Calcium in PDB 8h4v: Mincle Crd Complex with Pgl Trisaccharide

The structure of Mincle Crd Complex with Pgl Trisaccharide, PDB code: 8h4v was solved by S.Ishizuka, M.Nagae, S.Yamasaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.35 / 2.40
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	75.298, 75.298, 111.4, 90, 90, 120
R / Rfree (%)	25.6 / 28.9

The binding sites of Calcium atom in the Mincle Crd Complex with Pgl Trisaccharide (pdb code 8h4v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Mincle Crd Complex with Pgl Trisaccharide, PDB code: 8h4v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Mincle Crd Complex with Pgl Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mincle Crd Complex with Pgl Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:92.4 occ:1.00 OD1 A:ASP193 2.3 97.4 1.0 OE2 A:GLU168 2.3 105.6 1.0 O4 E:L6N3 2.4 98.9 1.0 OE1 A:GLU176 2.4 105.0 1.0 OD1 A:ASN192 2.6 92.2 1.0 O3 E:L6N3 2.8 100.9 1.0 O A:ASP193 2.9 91.7 1.0 CD A:GLU176 3.0 97.8 1.0 OD1 A:ASN170 3.0 114.2 1.0 C4 E:L6N3 3.2 95.0 1.0 O A:PRO169 3.2 103.7 1.0 CD A:GLU168 3.3 99.5 1.0 C3 E:L6N3 3.3 99.6 1.0 CG A:ASP193 3.5 94.5 1.0 OE2 A:GLU176 3.6 93.5 1.0 OE1 A:GLU168 3.7 99.2 1.0 CG A:ASN192 3.7 92.0 1.0 CG A:GLU176 3.8 98.0 1.0 CG A:ASN170 3.8 114.0 1.0 C A:ASP193 3.9 91.4 1.0 N A:ASP193 3.9 89.8 1.0 ND2 A:ASN170 4.1 109.4 1.0 OD2 A:ASP193 4.3 92.5 1.0 CA A:ASP193 4.3 90.4 1.0 ND2 A:ASN192 4.3 87.4 1.0 C A:PRO169 4.4 105.8 1.0 CG A:GLU168 4.5 97.0 1.0 CB A:ASP193 4.5 88.5 1.0 C5 E:L6N3 4.6 98.1 1.0 CG A:LEU172 4.8 112.0 1.0 C2 E:L6N3 4.8 106.3 1.0 CB A:GLU176 4.8 98.2 1.0 N A:ASN171 4.9 111.3 1.0 C A:ASN192 4.9 86.8 1.0 CB A:ASN192 5.0 87.8 1.0 CA A:PRO169 5.0 104.2 1.0

Calcium binding site 2 out of 6 in the Mincle Crd Complex with Pgl Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mincle Crd Complex with Pgl Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:105.8 occ:1.00 OE1 A:GLU146 2.4 104.7 1.0 OD2 A:ASP142 2.5 97.1 1.0 O A:GLU176 2.5 89.7 1.0 OE2 A:GLU146 2.6 100.2 1.0 OD1 A:ASP142 2.8 99.4 1.0 CD A:GLU146 2.9 105.5 1.0 ND2 A:ASN171 2.9 113.0 1.0 OD2 A:ASP177 3.0 95.3 1.0 CG A:ASP142 3.0 100.6 1.0 CG A:ASN171 3.2 115.7 1.0 OD1 A:ASN171 3.6 124.8 1.0 C A:GLU176 3.6 92.3 1.0 CB A:ASN171 3.9 117.9 1.0 CA A:ASP177 3.9 91.3 1.0 CG A:ASP177 4.1 99.3 1.0 CZ2 A:TRP149 4.2 84.7 1.0 N A:ASP177 4.3 87.6 1.0 CG A:GLU146 4.4 106.7 1.0 OD2 A:ASP193 4.5 92.5 1.0 CB A:ASP177 4.5 91.8 1.0 CB A:ASP142 4.5 97.7 1.0 CA A:ASN171 4.7 109.2 1.0 CA A:GLU176 4.7 101.8 1.0 N A:GLY147 4.8 103.2 1.0 CH2 A:TRP149 4.8 89.2 1.0 CE2 A:TRP149 4.9 94.1 1.0 CA A:GLU146 4.9 104.2 1.0 N A:GLU176 5.0 97.2 1.0

Calcium binding site 3 out of 6 in the Mincle Crd Complex with Pgl Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mincle Crd Complex with Pgl Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:79.7 occ:1.00 OE2 A:GLU205 2.3 74.1 1.0 OD1 A:ASN118 2.4 70.1 1.0 O A:VAL116 2.5 73.6 1.0 OE1 A:GLU205 2.6 75.7 1.0 OE2 A:GLU122 2.8 59.9 1.0 CD A:GLU205 2.8 73.1 1.0 OE1 A:GLU122 3.5 74.7 1.0 CD A:GLU122 3.5 76.1 1.0 CG A:ASN118 3.5 73.0 1.0 C A:VAL116 3.6 76.0 1.0 CB A:VAL116 4.1 78.0 1.0 ND2 A:ASN118 4.1 75.9 1.0 N A:VAL116 4.2 68.5 1.0 CA A:VAL116 4.2 73.3 1.0 CG A:GLU205 4.3 75.2 1.0 N A:ASN118 4.6 75.8 1.0 N A:ILE117 4.7 71.0 1.0 CB A:ASN118 4.7 80.5 1.0 OH A:TYR91 4.8 74.1 1.0 CE1 A:HIS113 4.8 76.3 1.0 CG1 A:VAL116 4.9 76.2 1.0 CA A:ILE117 5.0 75.6 1.0

Calcium binding site 4 out of 6 in the Mincle Crd Complex with Pgl Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mincle Crd Complex with Pgl Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:82.8 occ:1.00 OD1 B:ASP193 2.3 92.6 1.0 O3 C:L6N3 2.3 88.7 1.0 OE1 B:GLU176 2.4 87.2 1.0 OD1 B:ASN192 2.7 80.2 1.0 OD1 B:ASN170 2.7 91.2 1.0 OE1 B:GLU168 2.8 96.4 1.0 O B:ASP193 2.9 87.6 1.0 O4 C:L6N3 2.9 78.3 1.0 C3 C:L6N3 3.1 88.5 1.0 OE2 B:GLU168 3.1 91.0 1.0 C4 C:L6N3 3.3 84.2 1.0 CD B:GLU176 3.3 88.5 1.0 CD B:GLU168 3.3 92.0 1.0 CG B:ASN170 3.4 91.0 1.0 CG B:ASP193 3.4 89.4 1.0 ND2 B:ASN170 3.4 87.4 1.0 OE2 B:GLU176 3.6 84.0 1.0 CG B:ASN192 3.7 83.7 1.0 N B:ASP193 3.9 87.5 1.0 C B:ASP193 3.9 83.4 1.0 ND2 B:ASN192 4.0 81.0 1.0 OD2 B:ASP193 4.1 95.7 1.0 CA B:ASP193 4.3 89.5 1.0 N B:ASN170 4.5 101.0 1.0 CB B:ASP193 4.5 87.4 1.0 C2 C:L6N3 4.5 95.5 1.0 CG B:GLU176 4.6 92.4 1.0 CG B:GLU168 4.8 93.7 1.0 CB B:ASN170 4.8 90.7 1.0 C5 C:L6N3 4.8 85.4 1.0 CB B:GLU176 4.8 89.2 1.0 N B:ASN171 4.9 98.3 1.0 CG B:LEU172 4.9 97.5 1.0 CB B:ASN192 5.0 79.1 1.0 C B:ASN192 5.0 83.4 1.0

Calcium binding site 5 out of 6 in the Mincle Crd Complex with Pgl Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mincle Crd Complex with Pgl Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:109.4 occ:1.00 OE2 B:GLU146 2.4 99.9 1.0 OD2 B:ASP142 2.7 108.7 1.0 O B:GLU176 3.1 96.6 1.0 OD1 B:ASP177 3.2 100.7 1.0 CZ2 B:TRP149 3.4 95.2 1.0 CG B:ASP142 3.4 110.4 1.0 ND2 B:ASN171 3.4 104.1 1.0 OD1 B:ASP142 3.4 104.7 1.0 CD B:GLU146 3.5 114.8 1.0 CG B:ASN171 3.6 105.3 1.0 CB B:ASN171 3.7 100.9 1.0 CH2 B:TRP149 3.8 99.9 1.0 OD2 B:ASP193 3.9 95.7 1.0 OE1 B:GLU146 4.1 114.4 1.0 CE2 B:TRP149 4.3 103.4 1.0 OD1 B:ASN171 4.3 111.8 1.0 C B:GLU176 4.3 98.5 1.0 CA B:ASN171 4.4 98.7 1.0 CG B:ASP177 4.4 107.5 1.0 N B:GLY147 4.5 118.9 1.0 CA B:ASP177 4.5 101.8 1.0 N B:ASN171 4.7 98.3 1.0 CB B:ASP142 4.7 114.4 1.0 CG B:GLU146 4.7 115.2 1.0 NE1 B:TRP149 4.7 107.3 1.0 CB B:PRO169 4.8 97.0 1.0 N B:ASP177 4.9 95.2 1.0 CA B:GLY147 4.9 122.5 1.0 CZ3 B:TRP149 4.9 101.2 1.0 CG B:ASP193 5.0 89.4 1.0

Calcium binding site 6 out of 6 in the Mincle Crd Complex with Pgl Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mincle Crd Complex with Pgl Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:99.0 occ:1.00 O B:VAL116 2.2 98.5 1.0 OE2 B:GLU122 2.4 90.4 1.0 OD1 B:ASN118 2.4 96.0 1.0 OE2 B:GLU205 2.5 107.7 1.0 OE1 B:GLU122 2.8 96.6 1.0 CD B:GLU122 2.9 92.0 1.0 OE1 B:GLU205 3.0 102.1 1.0 CD B:GLU205 3.1 105.0 1.0 C B:VAL116 3.4 98.6 1.0 CG B:ASN118 3.6 99.3 1.0 CA B:VAL116 4.2 96.9 1.0 N B:VAL116 4.2 93.5 1.0 OH B:TYR91 4.3 101.8 1.0 CB B:VAL116 4.3 99.1 1.0 N B:ASN118 4.3 97.8 1.0 ND2 B:ASN118 4.4 98.0 1.0 N B:ILE117 4.4 93.6 1.0 CG B:GLU122 4.4 92.6 1.0 CA B:ILE117 4.6 93.0 1.0 CG B:GLU205 4.6 104.3 1.0 CB B:ASN118 4.6 95.1 1.0 C B:ILE117 4.9 96.8 1.0 CG2 B:VAL115 4.9 93.1 1.0 CE1 B:HIS113 5.0 106.8 1.0

S.Ishizuka, J.H.M.Van Dijk, T.Kawakita, Y.Miyamoto, Y.Maeda, M.Goto, G.Le Calvez, L.M.Groot, M.D.Witte, A.J.Minnaard, G.A.Van Der Marel, M.Ato, M.Nagae, J.D.C.Codee, S.Yamasaki. Pgl-III, A Rare Intermediate of Mycobacterium Leprae Phenolic Glycolipid Biosynthesis, Is A Potent Mincle Ligand. Acs Cent.Sci. V. 9 1388 2023.
ISSN: ESSN 2374-7951
PubMed: 37521780
DOI: 10.1021/ACSCENTSCI.3C00040