Calcium in PDB 8khv: The Crystal Structure of Glycosaminoglycan Lyase Gagase II

The structure of The Crystal Structure of Glycosaminoglycan Lyase Gagase II, PDB code: 8khv was solved by L.Wei, H.Y.Cao, F.C.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.01 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.917, 82.096, 79.885, 90, 106.59, 90
R / Rfree (%)	15.9 / 19.2

The structure of The Crystal Structure of Glycosaminoglycan Lyase Gagase II also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the The Crystal Structure of Glycosaminoglycan Lyase Gagase II (pdb code 8khv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Crystal Structure of Glycosaminoglycan Lyase Gagase II, PDB code: 8khv:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The Crystal Structure of Glycosaminoglycan Lyase Gagase II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Glycosaminoglycan Lyase Gagase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:19.2 occ:1.00 O A:HOH1026 2.4 15.2 1.0 O A:HOH1101 2.5 17.5 1.0 OE2 A:GLU160 2.5 14.6 1.0 O A:HOH1240 2.8 32.7 1.0 CD A:GLU160 3.4 18.0 1.0 OE1 A:GLU160 3.6 17.5 1.0 O A:HOH881 4.3 16.4 1.0 O A:HOH912 4.4 15.0 1.0 O A:HOH1011 4.4 22.3 1.0 OG A:SER164 4.5 16.5 1.0 NZ A:LYS167 4.6 19.0 1.0 CG A:GLU160 4.8 13.7 1.0

Calcium binding site 2 out of 3 in the The Crystal Structure of Glycosaminoglycan Lyase Gagase II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Glycosaminoglycan Lyase Gagase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:21.1 occ:1.00 O A:HOH1263 2.3 22.6 1.0 O A:HOH1269 2.4 20.3 1.0 OD2 A:ASP233 2.4 19.6 1.0 O A:SER190 2.4 13.1 1.0 O A:HOH1187 2.5 22.1 1.0 O A:HOH1016 2.5 14.7 1.0 O A:HOH1097 2.8 19.7 1.0 CG A:ASP233 3.3 20.1 1.0 C A:SER190 3.5 14.8 1.0 CB A:ASP233 3.8 16.4 1.0 CA A:ASN191 4.1 11.3 1.0 O A:HOH841 4.3 29.9 1.0 N A:ASN191 4.3 15.6 1.0 OD1 A:ASP233 4.3 25.0 1.0 OE1 A:GLU242 4.3 19.4 1.0 CB A:SER190 4.4 13.0 1.0 O A:HOH932 4.4 12.3 1.0 O A:HOH1071 4.5 27.2 1.0 O A:HOH818 4.6 13.4 1.0 CA A:SER190 4.6 12.6 1.0 O A:PRO230 4.7 8.6 1.0 CB A:ASN191 4.8 14.5 1.0 CA A:PRO230 4.9 8.1 1.0

Calcium binding site 3 out of 3 in the The Crystal Structure of Glycosaminoglycan Lyase Gagase II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of Glycosaminoglycan Lyase Gagase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:27.3 occ:1.00 O A:HOH1295 2.7 26.0 1.0 N A:ASN583 2.9 10.5 1.0 O A:HOH1222 3.1 13.7 1.0 C A:ASN583 3.7 11.1 1.0 CD A:PRO575 3.7 8.6 1.0 CA A:PRO582 3.7 11.4 1.0 C A:PRO582 3.8 10.3 1.0 CA A:GLU574 3.8 9.5 1.0 CA A:ASN583 3.8 10.2 1.0 N A:PRO584 3.9 14.2 1.0 CB A:PRO582 4.0 13.3 1.0 O A:ASN583 4.1 11.6 1.0 O A:THR573 4.3 9.2 1.0 CB A:GLU574 4.4 12.9 1.0 CB A:ASN583 4.4 10.0 1.0 CA A:PRO584 4.5 13.2 1.0 N A:GLU574 4.5 7.1 1.0 CD A:PRO584 4.5 14.0 1.0 N A:PRO575 4.6 5.8 1.0 C A:GLU574 4.7 6.5 1.0 C A:THR573 4.7 9.4 1.0 CG A:PRO575 4.7 9.1 1.0 O A:PRO582 5.0 11.2 1.0

L.Wei, H.Y.Cao, F.C.Li. The Crystal Structure of Glycosaminoglycan Lyase Gagase VII To Be Published.