Calcium in PDB 9dq9: Borrelia Burgdorferi Ldh with Nadh and Oxamate

All present enzymatic activity of Borrelia Burgdorferi Ldh with Nadh and Oxamate:
1.1.1.27;

The structure of Borrelia Burgdorferi Ldh with Nadh and Oxamate, PDB code: 9dq9 was solved by M.J.Lynch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.47 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.528, 90.348, 167.361, 90, 90, 90
R / Rfree (%)	20 / 23

The binding sites of Calcium atom in the Borrelia Burgdorferi Ldh with Nadh and Oxamate (pdb code 9dq9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Borrelia Burgdorferi Ldh with Nadh and Oxamate, PDB code: 9dq9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Borrelia Burgdorferi Ldh with Nadh and Oxamate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Borrelia Burgdorferi Ldh with Nadh and Oxamate within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca403 b:57.8 occ:1.00 OD1 P:ASP161 2.5 62.7 1.0 O P:ASP161 2.5 44.5 1.0 OD1 P:ASN164 2.7 56.1 1.0 HD22 P:ASN164 3.3 74.2 1.0 CG P:ASN164 3.5 51.2 1.0 CG P:ASP161 3.6 47.8 1.0 C P:ASP161 3.6 44.6 1.0 ND2 P:ASN164 3.8 61.9 1.0 HA P:ASP161 3.8 49.2 1.0 CA P:ASP161 4.2 41.0 1.0 OD2 P:ASP161 4.3 57.7 1.0 HA P:HIS162 4.5 46.8 1.0 CB P:ASP161 4.5 45.9 1.0 HD21 P:ASN164 4.6 74.2 1.0 H P:ASN164 4.7 54.2 1.0 N P:HIS162 4.7 44.8 1.0 O P:HIS162 4.8 41.6 1.0 HA P:ASN164 4.8 54.1 1.0 CB P:ASN164 4.9 40.4 1.0 CA P:HIS162 4.9 39.0 1.0

Calcium binding site 2 out of 5 in the Borrelia Burgdorferi Ldh with Nadh and Oxamate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Borrelia Burgdorferi Ldh with Nadh and Oxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:51.8 occ:1.00 OD1 A:ASP161 2.3 47.2 1.0 OD1 A:ASN164 2.4 56.4 1.0 O A:ASP161 2.5 38.8 1.0 O A:HOH527 2.7 45.3 1.0 HA A:ASP161 3.3 45.7 1.0 CG A:ASN164 3.4 48.8 1.0 CG A:ASP161 3.5 42.2 1.0 C A:ASP161 3.5 36.7 1.0 HD22 A:ASN164 3.8 66.1 1.0 CA A:ASP161 3.8 38.0 1.0 ND2 A:ASN164 4.0 55.0 1.0 HA A:ASN164 4.1 45.1 1.0 H A:ASN164 4.2 43.6 1.0 CB A:ASP161 4.3 38.9 1.0 OD2 A:ASP161 4.4 42.0 1.0 CB A:ASN164 4.6 38.5 1.0 CA A:ASN164 4.6 37.6 1.0 N A:ASN164 4.7 36.3 1.0 N A:HIS162 4.7 36.2 1.0 HD21 A:ASN164 4.8 66.1 1.0 HB2 A:ASP161 4.9 46.7 1.0 HA A:HIS162 4.9 41.5 1.0 HB3 A:ASN164 4.9 46.2 1.0 HB3 A:ASP161 4.9 46.7 1.0 O A:SER160 4.9 33.8 1.0

Calcium binding site 3 out of 5 in the Borrelia Burgdorferi Ldh with Nadh and Oxamate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Borrelia Burgdorferi Ldh with Nadh and Oxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:104.4 occ:1.00 OE2 A:GLU209 2.2 66.8 1.0 HG2 A:GLU209 3.3 61.3 1.0 CD A:GLU209 3.3 57.2 1.0 CG A:GLU209 3.8 51.1 1.0 HG3 A:GLU209 4.0 61.3 1.0 OE1 A:GLU209 4.4 47.7 1.0

Calcium binding site 4 out of 5 in the Borrelia Burgdorferi Ldh with Nadh and Oxamate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Borrelia Burgdorferi Ldh with Nadh and Oxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:62.9 occ:1.00 OD1 B:ASP161 2.2 66.1 1.0 HD22 B:ASN164 2.4 79.2 1.0 O B:ASP161 2.4 51.5 1.0 OD1 B:ASN164 2.5 61.1 1.0 ND2 B:ASN164 2.9 66.0 1.0 CG B:ASN164 3.0 56.0 1.0 C B:ASP161 3.5 48.7 1.0 CG B:ASP161 3.5 64.0 1.0 HA B:ASP161 3.6 58.6 1.0 HD21 B:ASN164 3.6 79.2 1.0 CA B:ASP161 4.0 48.8 1.0 CB B:ASP161 4.3 44.8 1.0 OD2 B:ASP161 4.3 71.2 1.0 H B:ASN164 4.3 60.9 1.0 HA B:ASN164 4.4 59.5 1.0 CB B:ASN164 4.4 46.0 1.0 HA B:HIS162 4.5 59.6 1.0 N B:HIS162 4.6 53.1 1.0 O B:HIS162 4.8 54.1 1.0 CA B:ASN164 4.8 49.6 1.0 N B:ASN164 4.8 50.8 1.0 HB3 B:ASP161 4.8 53.8 1.0 HB2 B:ASN164 4.9 55.2 1.0 CA B:HIS162 4.9 49.7 1.0 HB3 B:ASN164 4.9 55.2 1.0 C B:HIS162 5.0 47.4 1.0

Calcium binding site 5 out of 5 in the Borrelia Burgdorferi Ldh with Nadh and Oxamate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Borrelia Burgdorferi Ldh with Nadh and Oxamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:63.6 occ:1.00 OD1 C:ASP161 2.2 65.4 1.0 OD1 C:ASN164 2.4 65.2 1.0 O C:ASP161 2.8 47.0 1.0 HD22 C:ASN164 3.1 77.1 1.0 CG C:ASN164 3.3 58.0 1.0 CG C:ASP161 3.4 56.1 1.0 ND2 C:ASN164 3.5 64.3 1.0 HA C:ASP161 3.5 55.1 1.0 C C:ASP161 3.8 47.8 1.0 CA C:ASP161 4.0 45.9 1.0 OD2 C:ASP161 4.2 53.8 1.0 CB C:ASP161 4.3 48.4 1.0 HD21 C:ASN164 4.4 77.1 1.0 O C:HOH502 4.4 51.5 1.0 HA C:ASN164 4.5 60.4 1.0 O C:HOH522 4.5 54.4 1.0 H C:ASN164 4.5 54.9 1.0 CB C:ASN164 4.6 50.3 1.0 HB2 C:ASP161 4.9 58.1 1.0 CA C:ASN164 4.9 50.3 1.0 N C:HIS162 5.0 49.1 1.0 HB3 C:ASP161 5.0 58.1 1.0

M.J.Lynch, M.J.Lynch. N/A N/A.