Magnesium in PDB 5l44: Structure of K-26-Dcp in Complex with the K-26 Tripeptide

The structure of Structure of K-26-Dcp in Complex with the K-26 Tripeptide, PDB code: 5l44 was solved by G.Masuyer, K.R.Acharya, G.J.Kramer, B.O.Bachmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 1.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.580, 66.940, 102.000, 97.72, 90.71, 117.37
R / Rfree (%)	18.5 / 21.3

The structure of Structure of K-26-Dcp in Complex with the K-26 Tripeptide also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Structure of K-26-Dcp in Complex with the K-26 Tripeptide (pdb code 5l44). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of K-26-Dcp in Complex with the K-26 Tripeptide, PDB code: 5l44:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of K-26-Dcp in Complex with the K-26 Tripeptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of K-26-Dcp in Complex with the K-26 Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:8.1 occ:1.00 OD2 A:ASP527 2.0 8.6 1.0 OD1 A:ASP524 2.1 9.1 1.0 O B:HOH1161 2.1 6.7 1.0 O B:HOH1211 2.1 8.1 1.0 O A:HOH1431 2.2 9.6 1.0 O B:HOH1153 2.2 7.2 1.0 CG A:ASP527 3.1 9.5 1.0 CG A:ASP524 3.2 8.6 1.0 CB A:ASP527 3.5 9.2 1.0 CB A:ASP524 3.9 9.0 1.0 CA A:ASP524 3.9 9.1 1.0 OE2 B:GLU354 4.0 13.8 1.0 OD2 A:ASP524 4.1 8.5 1.0 OD2 B:ASP356 4.1 9.7 1.0 OD1 A:ASP527 4.2 9.8 1.0 O A:HOH1276 4.2 22.2 1.0 NZ A:LYS523 4.2 9.6 1.0 OG1 B:THR451 4.2 8.3 1.0 OD1 B:ASP356 4.3 9.8 1.0 O B:GLU449 4.4 11.0 1.0 CE A:LYS523 4.4 9.4 1.0 O A:ASP524 4.4 9.4 1.0 O B:HOH1461 4.5 17.0 1.0 CD A:LYS523 4.5 9.5 1.0 CG B:ASP356 4.6 9.4 1.0 OH B:TYR409 4.6 6.7 1.0 C A:ASP524 4.7 9.1 1.0 N B:THR451 4.8 8.7 1.0 O A:LYS523 4.9 8.8 1.0 N A:ASP524 4.9 8.8 1.0 NH2 B:ARG389 4.9 9.5 1.0 CD B:GLU354 5.0 12.1 1.0

Magnesium binding site 2 out of 4 in the Structure of K-26-Dcp in Complex with the K-26 Tripeptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of K-26-Dcp in Complex with the K-26 Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:27.1 occ:1.00 O A:HOH1237 2.0 22.4 1.0 O A:HOH1369 2.0 23.0 1.0 O A:HOH1585 2.1 23.1 1.0 O A:HOH1117 2.2 20.7 1.0 O A:HOH1535 2.3 29.3 1.0 O A:HOH1134 2.3 22.1 1.0 OE1 A:GLU499 4.0 13.4 1.0 OE1 A:GLN496 4.1 9.8 1.0 OE2 A:GLU499 4.3 11.2 1.0 O A:HOH1114 4.3 22.5 1.0 O A:HOH1502 4.3 24.0 1.0 O A:HOH1552 4.4 28.8 1.0 O A:HOH1124 4.5 15.6 1.0 NH2 A:ARG668 4.5 21.1 1.0 CD A:GLU499 4.6 10.7 1.0 O A:HOH1521 4.7 36.9 1.0 ND2 A:ASN459 4.7 8.7 0.5 O A:HOH1529 4.8 35.2 1.0 O A:HOH1159 4.9 17.5 1.0 O A:HOH1548 4.9 26.9 1.0

Magnesium binding site 3 out of 4 in the Structure of K-26-Dcp in Complex with the K-26 Tripeptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of K-26-Dcp in Complex with the K-26 Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:8.8 occ:1.00 OD1 B:ASP524 2.0 7.9 1.0 OD2 B:ASP527 2.1 8.4 1.0 O B:HOH1460 2.2 8.7 1.0 CG B:ASP527 3.2 9.2 1.0 CG B:ASP524 3.2 8.2 1.0 CB B:ASP527 3.6 9.0 1.0 CB B:ASP524 3.9 8.2 1.0 CA B:ASP524 4.0 8.2 1.0 OD2 B:ASP524 4.0 8.8 1.0 NZ B:LYS523 4.2 9.4 1.0 O B:HOH1234 4.2 30.6 1.0 OD1 B:ASP527 4.2 8.8 1.0 CE B:LYS523 4.4 9.1 1.0 O B:ASP524 4.4 8.3 1.0 CD B:LYS523 4.5 9.2 1.0 C B:ASP524 4.7 8.3 1.0 N B:ASP524 4.9 8.2 1.0

Magnesium binding site 4 out of 4 in the Structure of K-26-Dcp in Complex with the K-26 Tripeptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of K-26-Dcp in Complex with the K-26 Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:25.4 occ:1.00 O B:HOH1436 2.0 18.6 1.0 O B:HOH1167 2.0 19.7 1.0 O B:HOH1574 2.1 29.1 1.0 O B:HOH1134 2.1 17.4 1.0 O B:HOH1570 2.2 24.7 1.0 O B:HOH1113 2.2 22.2 1.0 OE1 B:GLU499 3.9 12.8 1.0 OE1 B:GLN496 4.1 11.0 1.0 OE2 B:GLU499 4.2 10.3 1.0 O B:HOH1364 4.4 18.4 1.0 O B:HOH1193 4.4 21.8 1.0 O B:HOH1518 4.5 25.8 1.0 O B:HOH1571 4.5 35.6 1.0 CD B:GLU499 4.6 10.1 1.0 NH2 B:ARG668 4.6 23.3 1.0 O B:HOH1554 4.6 33.0 1.0 ND2 B:ASN459 4.6 8.1 0.5 O B:HOH1250 4.8 15.2 1.0 O B:HOH1536 4.9 29.5 1.0

G.Masuyer, G.E.Cozier, G.J.Kramer, B.O.Bachmann, K.R.Acharya. Crystal Structure of A Peptidyl-Dipeptidase K-26-Dcp From Actinomycete in Complex with Its Natural Inhibitor. Febs J. V. 283 4357 2016.
ISSN: ISSN 1742-4658
PubMed: 27754586
DOI: 10.1111/FEBS.13928