Magnesium 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:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium, PDB code: 6san:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg2001 b:16.1 occ:1.00 O A:HOH2157 2.0 18.8 1.0 O A:SER1021 2.1 14.0 1.0 OD2 A:ASP1026 2.2 14.4 1.0 O A:HOH2160 2.2 18.2 1.0 O A:VAL1060 2.2 12.7 1.0 OD2 A:ASP1023 2.3 17.4 1.0 HA A:ARG1061 2.8 15.8 1.0 CG A:ASP1026 3.0 12.2 1.0 CG A:ASP1023 3.1 16.0 1.0 OD1 A:ASP1026 3.2 12.8 1.0 C A:SER1021 3.3 12.5 1.0 C A:VAL1060 3.4 10.9 1.0 OD1 A:ASP1023 3.4 18.3 1.0 HB3 A:SER1021 3.5 19.5 1.0 H A:ASP1023 3.5 14.8 1.0 HA A:TRP1022 3.5 13.8 1.0 CA A:ARG1061 3.7 13.2 1.0 N A:ARG1061 4.0 12.1 1.0 N A:ASP1023 4.0 12.3 1.0 H A:CYS1062 4.0 14.0 1.0 O A:HOH2253 4.0 33.2 1.0 O A:HOH2136 4.1 34.3 1.0 HG2 A:ARG1061 4.1 21.1 1.0 CB A:SER1021 4.2 16.3 1.0 CA A:TRP1022 4.2 11.5 1.0 N A:TRP1022 4.2 11.2 1.0 HB2 A:SER1021 4.2 19.5 1.0 CA A:SER1021 4.3 12.6 1.0 CB A:ASP1023 4.3 14.1 1.0 HB3 A:ASP1023 4.4 16.9 1.0 CB A:ASP1026 4.4 12.9 1.0 N A:CYS1062 4.4 11.7 1.0 C A:TRP1022 4.4 14.4 1.0 HB A:VAL1060 4.4 13.8 1.0 H A:ASP1026 4.5 14.4 1.0 HA A:SER1021 4.5 15.1 1.0 HB2 A:ASP1026 4.5 15.4 1.0 C A:ARG1061 4.5 12.2 1.0 CA A:VAL1060 4.6 9.2 1.0 HG12 A:VAL1060 4.6 15.6 1.0 O A:HOH2165 4.6 36.9 1.0 CG A:ARG1061 4.7 17.6 1.0 HG3 A:ARG1061 4.7 21.1 1.0 CB A:ARG1061 4.7 16.4 1.0 CA A:ASP1023 4.7 13.2 1.0 H A:ARG1061 4.8 14.5 1.0 HB2 A:ASN1025 4.9 20.3 1.0 N A:VAL1060 4.9 9.9 1.0 H A:VAL1060 4.9 11.8 1.0 HB3 A:ASP1026 5.0 15.4 1.0 CB A:VAL1060 5.0 11.5 1.0 HB3 A:ARG1061 5.0 19.7 1.0

Magnesium binding site 2 out of 6 in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg2002 b:14.1 occ:1.00 OE1 A:GLU1086 2.0 12.1 1.0 OD1 A:ASP1019 2.1 11.4 1.0 O A:HOH2144 2.1 15.5 1.0 O A:HOH2186 2.1 17.2 1.0 OD1 A:ASP1020 2.1 13.3 1.0 CG A:ASP1019 3.1 9.7 1.0 CD A:GLU1086 3.2 12.5 1.0 CG A:ASP1020 3.4 14.8 1.0 HG2 A:GLU1086 3.5 14.0 1.0 HB3 A:GLU1086 3.5 12.8 1.0 OD2 A:ASP1019 3.6 10.9 1.0 HA A:ASP1020 3.8 12.1 1.0 CG A:GLU1086 3.8 11.7 1.0 N A:ASP1020 4.0 8.4 1.0 H A:ASP1020 4.1 10.1 1.0 OD2 A:ASP1020 4.1 18.1 1.0 CB A:GLU1086 4.2 10.7 1.0 OE2 A:GLU1086 4.2 15.6 1.0 CA A:ASP1020 4.2 10.1 1.0 C A:ASP1019 4.3 9.2 1.0 O A:HOH2120 4.3 22.9 1.0 O A:HOH2203 4.3 29.3 1.0 CB A:ASP1020 4.4 12.6 1.0 CB A:ASP1019 4.5 10.4 1.0 H A:ASP1019 4.5 9.6 1.0 O A:HOH2170 4.6 43.2 1.0 SG A:CYS1018 4.6 15.5 1.0 HG3 A:GLU1086 4.7 14.0 1.0 CA A:ASP1019 4.7 7.6 1.0 O A:ASP1019 4.7 10.5 1.0 HB2 A:GLU1086 4.8 12.8 1.0 HB2 A:ASP1019 4.8 12.4 1.0 N A:ASP1019 4.9 8.0 1.0 HB2 A:ASP1020 5.0 15.2 1.0 HA A:GLU1086 5.0 11.9 1.0

Magnesium binding site 3 out of 6 in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2003 b:24.3 occ:1.00 OD1 A:ASN1081 2.2 20.7 1.0 OD2 A:ASP1058 2.4 16.6 1.0 OD2 A:ASP1020 2.5 18.1 1.0 OD2 A:ASP1059 2.6 24.6 1.0 OD1 A:ASP1058 2.6 16.9 1.0 CG A:ASP1058 2.9 15.7 1.0 HB2 A:ASP1020 2.9 15.2 1.0 HB3 A:ASP1020 3.3 15.2 1.0 CG A:ASP1020 3.3 14.8 1.0 CB A:ASP1020 3.4 12.6 1.0 CG A:ASN1081 3.4 17.8 1.0 H A:ASN1081 3.6 12.8 1.0 CG A:ASP1059 3.6 18.9 1.0 HD21 A:ASN1081 3.8 23.1 1.0 HD21 A:ASN1075 3.8 22.7 1.0 SG A:CYS1082 3.9 17.7 1.0 OD1 A:ASP1059 4.0 19.4 1.0 ND2 A:ASN1081 4.0 19.3 1.0 O A:HOH2205 4.2 51.5 1.0 HD22 A:ASN1075 4.3 22.7 1.0 N A:ASN1081 4.3 10.7 1.0 CB A:ASP1058 4.4 11.7 1.0 ND2 A:ASN1075 4.4 18.9 1.0 H A:ASP1059 4.4 13.4 1.0 CB A:ASN1081 4.5 14.5 1.0 OD1 A:ASP1020 4.6 13.3 1.0 HB3 A:ASP1058 4.6 14.0 1.0 HA A:HIS1080 4.6 13.8 1.0 SG A:CYS1018 4.6 15.5 1.0 HB3 A:ASN1081 4.6 17.4 1.0 HB2 A:ASP1059 4.8 17.3 1.0 CB A:ASP1059 4.8 14.4 1.0 N A:ASP1059 4.8 11.1 1.0 CA A:ASN1081 4.8 9.8 1.0 HB2 A:ASP1058 4.8 14.0 1.0 CA A:ASP1020 4.8 10.1 1.0 HD22 A:ASN1081 4.9 23.1 1.0 HB3 A:CYS1018 4.9 15.8 1.0 H A:ASP1020 4.9 10.1 1.0 C A:ASN1081 4.9 10.5 1.0

Magnesium binding site 4 out of 6 in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:15.7 occ:1.00 O B:HOH2159 2.0 18.1 1.0 O B:SER1021 2.1 15.2 1.0 OD2 B:ASP1026 2.1 14.6 1.0 O B:VAL1060 2.2 14.7 1.0 O B:HOH2153 2.2 20.3 1.0 OD2 B:ASP1023 2.2 16.7 1.0 HA B:ARG1061 2.9 17.1 1.0 CG B:ASP1026 3.0 13.3 1.0 OD1 B:ASP1026 3.1 14.1 1.0 CG B:ASP1023 3.1 16.7 1.0 C B:VAL1060 3.3 14.1 1.0 C B:SER1021 3.3 13.0 1.0 OD1 B:ASP1023 3.5 16.6 1.0 HA B:TRP1022 3.5 13.4 1.0 HB3 B:SER1021 3.6 22.4 1.0 H B:ASP1023 3.7 17.2 1.0 CA B:ARG1061 3.7 14.2 1.0 H B:CYS1062 3.9 17.1 1.0 N B:ARG1061 3.9 14.1 1.0 HG2 B:ARG1061 4.0 28.9 1.0 O B:HOH2223 4.0 42.7 1.0 O B:HOH2222 4.1 59.6 1.0 N B:ASP1023 4.1 14.3 1.0 CA B:TRP1022 4.2 11.2 1.0 N B:TRP1022 4.2 11.7 1.0 CB B:SER1021 4.2 18.7 1.0 HB2 B:SER1021 4.2 22.4 1.0 CA B:SER1021 4.3 12.0 1.0 O B:HOH2164 4.3 22.6 1.0 CB B:ASP1023 4.3 15.8 1.0 N B:CYS1062 4.4 14.2 1.0 CB B:ASP1026 4.4 12.7 1.0 HB B:VAL1060 4.4 15.7 1.0 H B:ASP1026 4.4 16.3 1.0 HB3 B:ASP1023 4.4 19.0 1.0 HA B:SER1021 4.4 14.4 1.0 HG12 B:VAL1060 4.5 16.1 1.0 C B:TRP1022 4.5 14.0 1.0 C B:ARG1061 4.5 15.3 1.0 CA B:VAL1060 4.5 12.5 1.0 HB2 B:ASP1026 4.5 15.3 1.0 CG B:ARG1061 4.7 24.1 1.0 CB B:ARG1061 4.7 18.6 1.0 H B:ARG1061 4.8 16.9 1.0 HB2 B:ASN1025 4.8 21.7 1.0 CA B:ASP1023 4.8 14.3 1.0 N B:VAL1060 4.8 12.2 1.0 H B:VAL1060 4.9 14.6 1.0 HB3 B:ASP1026 4.9 15.3 1.0 CB B:VAL1060 4.9 13.1 1.0 HG3 B:ARG1061 4.9 28.9 1.0 O B:CYS1062 5.0 15.8 1.0 HB3 B:ARG1061 5.0 22.3 1.0

Magnesium binding site 5 out of 6 in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:16.6 occ:1.00 O B:HOH2166 2.0 20.4 1.0 OD1 B:ASP1019 2.0 14.7 1.0 OE2 B:GLU1086 2.1 15.9 1.0 O B:HOH2135 2.1 21.3 1.0 OD1 B:ASP1020 2.1 16.3 1.0 CG B:ASP1019 3.1 13.7 1.0 CD B:GLU1086 3.2 16.5 1.0 CG B:ASP1020 3.3 17.7 1.0 HB3 B:GLU1086 3.5 18.2 1.0 HG2 B:GLU1086 3.5 20.4 1.0 OD2 B:ASP1019 3.5 14.0 1.0 HA B:ASP1020 3.8 15.3 1.0 CG B:GLU1086 3.8 17.0 1.0 N B:ASP1020 4.0 12.6 1.0 H B:ASP1020 4.0 15.1 1.0 OD2 B:ASP1020 4.1 22.2 1.0 CB B:GLU1086 4.1 15.1 1.0 CA B:ASP1020 4.2 12.8 1.0 OE1 B:GLU1086 4.2 17.6 1.0 C B:ASP1019 4.3 12.2 1.0 CB B:ASP1020 4.4 15.5 1.0 H B:ASP1019 4.4 16.6 1.0 CB B:ASP1019 4.4 12.4 1.0 O B:HOH2121 4.5 37.5 1.0 SG B:CYS1018 4.6 18.5 1.0 HG3 B:GLU1086 4.7 20.4 1.0 O B:ASP1019 4.7 13.3 1.0 HB2 B:GLU1086 4.7 18.2 1.0 CA B:ASP1019 4.8 12.2 1.0 HB2 B:ASP1019 4.8 14.8 1.0 N B:ASP1019 4.9 13.9 1.0 HB3 B:ASP1020 4.9 18.6 1.0 HB2 B:ASP1020 5.0 18.6 1.0 HA B:GLU1086 5.0 15.8 1.0

Magnesium binding site 6 out of 6 in the Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Salsa / DMBT1 / GP340 Srcr Domain 8 Soaked in Calcium and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2003 b:24.6 occ:1.00 OD1 B:ASN1081 2.2 23.4 1.0 OD2 B:ASP1058 2.3 20.4 1.0 OD1 B:ASP1058 2.5 20.0 1.0 OD2 B:ASP1020 2.6 22.2 1.0 OD2 B:ASP1059 2.6 26.4 1.0 CG B:ASP1058 2.7 19.7 1.0 HB2 B:ASP1020 2.9 18.6 1.0 HB3 B:ASP1020 3.3 18.6 1.0 CB B:ASP1020 3.4 15.5 1.0 CG B:ASP1020 3.4 17.7 1.0 CG B:ASN1081 3.4 20.5 1.0 CG B:ASP1059 3.5 22.5 1.0 H B:ASN1081 3.5 17.0 1.0 OD1 B:ASP1059 3.8 21.1 1.0 SG B:CYS1082 3.8 21.7 1.0 HD21 B:ASN1081 3.8 26.7 1.0 HD21 B:ASN1075 3.9 28.4 1.0 ND2 B:ASN1081 4.0 22.2 1.0 N B:ASN1081 4.2 14.2 1.0 HD22 B:ASN1075 4.3 28.4 1.0 CB B:ASP1058 4.3 16.2 1.0 H B:ASP1059 4.4 18.4 1.0 ND2 B:ASN1075 4.4 23.7 1.0 CB B:ASN1081 4.5 17.2 1.0 HA B:HIS1080 4.5 19.8 1.0 HB3 B:ASP1058 4.5 19.5 1.0 OD1 B:ASP1020 4.6 16.3 1.0 SG B:CYS1018 4.6 18.5 1.0 HB3 B:ASN1081 4.7 20.6 1.0 HB2 B:ASP1058 4.7 19.5 1.0 CB B:ASP1059 4.7 18.6 1.0 N B:ASP1059 4.7 15.3 1.0 CA B:ASN1081 4.8 15.1 1.0 HB3 B:CYS1018 4.8 18.8 1.0 HB2 B:ASP1059 4.8 22.4 1.0 CA B:ASP1020 4.8 12.8 1.0 HD22 B:ASN1081 4.9 26.7 1.0 H B:ASP1020 4.9 15.1 1.0 C B:ASN1081 4.9 15.2 1.0 O B:ASN1081 5.0 16.6 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