Chlorine in PDB 6san: Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium

The structure of Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium, PDB code: 6san was solved by M.P.Reichhardt, S.Johnson, V.Loimaranta, S.M.Lea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.95 / 1.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.235, 46.643, 93.628, 90.00, 97.37, 90.00
R / Rfree (%)	18.9 / 22.6

The structure of Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Chlorine atom in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium (pdb code 6san). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium, PDB code: 6san:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2004 b:20.2 occ:1.00 H A:VAL1017 2.2 11.2 1.0 O A:VAL1006 2.7 10.4 1.0 HB A:THR1016 2.7 15.7 1.0 H A:ALA1088 2.7 10.6 1.0 O A:ALA1088 2.9 10.3 1.0 HG3 A:ARG1005 2.9 12.5 1.0 HB3 A:ASP1087 3.0 14.3 1.0 N A:VAL1017 3.1 9.3 1.0 HG2 A:ARG1005 3.2 12.5 1.0 N A:ALA1088 3.2 8.8 1.0 H A:VAL1006 3.3 11.5 1.0 HB A:VAL1017 3.3 13.0 1.0 O A:VAL1017 3.3 10.3 1.0 HA A:THR1016 3.3 12.8 1.0 HB A:VAL1006 3.4 12.5 1.0 CG A:ARG1005 3.5 10.4 1.0 CB A:THR1016 3.5 13.1 1.0 HB3 A:ALA1088 3.6 11.7 1.0 HA A:ASP1087 3.7 11.6 1.0 C A:VAL1006 3.7 9.8 1.0 HD2 A:ARG1005 3.7 12.4 1.0 N A:VAL1006 3.7 9.6 1.0 CA A:THR1016 3.7 10.7 1.0 C A:ALA1088 3.8 8.6 1.0 CB A:ASP1087 3.8 11.9 1.0 HG22 A:THR1016 3.8 19.6 1.0 CA A:VAL1017 3.9 10.5 1.0 C A:ASP1087 3.9 9.6 1.0 C A:THR1016 3.9 8.9 1.0 CA A:ALA1088 3.9 7.2 1.0 CB A:VAL1017 4.0 10.8 1.0 C A:VAL1017 4.0 11.5 1.0 CA A:ASP1087 4.0 9.7 1.0 HG23 A:VAL1017 4.0 17.0 1.0 CA A:VAL1006 4.1 9.6 1.0 CG2 A:THR1016 4.1 16.3 1.0 CD A:ARG1005 4.2 10.3 1.0 CB A:VAL1006 4.2 10.4 1.0 CB A:ALA1088 4.2 9.8 1.0 CG A:ASP1087 4.3 15.3 1.0 HG21 A:THR1016 4.4 19.6 1.0 HG2 A:GLU1007 4.5 16.6 1.0 HA A:ARG1005 4.5 10.4 1.0 C A:ARG1005 4.5 9.2 1.0 CG2 A:VAL1017 4.6 14.2 1.0 OD1 A:ASP1087 4.6 16.0 1.0 HB2 A:ASP1087 4.6 14.3 1.0 OG1 A:THR1016 4.6 12.9 1.0 HG12 A:VAL1006 4.6 14.6 1.0 HB2 A:ALA1088 4.7 11.7 1.0 HA A:GLU1007 4.7 12.3 1.0 CB A:ARG1005 4.7 9.7 1.0 O A:HOH2118 4.7 41.2 1.0 HA A:VAL1017 4.8 12.6 1.0 HD3 A:ARG1005 4.8 12.4 1.0 O A:ASP1087 4.8 11.8 1.0 HG1 A:THR1016 4.8 15.4 1.0 HA A:ALA1088 4.8 8.7 1.0 CA A:ARG1005 4.8 8.6 1.0 N A:GLU1007 4.9 9.8 1.0 OD2 A:ASP1087 4.9 15.4 1.0 HB1 A:ALA1088 4.9 11.7 1.0

Chlorine binding site 2 out of 2 in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2004 b:26.1 occ:1.00 H B:GLY1037 2.4 24.4 1.0 HH11 B:ARG1032 2.6 22.4 1.0 HA2 B:GLY1037 3.0 22.4 1.0 O B:HOH2214 3.1 43.8 1.0 HA2 B:GLY1035 3.2 23.7 1.0 N B:GLY1037 3.2 20.4 1.0 HD3 B:ARG1032 3.3 21.0 1.0 NH1 B:ARG1032 3.4 18.7 1.0 HA B:ARG1032 3.4 20.0 1.0 HD2 B:ARG1032 3.5 21.0 1.0 CA B:GLY1037 3.5 18.7 1.0 O B:HOH2124 3.5 36.4 1.0 HH12 B:ARG1032 3.7 22.4 1.0 CD B:ARG1032 3.8 17.5 1.0 O B:GLY1037 3.9 20.6 1.0 C B:GLY1035 3.9 21.9 1.0 H B:CYS1036 3.9 25.1 1.0 CA B:GLY1035 3.9 19.8 1.0 N B:CYS1036 4.0 20.9 1.0 C B:GLY1037 4.0 19.6 1.0 O A:HOH2238 4.3 35.1 1.0 CA B:ARG1032 4.4 16.7 1.0 C B:CYS1036 4.4 20.5 1.0 O B:GLY1035 4.4 22.4 1.0 HA3 B:GLY1037 4.4 22.4 1.0 CZ B:ARG1032 4.5 16.9 1.0 O B:ARG1032 4.5 16.2 1.0 H B:GLY1035 4.5 22.8 1.0 HA3 B:GLY1035 4.6 23.7 1.0 NE B:ARG1032 4.6 17.5 1.0 O B:CYS1031 4.7 17.1 1.0 N B:GLY1035 4.8 19.0 1.0 CA B:CYS1036 4.8 19.4 1.0 HB3 B:ARG1032 4.8 20.5 1.0 C B:ARG1032 5.0 16.5 1.0 CB B:ARG1032 5.0 17.1 1.0

M.P.Reichhardt, V.Loimaranta, S.M.Lea, S.Johnson. Structures of Salsa/DMBT1 Srcr Domains Reveal the Conserved Ligand-Binding Mechanism of the Ancient Srcr Fold. Life Sci Alliance V. 3 2020.
ISSN: ESSN 2575-1077
PubMed: 32098784
DOI: 10.26508/LSA.201900502