Magnesium in PDB 2a31: Trypsin in Complex with Borate

All present enzymatic activity of Trypsin in Complex with Borate:
3.4.21.4;

The structure of Trypsin in Complex with Borate, PDB code: 2a31 was solved by T.R.Transue, S.A.Gabel, R.E.London, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.90 / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.304, 53.446, 46.466, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 16.2

The structure of Trypsin in Complex with Borate also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Trypsin in Complex with Borate (pdb code 2a31). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Trypsin in Complex with Borate, PDB code: 2a31:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Trypsin in Complex with Borate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trypsin in Complex with Borate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:9.0 occ:0.60 CA A:CA502 0.5 8.2 0.4 H2 A:HOH975 1.8 9.8 0.9 O A:HOH1215 1.8 3.7 0.3 OE2 A:GLU80 1.9 12.4 1.0 OE1 A:GLU70 2.1 9.3 1.0 OE1 A:GLU77 2.1 20.1 0.7 O A:VAL75 2.2 11.8 1.0 H2 A:HOH1215 2.2 2.5 0.3 O A:ASN72 2.4 10.1 1.0 O A:HOH975 2.4 9.9 0.9 H1 A:HOH975 2.4 10.4 0.9 H1 A:HOH1215 2.6 2.2 0.3 HG3 A:GLU77 3.0 38.2 0.7 CD A:GLU80 3.1 12.4 1.0 CD A:GLU77 3.1 15.7 0.7 H A:GLU77 3.1 15.3 1.0 HA A:LEU76 3.2 17.1 1.0 CD A:GLU70 3.2 10.1 1.0 HG2 A:GLU80 3.3 10.1 1.0 C A:VAL75 3.4 11.2 1.0 C A:ASN72 3.4 9.3 1.0 H1 A:HOH1004 3.5 11.3 0.7 HG3 A:GLU80 3.5 10.1 1.0 CG A:GLU77 3.5 37.1 0.7 H A:HIS71 3.5 8.8 1.0 CG A:GLU80 3.5 10.2 1.0 HG3 A:GLU77 3.6 6.2 0.3 HA A:ILE73 3.7 8.3 1.0 OE2 A:GLU70 3.7 9.6 1.0 HB2 A:GLU77 3.7 23.3 0.3 HA A:GLU70 3.7 8.0 1.0 H A:VAL75 3.7 9.3 1.0 HB3 A:ASN72 3.8 8.7 1.0 H A:ASN72 3.8 9.1 1.0 H2 A:HOH1004 3.8 11.0 0.7 N A:GLU77 4.0 15.5 1.0 CA A:LEU76 4.0 17.5 1.0 H1 A:HOH1039 4.0 17.6 0.9 O A:HOH1004 4.1 12.5 0.7 N A:LEU76 4.1 12.9 1.0 OE2 A:GLU77 4.2 16.8 0.7 OE1 A:GLU80 4.2 14.8 1.0 HB2 A:GLU77 4.2 25.6 0.7 OE1 A:GLU77 4.2 5.2 0.3 N A:ASN72 4.2 9.2 1.0 HD12 A:LEU76 4.2 19.2 1.0 CA A:ASN72 4.3 8.3 1.0 N A:ILE73 4.3 8.8 1.0 N A:VAL75 4.4 9.4 1.0 CB A:GLU77 4.4 25.6 0.7 HG2 A:GLU77 4.4 38.2 0.7 CG A:GLU77 4.4 7.1 0.3 HB3 A:GLU70 4.4 8.4 1.0 H2 A:HOH1039 4.4 16.9 0.9 CA A:ILE73 4.4 8.8 1.0 CB A:GLU77 4.4 22.3 0.3 C A:LEU76 4.5 17.4 1.0 CA A:VAL75 4.5 11.3 1.0 N A:HIS71 4.5 8.1 1.0 CB A:ASN72 4.5 9.0 1.0 CG A:GLU70 4.5 9.2 1.0 CA A:GLU70 4.6 8.0 1.0 HB A:VAL75 4.6 10.1 1.0 O A:HOH1039 4.7 17.7 0.9 CB A:GLU70 4.7 8.1 1.0 C A:ILE73 4.8 11.4 1.0 CD A:GLU77 4.8 9.4 0.3 CA A:GLU77 4.8 19.4 1.0 HG2 A:GLU70 4.9 9.0 1.0

Magnesium binding site 2 out of 3 in the Trypsin in Complex with Borate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trypsin in Complex with Borate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:25.7 occ:0.77 H2 A:HOH1159 1.9 24.0 0.7 H1 A:HOH1160 2.0 30.9 0.8 O A:HOH1158 2.0 23.9 0.8 H1 A:HOH1161 2.0 24.1 0.7 H1 A:HOH1115 2.0 28.5 1.0 O A:HOH1161 2.1 24.2 0.7 O A:HOH1162 2.2 26.5 0.5 O A:HOH1115 2.3 27.9 1.0 O A:HOH1159 2.3 24.0 0.7 O A:HOH1160 2.3 30.5 0.8 H2 A:HOH1158 2.5 24.3 0.8 H2 A:HOH1160 2.8 30.7 0.8 H1 A:HOH1158 2.8 24.3 0.8 H2 A:HOH1162 2.8 26.5 0.5 H1 A:HOH1162 2.9 26.5 0.5 H1 A:HOH1159 2.9 24.1 0.7 H2 A:HOH1161 3.1 24.2 0.7 H2 A:HOH1115 3.2 28.6 1.0 O A:TYR151 4.0 17.8 1.0 OD2 A:ASP74 4.0 15.1 1.0 H1 A:HOH920 4.1 26.4 0.8 H1 A:HOH1147 4.2 14.5 0.5 HB2 A:TYR151 4.2 12.7 1.0 H2 A:HOH1220 4.2 16.1 0.6 OD1 A:ASP74 4.3 16.8 1.0 O A:HOH1147 4.4 13.9 0.5 O A:HOH1220 4.4 16.2 0.6 CG A:ASP74 4.5 15.3 1.0 HB3 A:TYR151 4.7 12.4 1.0 H2 A:HOH1096 4.7 22.4 0.8 H1 A:HOH1220 4.8 16.2 0.6 HG A:SER153 4.8 14.8 1.0 CB A:TYR151 4.9 12.1 1.0 O A:HOH920 5.0 26.7 0.8

Magnesium binding site 3 out of 3 in the Trypsin in Complex with Borate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trypsin in Complex with Borate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:22.2 occ:0.50 H1 A:HOH1138 2.0 15.4 0.5 H1 A:HOH1168 2.0 21.5 0.6 O A:HOH1233 2.0 17.3 0.4 H2 A:HOH1233 2.1 17.4 0.4 O A:HOH1170 2.1 16.2 0.3 O A:HOH1138 2.1 15.8 0.5 H1 A:HOH1169 2.2 20.0 0.6 O A:HOH1168 2.2 21.3 0.6 O A:HOH1167 2.2 18.5 0.6 H2 A:HOH1168 2.4 21.2 0.6 H1 A:HOH1170 2.6 17.0 0.3 O A:HOH1169 2.6 20.1 0.6 H2 A:HOH1138 2.7 15.8 0.5 H1 A:HOH1167 2.7 18.3 0.6 H2 A:HOH1170 2.8 17.0 0.3 H1 A:HOH1233 2.9 17.5 0.4 H2 A:HOH1167 2.9 18.5 0.6 H2 A:HOH1169 3.1 20.0 0.6 O A:HOH997 3.8 23.1 0.8 H1 A:HOH997 3.9 23.5 0.8 H2 A:HOH997 4.6 23.5 0.8

T.R.Transue, S.A.Gabel, R.E.London. uc(Nmr) and Crystallographic Characterization of Adventitious Borate Binding By Trypsin. Bioconjug.Chem. V. 17 300 2006.
ISSN: ISSN 1043-1802
PubMed: 16536459
DOI: 10.1021/BC0502210