Magnesium in PDB 4qql: Crystal Structure of C1QL3 in P1 Space Group

The structure of Crystal Structure of C1QL3 in P1 Space Group, PDB code: 4qql was solved by S.Ressl, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.34 / 2.39
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.590, 82.600, 86.200, 61.44, 84.50, 74.93
R / Rfree (%)	22.4 / 25.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of C1QL3 in P1 Space Group (pdb code 4qql). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Crystal Structure of C1QL3 in P1 Space Group, PDB code: 4qql:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:19.8 occ:1.00 OD2 A:ASP114 1.9 16.1 1.0 OD2 A:ASP72 2.1 23.9 1.0 O B:HOH381 2.4 22.1 1.0 O A:HOH345 2.4 17.9 1.0 O B:HOH322 2.4 19.6 1.0 O A:HOH343 2.6 17.9 1.0 CG A:ASP114 3.0 16.1 1.0 CG A:ASP72 3.2 20.0 1.0 O B:HOH353 3.4 26.1 1.0 HG21 A:VAL79 3.7 18.7 1.0 HB2 A:ASP114 3.7 18.5 1.0 OD1 A:ASP72 3.8 18.4 1.0 CB A:ASP114 3.8 16.2 1.0 HB3 A:ASP114 3.8 18.5 1.0 OD1 A:ASP114 3.8 16.1 1.0 O A:HOH387 3.9 20.5 1.0 O A:HOH379 4.0 18.8 1.0 O A:HOH358 4.2 20.5 1.0 OG A:SER82 4.2 18.5 1.0 OD1 B:ASN124 4.2 26.1 1.0 HG11 A:VAL79 4.3 18.6 1.0 O B:HOH392 4.4 20.5 1.0 O A:HOH338 4.4 20.1 1.0 CB A:ASP72 4.4 18.0 1.0 HB3 A:SER82 4.4 18.3 1.0 O B:HOH362 4.5 19.1 1.0 HB2 A:ASP72 4.5 18.6 1.0 HB3 A:ASP72 4.5 18.6 1.0 CG2 A:VAL79 4.5 20.7 1.0 HG22 A:VAL79 4.6 18.7 1.0 HG A:SER82 4.9 18.4 1.0 CB A:SER82 4.9 18.3 1.0 CG B:ASN124 4.9 28.8 1.0 HB3 A:TRP70 5.0 18.3 1.0

Magnesium binding site 2 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:18.5 occ:1.00 OD2 A:ASP89 2.2 16.7 1.0 OD2 B:ASP89 2.3 15.3 1.0 OD2 C:ASP89 2.4 16.1 1.0 O A:HOH301 2.4 14.6 1.0 OD1 A:ASP89 2.8 18.8 1.0 CG A:ASP89 2.8 16.7 1.0 OD1 B:ASP89 3.1 15.3 1.0 CG B:ASP89 3.1 15.3 1.0 CG C:ASP89 3.2 16.1 1.0 OD1 C:ASP89 3.3 16.1 1.0 MG A:MG203 4.2 16.7 1.0 HB3 C:ALA88 4.2 17.9 1.0 CB A:ASP89 4.3 16.7 1.0 HB2 A:ALA88 4.3 17.9 1.0 O B:HOH327 4.5 16.2 1.0 HB2 B:ALA88 4.5 17.5 1.0 CB B:ASP89 4.5 15.3 1.0 HB2 A:ASP89 4.5 17.9 1.0 CB C:ASP89 4.6 16.1 1.0 O C:HOH329 4.7 16.2 1.0 HB3 A:ASP89 4.7 17.9 1.0 HB2 B:ASP89 4.8 17.7 1.0 HB2 C:ASP89 4.8 17.6 1.0 H A:ASP89 4.9 18.5 1.0 H C:ASP89 5.0 17.7 1.0 HB3 B:ASP89 5.0 17.7 1.0

Magnesium binding site 3 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:16.7 occ:1.00 O B:HOH354 2.0 14.8 1.0 OD2 A:ASP89 2.6 16.7 1.0 H C:ALA88 2.6 17.8 1.0 OD1 A:ASN91 2.9 16.7 1.0 HB2 A:ASP89 2.9 17.9 1.0 OD2 A:ASP87 2.9 14.7 1.0 OD2 C:ASP87 3.1 15.6 1.0 O B:HOH327 3.1 16.2 1.0 OD1 A:ASP87 3.2 14.9 1.0 H C:ASP89 3.2 17.7 1.0 CG C:ASP87 3.3 15.6 1.0 HB3 C:ALA88 3.3 17.9 1.0 N C:ALA88 3.3 16.2 1.0 OD1 C:ASP87 3.3 15.6 1.0 O C:HOH329 3.4 16.2 1.0 HA C:ASP87 3.4 17.8 1.0 CG A:ASP87 3.4 14.8 1.0 CG A:ASP89 3.5 16.7 1.0 CB A:ASP89 3.6 16.7 1.0 OD2 C:ASP89 3.8 16.1 1.0 H A:ASP89 3.8 18.5 1.0 N C:ASP89 4.0 16.2 1.0 CB C:ALA88 4.0 16.3 1.0 CA C:ASP87 4.0 15.7 1.0 C C:ASP87 4.0 15.7 1.0 CG A:ASN91 4.0 16.7 1.0 OD2 B:ASP89 4.1 15.3 1.0 CA C:ALA88 4.1 16.2 1.0 HB2 C:ALA88 4.2 17.9 1.0 MG A:MG202 4.2 18.5 1.0 OD1 B:ASP87 4.2 14.8 1.0 HB3 A:ASP89 4.2 17.9 1.0 HB2 A:ASN91 4.2 17.9 1.0 CB C:ASP87 4.2 15.6 1.0 HB2 C:ASP89 4.2 17.6 1.0 CG C:ASP89 4.3 16.1 1.0 N A:ASP89 4.5 16.9 1.0 C C:ALA88 4.6 16.1 1.0 OD1 A:ASP89 4.6 18.8 1.0 CA A:ASP89 4.7 16.6 1.0 HB2 C:ASP87 4.7 17.7 1.0 CB C:ASP89 4.7 16.1 1.0 CB A:ASN91 4.7 16.7 1.0 HB1 C:ALA88 4.8 17.9 1.0 CB A:ASP87 4.9 14.9 1.0 H A:ALA88 4.9 17.9 1.0 HB3 C:ASP87 4.9 17.7 1.0 HA C:ALA88 5.0 17.8 1.0 CA C:ASP89 5.0 16.2 1.0

Magnesium binding site 4 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:17.9 occ:1.00 O B:HOH374 2.0 21.3 1.0 OD2 B:ASP72 2.1 23.0 1.0 O B:HOH364 2.1 18.8 1.0 OD2 B:ASP114 2.3 20.1 1.0 O B:HOH347 2.5 15.8 1.0 O B:HOH340 2.8 23.4 1.0 CG B:ASP114 3.2 20.2 1.0 CG B:ASP72 3.3 20.6 1.0 HB2 B:ASP114 3.7 17.3 1.0 OD1 B:ASP72 3.8 21.4 1.0 HB3 B:ASP114 3.8 17.3 1.0 CB B:ASP114 3.9 20.3 1.0 HG21 B:VAL79 4.0 17.5 1.0 HG B:SER82 4.0 17.5 1.0 HH C:TYR126 4.0 17.4 1.0 OH C:TYR126 4.2 17.3 1.0 OD1 B:ASP114 4.2 20.1 1.0 O B:HOH383 4.2 21.5 1.0 OG B:SER82 4.2 18.1 1.0 HB3 B:SER82 4.2 17.5 1.0 O B:HOH375 4.3 20.2 1.0 HG11 B:VAL79 4.4 17.6 1.0 CB B:ASP72 4.4 20.7 1.0 O C:HOH305 4.5 24.0 1.0 HB2 B:ASP72 4.5 18.2 1.0 O D:HOH368 4.5 22.9 1.0 HB3 B:ASP72 4.6 18.2 1.0 O B:HOH402 4.6 20.2 1.0 HZ1 B:LYS112 4.7 37.5 1.0 CB B:SER82 4.8 18.2 1.0 HB3 B:TRP70 4.8 17.4 1.0 CG2 B:VAL79 4.9 21.9 1.0 HE3 B:LYS112 4.9 35.2 1.0 HG22 B:VAL79 5.0 17.5 1.0

Magnesium binding site 5 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:16.8 occ:1.00 OD2 B:ASP93 1.9 14.5 1.0 O C:HOH315 2.0 16.1 1.0 OD2 C:ASP93 2.1 15.1 1.0 OD2 A:ASP93 2.2 13.7 1.0 CG B:ASP93 2.9 14.6 1.0 CG C:ASP93 3.0 15.1 1.0 O B:HOH380 3.2 18.4 1.0 CG A:ASP93 3.3 13.7 1.0 OD1 B:ASP93 3.4 14.6 1.0 OD1 C:ASP93 3.4 15.1 1.0 OD1 A:ASP93 3.7 13.7 1.0 O B:HOH337 3.8 14.0 1.0 HB2 B:ASP93 3.8 17.7 1.0 HB2 C:ASP93 3.9 17.7 1.0 CB B:ASP93 4.0 14.6 1.0 O C:HOH303 4.0 14.2 1.0 O B:HOH336 4.1 13.2 1.0 HB2 B:ASP87 4.1 17.6 1.0 CB C:ASP93 4.1 15.1 1.0 O B:GLN86 4.2 16.2 1.0 OD1 B:ASP87 4.2 14.8 1.0 HB2 A:ASP93 4.4 18.0 1.0 OD2 C:ASP87 4.4 15.6 1.0 O A:HOH304 4.4 13.7 1.0 CB A:ASP93 4.5 13.8 1.0 HB2 C:ASP87 4.5 17.7 1.0 O A:GLN86 4.5 14.4 1.0 HB3 B:ASP93 4.6 17.7 1.0 OD2 A:ASP87 4.6 14.7 1.0 HB2 A:ASP87 4.6 17.9 1.0 HB3 C:ASP93 4.7 17.7 1.0 O C:GLN86 4.8 17.3 1.0 HA C:ASP93 4.8 17.7 1.0 HA B:ASP93 4.8 17.8 1.0 CB B:ASP87 4.9 14.7 1.0 HB3 A:ASP93 5.0 18.0 1.0 O C:TYR92 5.0 15.9 1.0

Magnesium binding site 6 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:13.8 occ:1.00 O B:HOH334 2.5 14.3 1.0 HB2 C:TYR94 2.6 17.8 1.0 O B:HOH336 2.6 13.2 1.0 O B:TYR94 2.7 14.8 1.0 H C:TYR94 2.9 17.8 1.0 OD1 C:ASP93 3.0 15.1 1.0 HD1 C:TYR94 3.1 17.7 1.0 OD1 B:ASP93 3.3 14.6 1.0 H B:TYR94 3.4 17.8 1.0 CB C:TYR94 3.5 15.2 1.0 O C:HOH319 3.6 14.2 1.0 N C:TYR94 3.6 15.1 1.0 HB2 B:TYR94 3.7 17.9 1.0 C B:TYR94 3.7 14.8 1.0 HA C:ASP93 3.8 17.7 1.0 CD1 C:TYR94 3.9 15.1 1.0 N B:TYR94 4.0 14.9 1.0 HB3 C:TYR94 4.1 17.8 1.0 CG C:TYR94 4.1 15.1 1.0 CA C:TYR94 4.2 15.2 1.0 CA B:TYR94 4.2 14.9 1.0 CG B:ASP93 4.2 14.6 1.0 CG C:ASP93 4.2 15.1 1.0 CB B:TYR94 4.3 15.0 1.0 HB3 B:TYR94 4.3 17.9 1.0 O C:HOH303 4.3 14.2 1.0 C C:ASP93 4.5 15.2 1.0 CA C:ASP93 4.6 15.2 1.0 OD2 B:ASP93 4.6 14.5 1.0 HA B:ALA85 4.7 17.6 1.0 HA B:ALA95 4.7 17.7 1.0 OD1 A:ASP93 4.7 13.7 1.0 O B:ILE84 4.7 16.7 1.0 O C:TYR94 4.8 15.3 1.0 N B:ALA95 4.9 16.7 1.0 O C:HOH336 4.9 14.3 1.0 HA C:TYR94 4.9 17.8 1.0 C C:TYR94 5.0 15.2 1.0 H B:SER96 5.0 19.0 0.7 H B:SER96 5.0 19.0 0.3

Magnesium binding site 7 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:22.6 occ:1.00 O C:HOH387 2.0 20.2 1.0 OD2 C:ASP114 2.2 18.2 1.0 O C:HOH376 2.3 24.3 1.0 OD2 C:ASP72 2.3 17.8 1.0 CG C:ASP114 3.3 18.2 1.0 CG C:ASP72 3.4 17.8 1.0 HG C:SER82 3.6 18.3 1.0 OD1 C:ASP72 3.8 19.3 1.0 HG23 C:VAL79 3.9 18.3 1.0 HB3 C:ASP114 4.0 18.1 1.0 HB2 C:ASP114 4.0 18.1 1.0 CB C:ASP114 4.0 18.2 1.0 HG11 C:VAL79 4.0 18.4 1.0 OG C:SER82 4.1 17.2 1.0 OD1 C:ASP114 4.2 18.2 1.0 HB3 C:SER82 4.3 18.3 1.0 OH A:TYR126 4.3 16.5 1.0 HH A:TYR126 4.3 18.2 1.0 CB C:ASP72 4.6 17.9 1.0 HG22 C:VAL79 4.7 18.3 1.0 HB3 C:ASP72 4.7 18.2 1.0 O A:HOH373 4.7 19.7 1.0 CG2 C:VAL79 4.7 19.7 1.0 O C:HOH356 4.7 23.3 1.0 O C:HOH364 4.8 19.4 1.0 CB C:SER82 4.8 17.2 1.0 HB2 C:ASP72 4.8 18.2 1.0 HB3 A:ASN124 4.8 18.4 1.0 CG1 C:VAL79 4.9 19.7 1.0 HG13 C:VAL79 4.9 18.4 1.0 HB3 C:TRP70 5.0 18.0 1.0

Magnesium binding site 8 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:18.3 occ:1.00 O D:HOH356 2.0 14.9 1.0 OD2 D:ASP89 2.2 16.0 1.0 O D:HOH316 2.4 14.7 1.0 OD2 F:ASP89 2.4 19.1 1.0 CG D:ASP89 3.0 16.2 1.0 OD1 D:ASP89 3.0 16.2 1.0 CG F:ASP89 3.2 17.7 1.0 OD1 F:ASP89 3.3 16.4 1.0 MG D:MG202 4.1 15.9 1.0 HB1 D:ALA88 4.2 15.9 1.0 HB1 F:ALA88 4.3 16.1 1.0 CB D:ASP89 4.4 16.4 1.0 HB2 D:ASP89 4.6 16.1 1.0 CB F:ASP89 4.7 16.1 1.0 HB2 F:ASP89 4.8 17.9 1.0 H D:ASP89 4.9 16.1 1.0 HB3 D:ASP89 4.9 16.1 1.0

Magnesium binding site 9 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:15.9 occ:1.00 HD22 D:ASN91 2.3 16.2 1.0 OD2 D:ASP89 2.5 16.0 1.0 H F:ALA88 2.6 16.1 1.0 HD21 D:ASN91 2.7 16.2 1.0 HB2 D:ASP89 2.7 16.1 1.0 ND2 D:ASN91 2.8 16.8 1.0 OD1 D:ASP87 3.0 15.5 1.0 OD2 D:ASP87 3.0 15.3 1.0 HB1 F:ALA88 3.1 16.1 1.0 N F:ALA88 3.3 15.0 1.0 CG D:ASP87 3.4 15.4 1.0 OD2 F:ASP87 3.4 14.5 1.0 CG D:ASP89 3.4 16.2 1.0 H F:ASP89 3.4 18.0 1.0 CB D:ASP89 3.5 16.4 1.0 HA F:ASP87 3.5 16.1 1.0 CG F:ASP87 3.6 14.6 1.0 OD1 F:ASP87 3.6 14.5 1.0 H D:ASP89 3.7 16.1 1.0 OD2 F:ASP89 3.8 19.1 1.0 CB F:ALA88 3.8 15.1 1.0 HB3 F:ALA88 3.9 16.1 1.0 CG D:ASN91 4.0 16.6 1.0 HB3 D:ASP89 4.1 16.1 1.0 MG D:MG201 4.1 18.3 1.0 CA F:ALA88 4.1 15.1 1.0 HB2 D:ASN91 4.1 17.3 1.0 N F:ASP89 4.1 16.5 1.0 CA F:ASP87 4.2 15.0 1.0 C F:ASP87 4.2 15.0 1.0 N D:ASP89 4.4 16.1 1.0 CG F:ASP89 4.4 17.7 1.0 CB F:ASP87 4.5 14.7 1.0 HB2 F:ASP89 4.5 17.9 1.0 CA D:ASP89 4.5 16.3 1.0 OD1 D:ASP89 4.6 16.2 1.0 C F:ALA88 4.6 14.9 1.0 HB2 F:ALA88 4.7 16.1 1.0 CB D:ASN91 4.7 17.2 1.0 O D:HOH316 4.7 14.7 1.0 HD22 F:ASN91 4.9 15.9 1.0 CB D:ASP87 4.9 15.4 1.0 H D:ALA88 4.9 16.0 1.0 H D:ASN91 4.9 16.2 1.0 CB F:ASP89 4.9 16.1 1.0 HB2 F:ASP87 4.9 16.0 1.0 HA F:ALA88 4.9 16.1 1.0 OD1 D:ASN91 5.0 16.4 1.0

Magnesium binding site 10 out of 24 in the Crystal Structure of C1QL3 in P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of C1QL3 in P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:14.6 occ:1.00 OD2 F:ASP93 2.3 15.4 1.0 OD2 D:ASP93 2.6 13.3 1.0 O D:HOH352 3.2 18.0 1.0 O F:GLN86 3.2 15.1 1.0 OD2 D:ASP87 3.2 15.3 1.0 HB2 F:ASP87 3.3 16.0 1.0 OD2 F:ASP87 3.3 14.5 1.0 CG D:ASP93 3.5 13.5 1.0 CG F:ASP93 3.5 15.3 1.0 HB2 D:ASP87 3.7 16.1 1.0 HB2 D:ASP93 3.7 16.1 1.0 O D:HOH306 3.8 12.3 1.0 CB F:ASP87 4.1 14.7 1.0 HB2 F:ASP93 4.1 16.1 1.0 CG D:ASP87 4.1 15.4 1.0 CG F:ASP87 4.2 14.6 1.0 CB D:ASP93 4.2 13.6 1.0 OD1 D:ASP93 4.2 13.5 1.0 HA F:ASP87 4.2 16.1 1.0 C F:GLN86 4.3 15.2 1.0 OD1 F:ASP93 4.4 15.3 1.0 CB D:ASP87 4.4 15.4 1.0 HB2 D:ASN91 4.4 17.3 1.0 CB F:ASP93 4.4 15.3 1.0 O D:TYR92 4.4 15.4 1.0 CA F:ASP87 4.6 15.0 1.0 O D:GLN86 4.7 15.0 1.0 H F:GLN86 4.7 16.2 1.0 HB3 F:ASP93 4.7 16.1 1.0 HB3 D:ASP93 4.8 16.1 1.0 HB3 F:ASP87 4.9 16.0 1.0 HB3 D:ASN91 5.0 17.3 1.0 N F:ASP87 5.0 15.1 1.0 HB3 D:ASP87 5.0 16.1 1.0 HD22 D:ASN91 5.0 16.2 1.0 HA D:ASP93 5.0 16.2 1.0

S.Ressl, B.K.Vu, S.Vivona, D.C.Martinelli, T.C.Sudhof, A.T.Brunger. Structures of C1Q-Like Proteins Reveal Unique Features Among the C1Q/Tnf Superfamily. Structure V. 23 688 2015.
ISSN: ISSN 0969-2126
PubMed: 25752542
DOI: 10.1016/J.STR.2015.01.019