Calcium in PDB 4lmf: C1S CUB1-Egf-CUB2

All present enzymatic activity of C1S CUB1-Egf-CUB2:
3.4.21.42;

The structure of C1S CUB1-Egf-CUB2, PDB code: 4lmf was solved by R.Wallis, U.Venkatraman Girija, P.C.E.Moody, J.E.Marshall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.51 / 2.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.876, 71.668, 157.723, 90.00, 95.93, 90.00
R / Rfree (%)	20.8 / 25.2

The structure of C1S CUB1-Egf-CUB2 also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the C1S CUB1-Egf-CUB2 (pdb code 4lmf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the C1S CUB1-Egf-CUB2, PDB code: 4lmf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:57.7 occ:1.00 OD1 A:ASP98 2.4 47.6 1.0 OD2 A:ASP53 2.4 59.4 1.0 OD1 A:ASN101 2.7 46.9 1.0 OE2 A:GLU45 2.7 47.8 1.0 O A:SER100 2.8 58.8 1.0 CG A:ASP53 3.1 65.2 1.0 OD1 A:ASP53 3.2 72.9 1.0 CG A:ASN101 3.3 53.1 1.0 C A:SER100 3.5 61.1 1.0 CG A:ASP98 3.6 53.0 1.0 CD A:GLU45 3.9 53.5 1.0 CA A:ASN101 3.9 64.9 1.0 CB A:ASN101 3.9 61.0 1.0 N A:ASN101 4.0 62.6 1.0 N A:ASP98 4.0 54.4 1.0 ND2 A:ASN101 4.1 54.4 1.0 OH A:TYR17 4.2 27.8 1.0 OD2 A:ASP98 4.3 60.0 1.0 O A:ASP98 4.3 63.1 1.0 CE1 A:TYR17 4.3 27.2 1.0 N A:SER100 4.5 66.5 1.0 C A:ASP98 4.5 64.2 1.0 CB A:GLU45 4.5 45.3 1.0 CA A:SER100 4.6 65.6 1.0 OE1 A:GLU45 4.6 57.6 1.0 CA A:ASP98 4.6 56.8 1.0 CB A:ASP53 4.6 62.7 1.0 CB A:ASP98 4.6 51.5 1.0 CZ A:TYR17 4.7 28.4 1.0 CG A:GLU45 4.8 49.2 1.0 CB A:SER97 4.9 44.0 1.0 C A:SER97 4.9 44.8 1.0 CA A:SER97 5.0 43.0 1.0

Calcium binding site 2 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:31.3 occ:1.00 O A:ILE117 2.4 31.7 1.0 OD1 A:ASP116 2.4 40.8 1.0 O A:GLY138 2.5 34.0 1.0 O A:PHE135 2.5 44.6 1.0 OD1 A:ASN134 2.5 26.5 1.0 OE1 A:GLU119 2.6 37.9 1.0 CG A:ASP116 3.3 37.4 1.0 CD A:GLU119 3.3 34.6 1.0 OD2 A:ASP116 3.3 36.5 1.0 OE2 A:GLU119 3.4 32.6 1.0 C A:GLY138 3.4 29.9 1.0 N A:GLY138 3.4 31.8 1.0 C A:ILE117 3.6 27.9 1.0 CG A:ASN134 3.6 26.9 1.0 C A:PHE135 3.7 38.5 1.0 CA A:GLY138 3.8 32.9 1.0 N A:GLY137 4.0 30.9 1.0 ND2 A:ASN134 4.1 33.3 1.0 N A:ILE117 4.2 29.8 1.0 N A:PHE135 4.2 27.1 1.0 C A:GLY137 4.4 32.5 1.0 O A:GLY32 4.4 36.9 1.0 CA A:ILE117 4.4 24.4 1.0 N A:ASN118 4.5 26.1 1.0 CA A:ILE136 4.6 24.1 1.0 N A:GLU119 4.6 29.1 1.0 N A:TYR139 4.6 26.1 1.0 N A:ILE136 4.6 33.0 1.0 CA A:ASN118 4.6 27.9 1.0 CA A:PHE135 4.6 31.6 1.0 C A:ILE136 4.6 25.6 1.0 CA A:GLY137 4.7 31.4 1.0 CB A:ASP116 4.7 33.6 1.0 CG A:GLU119 4.8 29.5 1.0 CB A:ILE117 4.9 27.6 1.0 CB A:ASN134 4.9 22.1 1.0 C A:ASP116 5.0 29.5 1.0

Calcium binding site 3 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:31.6 occ:1.00 O A:THR262 2.3 43.7 1.0 OD1 A:ASP260 2.3 25.0 1.0 OD2 A:ASP221 2.3 36.6 1.0 O A:GLY263 2.4 40.1 1.0 OD1 A:ASP221 2.6 29.5 1.0 OE1 A:GLU211 2.7 36.2 1.0 CG A:ASP221 2.8 32.6 1.0 C A:THR262 3.3 37.1 1.0 OE1 A:GLN264 3.4 36.2 1.0 C A:GLY263 3.4 37.5 1.0 CG A:ASP260 3.6 24.0 1.0 O A:ASP260 3.8 35.6 1.0 CD A:GLU211 3.9 38.3 1.0 N A:ASP260 3.9 29.1 1.0 CA A:GLY263 3.9 31.1 1.0 N A:GLY263 4.0 31.9 1.0 C A:ASP260 4.2 32.7 1.0 CD A:GLN264 4.3 31.8 1.0 CB A:ASP221 4.3 30.4 1.0 OD2 A:ASP260 4.3 26.0 1.0 N A:THR262 4.3 28.8 1.0 CA A:ASP260 4.4 25.4 1.0 CA A:THR262 4.4 31.1 1.0 N A:GLN264 4.5 41.0 1.0 CE1 A:TYR181 4.5 22.8 1.0 OH A:TYR181 4.5 17.9 1.0 CB A:GLU211 4.5 24.7 1.0 CB A:ASP260 4.6 19.9 1.0 CB A:THR259 4.6 25.3 1.0 CG A:GLN264 4.6 32.0 1.0 OE2 A:GLU211 4.6 42.6 1.0 CA A:GLN264 4.8 36.8 1.0 C A:THR259 4.8 31.0 1.0 CG A:GLU211 4.8 30.0 1.0 CA A:THR259 4.9 29.1 1.0

Calcium binding site 4 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:76.3 occ:1.00 OD1 B:ASP98 2.4 0.5 1.0 OD1 B:ASN101 2.5 0.7 1.0 O B:SER100 2.5 0.9 1.0 OE2 B:GLU45 2.5 84.0 1.0 OD2 B:ASP53 2.6 0.7 1.0 CG B:ASN101 3.1 0.2 1.0 C B:SER100 3.2 0.7 1.0 CA B:ASN101 3.5 0.1 1.0 CG B:ASP98 3.5 0.0 1.0 CG B:ASP53 3.6 0.6 1.0 CB B:ASN101 3.6 0.6 1.0 CD B:GLU45 3.6 85.3 1.0 N B:ASN101 3.6 0.6 1.0 OD1 B:ASP53 3.9 0.5 1.0 OD2 B:ASP98 3.9 0.0 1.0 ND2 B:ASN101 4.1 0.7 1.0 OE1 B:GLU45 4.3 85.4 1.0 CA B:SER100 4.3 0.7 1.0 N B:SER100 4.3 0.5 1.0 CB B:GLU45 4.4 88.7 1.0 OH B:TYR17 4.6 57.8 1.0 N B:ASP98 4.6 0.9 1.0 CG B:GLU45 4.6 86.8 1.0 CE1 B:TYR17 4.7 65.0 1.0 O B:ASP98 4.8 1.0 1.0 CB B:ASP98 4.8 0.9 1.0 C B:ASP98 4.8 0.5 1.0 C B:ASN101 4.9 0.6 1.0 CB B:ASP53 4.9 1.0 1.0 CA B:ASP98 5.0 0.7 1.0

Calcium binding site 5 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:38.0 occ:1.00 O B:ILE117 2.4 33.0 1.0 O B:PHE135 2.4 45.9 1.0 OD1 B:ASP116 2.4 57.9 1.0 OD1 B:ASN134 2.5 28.4 1.0 O B:GLY138 2.5 59.9 1.0 OE1 B:GLU119 2.7 61.3 1.0 CG B:ASP116 3.3 55.0 1.0 N B:GLY138 3.3 48.8 1.0 OE2 B:GLU119 3.4 58.3 1.0 CD B:GLU119 3.4 56.5 1.0 C B:GLY138 3.4 57.6 1.0 OD2 B:ASP116 3.5 52.6 1.0 CG B:ASN134 3.6 32.1 1.0 C B:ILE117 3.6 35.5 1.0 C B:PHE135 3.7 44.1 1.0 CA B:GLY138 3.8 55.5 1.0 N B:GLY137 3.9 47.5 1.0 ND2 B:ASN134 4.1 35.5 1.0 N B:PHE135 4.2 33.3 1.0 N B:ILE117 4.2 42.4 1.0 C B:GLY137 4.3 49.6 1.0 O B:GLY32 4.5 64.8 1.0 CA B:ILE117 4.5 39.6 1.0 CA B:ILE136 4.5 40.6 1.0 N B:ASN118 4.5 32.6 1.0 N B:ILE136 4.5 42.8 1.0 C B:ILE136 4.5 43.2 1.0 CA B:ASN118 4.5 30.9 1.0 CA B:GLY137 4.6 51.2 1.0 CA B:PHE135 4.6 39.4 1.0 N B:GLU119 4.6 35.8 1.0 N B:TYR139 4.6 52.8 1.0 CB B:ASP116 4.7 52.9 1.0 CG B:GLU119 4.8 49.4 1.0 CB B:ASN134 4.8 27.4 1.0

Calcium binding site 6 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:26.9 occ:1.00 OD1 B:ASP260 2.3 33.0 1.0 O B:THR262 2.3 36.7 1.0 O B:GLY263 2.4 29.8 1.0 OD2 B:ASP221 2.4 19.5 1.0 OE1 B:GLU211 2.5 34.5 1.0 OD1 B:ASP221 2.5 17.4 1.0 CG B:ASP221 2.8 19.9 1.0 C B:THR262 3.4 33.4 1.0 C B:GLY263 3.4 26.8 1.0 NE2 B:GLN264 3.4 26.0 1.0 CG B:ASP260 3.5 26.0 1.0 CD B:GLU211 3.7 38.2 1.0 O B:ASP260 3.8 40.4 1.0 N B:ASP260 3.9 24.1 1.0 CA B:GLY263 3.9 27.2 1.0 N B:GLY263 4.0 31.9 1.0 C B:ASP260 4.2 31.4 1.0 OD2 B:ASP260 4.3 28.3 1.0 CB B:ASP221 4.3 22.0 1.0 N B:THR262 4.4 26.6 1.0 CB B:GLU211 4.4 24.8 1.0 OE2 B:GLU211 4.4 37.6 1.0 CA B:ASP260 4.4 23.0 1.0 CA B:THR262 4.5 26.4 1.0 N B:GLN264 4.5 27.1 1.0 CD B:GLN264 4.5 28.9 1.0 CB B:THR259 4.6 20.2 1.0 CB B:ASP260 4.6 18.6 1.0 OH B:TYR181 4.6 27.5 1.0 CE1 B:TYR181 4.6 30.3 1.0 CG B:GLU211 4.7 33.1 1.0 C B:THR259 4.8 26.0 1.0 CA B:THR259 4.9 25.0 1.0 CG B:GLN264 4.9 32.4 1.0 CA B:GLN264 4.9 31.5 1.0 N B:ASP221 5.0 28.5 1.0

Calcium binding site 7 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:0.6 occ:1.00 OD1 C:ASP98 2.8 0.7 1.0 OD1 C:ASN101 3.1 0.7 1.0 O C:SER100 3.1 0.5 1.0 OD2 C:ASP53 3.3 1.0 1.0 CG C:ASN101 3.4 1.0 1.0 C C:SER100 3.4 0.5 1.0 O C:ASP98 3.6 98.2 1.0 N C:ASP98 3.7 97.7 1.0 N C:ASN101 3.7 0.1 1.0 CB C:ASN101 3.7 0.1 1.0 OD1 C:ASP53 3.8 0.8 1.0 CA C:ASN101 3.8 0.0 1.0 CG C:ASP53 3.9 0.3 1.0 CA C:SER19 3.9 0.8 1.0 CE1 C:TYR17 4.0 67.8 1.0 CB C:SER97 4.0 83.6 1.0 CB C:SER19 4.0 0.6 1.0 CG C:ASP98 4.0 99.8 1.0 C C:ASP98 4.1 0.3 1.0 ND2 C:ASN101 4.2 99.5 1.0 N C:SER100 4.3 0.9 1.0 OE2 C:GLU45 4.3 82.9 1.0 CA C:SER100 4.3 0.4 1.0 C C:SER97 4.3 91.6 1.0 CA C:ASP98 4.4 0.8 1.0 OG C:SER97 4.4 84.4 1.0 CA C:SER97 4.5 88.7 1.0 O C:PRO18 4.5 95.0 1.0 CD1 C:TYR17 4.7 71.0 1.0 N C:SER19 4.7 0.5 1.0 CB C:ASP98 4.8 0.9 1.0 OH C:TYR17 4.8 62.9 1.0 CZ C:TYR17 4.8 64.8 1.0 OD2 C:ASP98 4.9 96.8 1.0 C C:PHE99 4.9 0.2 1.0 N C:GLU20 4.9 0.1 1.0 C C:PRO18 4.9 97.7 1.0 N C:PHE99 5.0 0.8 1.0

Calcium binding site 8 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:32.5 occ:1.00 O C:ILE117 2.4 34.5 1.0 O C:PHE135 2.5 41.0 1.0 O C:GLY138 2.5 48.1 1.0 OD1 C:ASP116 2.5 47.1 1.0 OE1 C:GLU119 2.6 56.7 1.0 OD1 C:ASN134 2.7 34.0 1.0 OD2 C:ASP116 3.2 49.8 1.0 CG C:ASP116 3.2 46.8 1.0 OE2 C:GLU119 3.3 55.1 1.0 CD C:GLU119 3.3 52.1 1.0 N C:GLY138 3.4 50.0 1.0 C C:GLY138 3.4 48.9 1.0 C C:ILE117 3.6 36.4 1.0 C C:PHE135 3.7 37.0 1.0 CA C:GLY138 3.8 50.0 1.0 CG C:ASN134 3.8 31.2 1.0 N C:GLY137 3.9 41.0 1.0 N C:ILE117 4.2 43.8 1.0 N C:PHE135 4.3 27.0 1.0 C C:GLY137 4.3 51.0 1.0 ND2 C:ASN134 4.3 36.4 1.0 CA C:ILE117 4.4 38.8 1.0 O C:GLY32 4.4 43.7 1.0 N C:ASN118 4.5 32.9 1.0 CA C:ILE136 4.5 35.2 1.0 N C:ILE136 4.5 35.8 1.0 C C:ILE136 4.6 36.7 1.0 CA C:ASN118 4.6 28.6 1.0 CA C:GLY137 4.6 46.6 1.0 N C:GLU119 4.6 33.3 1.0 N C:TYR139 4.6 44.5 1.0 CA C:PHE135 4.6 34.7 1.0 CB C:ASP116 4.7 43.0 1.0 CG C:GLU119 4.8 42.7 1.0 C C:ASP116 4.9 42.2 1.0 CB C:ILE117 5.0 39.3 1.0

Calcium binding site 9 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca304 b:31.1 occ:1.00 OD1 C:ASP260 2.3 36.4 1.0 OD2 C:ASP221 2.3 30.9 1.0 O C:THR262 2.3 44.5 1.0 O C:GLY263 2.4 34.1 1.0 OD1 C:ASP221 2.5 22.6 1.0 OE1 C:GLU211 2.6 39.9 1.0 CG C:ASP221 2.8 25.5 1.0 C C:GLY263 3.4 34.7 1.0 C C:THR262 3.4 35.7 1.0 CG C:ASP260 3.5 33.6 1.0 OE1 C:GLN264 3.7 38.7 1.0 CD C:GLU211 3.8 38.5 1.0 O C:ASP260 3.9 38.3 1.0 CA C:GLY263 3.9 31.4 1.0 N C:ASP260 4.0 28.5 1.0 N C:GLY263 4.0 29.6 1.0 OD2 C:ASP260 4.2 37.5 1.0 C C:ASP260 4.3 32.3 1.0 CB C:ASP221 4.3 21.5 1.0 N C:THR262 4.4 32.0 1.0 CB C:GLU211 4.4 26.8 1.0 CA C:ASP260 4.5 25.2 1.0 N C:GLN264 4.5 35.4 1.0 OE2 C:GLU211 4.5 35.3 1.0 CA C:THR262 4.5 30.6 1.0 CD C:GLN264 4.6 36.1 1.0 CB C:ASP260 4.6 26.5 1.0 CB C:THR259 4.6 19.7 1.0 CE1 C:TYR181 4.7 31.9 1.0 OH C:TYR181 4.7 23.4 1.0 CG C:GLU211 4.7 35.0 1.0 CA C:GLN264 4.9 33.9 1.0 CG C:GLN264 4.9 33.9 1.0 C C:THR259 4.9 27.0 1.0 CA C:THR259 5.0 21.9 1.0

Calcium binding site 10 out of 12 in the C1S CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of C1S CUB1-Egf-CUB2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:61.4 occ:1.00 OD1 D:ASP98 2.4 65.8 1.0 OD2 D:ASP53 2.4 52.0 1.0 OE2 D:GLU45 2.5 59.5 1.0 O D:SER100 2.5 63.7 1.0 OD1 D:ASN101 2.6 61.2 1.0 C D:SER100 3.3 66.5 1.0 CG D:ASN101 3.3 62.5 1.0 CG D:ASP53 3.3 58.4 1.0 OD1 D:ASP53 3.5 64.2 1.0 CG D:ASP98 3.6 66.9 1.0 CA D:ASN101 3.6 72.5 1.0 CD D:GLU45 3.7 61.9 1.0 N D:ASN101 3.7 70.4 1.0 CB D:ASN101 3.8 67.6 1.0 OD2 D:ASP98 4.2 72.6 1.0 OH D:TYR17 4.2 28.8 1.0 ND2 D:ASN101 4.2 58.4 1.0 N D:ASP98 4.3 60.5 1.0 CB D:GLU45 4.4 58.3 1.0 OE1 D:GLU45 4.4 65.0 1.0 CA D:SER100 4.4 66.6 1.0 CE1 D:TYR17 4.4 31.0 1.0 N D:SER100 4.5 69.3 1.0 O D:ASP98 4.6 68.3 1.0 CG D:GLU45 4.6 59.6 1.0 CB D:ASP98 4.7 62.5 1.0 CZ D:TYR17 4.7 30.1 1.0 CB D:ASP53 4.7 59.3 1.0 C D:ASP98 4.7 68.9 1.0 CA D:ASP98 4.8 63.9 1.0

U.Venkatraman Girija, A.R.Gingras, J.E.Marshall, R.Panchal, M.A.Sheikh, P.Gal, W.J.Schwaeble, D.A.Mitchell, P.C.Moody, R.Wallis. Structural Basis of the C1Q/C1S Interaction and Its Central Role in Assembly of the C1 Complex of Complement Activation. Proc.Natl.Acad.Sci.Usa V. 110 13916 2013.
ISSN: ISSN 0027-8424
PubMed: 23922389
DOI: 10.1073/PNAS.1311113110