4 45.0 1.0
CB A:SER22 4.4 57.4 1.0
CA A:ASN21 4.5 59.2 1.0
CB A:ASP104 4.6 48.6 1.0
CB A:ASP101 4.6 58.6 1.0
O A:ASN103 4.7 48.9 1.0
OD1 A:ASP104 4.7 49.4 1.0
C1 B:ZDC1 4.8 55.5 1.0
CB A:ASN103 4.9 54.2 1.0
N A:ASN103 4.9 58.5 1.0
CA A:ASN103 5.0 52.2 1.0
C5 B:ZDC1 5.0 54.0 1.0

Reference:

S.Baeriswyl, B.H.Gan, T.N.Siriwardena, R.Visini, M.Robadey, S.Javor, A.Stocker, T.Darbre, J.L.Reymond. X-Ray Crystal Structures of Short Antimicrobial Peptides As Pseudomonas Aeruginosa Lectin B Complexes. Acs Chem.Biol. V. 14 758 2019.
ISSN: ESSN 1554-8937
PubMed: 30830745
DOI: 10.1021/ACSCHEMBIO.9B00047
Page generated: Sat Dec 12 07:27:00 2020

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