Calcium in PDB 8qnd: Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri

The structure of Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri, PDB code: 8qnd was solved by I.O.Matyuta, M.E.Minyaev, L.A.Shaposhnikov, E.V.Pometun, V.I.Tishkov, V.O.Popov, K.M.Boyko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.38 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.112, 81.53, 86.847, 90, 95.76, 90
R / Rfree (%)	16.8 / 20.1

The binding sites of Calcium atom in the Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri (pdb code 8qnd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri, PDB code: 8qnd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:14.1 occ:1.00 OD1 A:ASP16 2.3 12.7 1.0 O A:HOH509 2.3 35.0 1.0 O A:THR128 2.4 14.0 1.0 O A:HOH560 2.5 13.2 1.0 OD1 A:ASP21 2.5 15.0 1.0 OD2 A:ASP238 2.5 16.8 1.0 OD2 A:ASP21 2.6 14.3 1.0 O A:HOH589 2.6 21.3 1.0 CG A:ASP21 2.9 15.6 1.0 C A:THR128 3.4 15.3 1.0 CG A:ASP16 3.5 13.2 1.0 CG A:ASP238 3.5 14.6 1.0 OD1 A:ASP238 3.8 15.2 1.0 OD2 A:ASP16 4.0 14.7 1.0 N A:GLY129 4.1 14.5 1.0 CA A:GLY129 4.2 12.9 1.0 OG1 A:THR128 4.3 14.2 1.0 CB A:ASP21 4.3 15.6 1.0 O A:ASP16 4.4 15.0 1.0 CB A:THR128 4.4 14.8 1.0 O A:HOH643 4.5 26.6 1.0 N A:ASP16 4.5 13.7 1.0 CA A:THR128 4.5 14.1 1.0 OD1 A:ASN170 4.6 14.0 1.0 C A:ASP16 4.7 14.6 1.0 N A:ASP21 4.7 16.2 1.0 ND2 A:ASN170 4.7 13.6 1.0 CB A:ASP16 4.7 14.3 1.0 CB A:ASP238 4.8 14.5 1.0 CA A:ASP16 4.9 13.7 1.0 CA A:ASP21 4.9 15.5 1.0 O A:HOH712 4.9 40.9 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:16.3 occ:1.00 OE1 C:GLU111 2.3 17.1 1.0 OE1 A:GLU111 2.3 17.6 1.0 OE1 C:GLU140 2.4 17.6 1.0 OE1 A:GLU140 2.4 14.6 1.0 OE2 C:GLU140 2.5 16.9 1.0 OE2 A:GLU140 2.5 16.0 1.0 CD C:GLU140 2.8 17.6 1.0 CD A:GLU140 2.8 15.3 1.0 CD C:GLU111 3.3 20.4 1.0 CD A:GLU111 3.3 18.4 1.0 CG C:GLU111 3.8 20.9 1.0 CG A:GLU111 3.8 15.3 1.0 CG1 C:VAL110 3.9 13.5 1.0 CG1 A:VAL110 4.0 15.2 1.0 O C:HOH621 4.2 15.4 1.0 CG C:GLU140 4.3 16.1 1.0 CE2 C:TYR141 4.3 17.4 1.0 CG A:GLU140 4.3 16.1 1.0 CE2 A:TYR141 4.3 16.7 1.0 OE2 C:GLU111 4.3 18.7 1.0 OH C:TYR141 4.3 18.9 1.0 OH A:TYR141 4.3 20.6 1.0 OE2 A:GLU111 4.4 17.4 1.0 CB A:VAL110 4.5 13.8 1.0 CB C:VAL110 4.6 15.0 1.0 OG1 C:THR108 4.7 14.1 1.0 OG1 A:THR108 4.7 17.2 1.0 CZ C:TYR141 4.8 17.4 1.0 CZ A:TYR141 4.8 18.6 1.0 N C:GLU111 5.0 17.2 1.0 N A:GLU111 5.0 15.0 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:15.2 occ:1.00 OD1 B:ASP16 2.3 17.0 1.0 O B:THR128 2.4 15.6 1.0 O B:HOH506 2.4 31.4 1.0 OD1 B:ASP21 2.5 16.6 1.0 OD2 B:ASP238 2.5 15.7 1.0 O B:HOH515 2.5 13.6 1.0 O B:HOH568 2.5 29.5 1.0 OD2 B:ASP21 2.6 15.6 1.0 CG B:ASP21 2.9 16.1 1.0 CG B:ASP238 3.5 18.0 1.0 C B:THR128 3.5 14.4 1.0 CG B:ASP16 3.5 16.5 1.0 OD1 B:ASP238 3.8 19.8 1.0 OD2 B:ASP16 4.0 18.2 1.0 N B:GLY129 4.2 15.0 1.0 CA B:GLY129 4.2 15.6 1.0 CB B:ASP21 4.3 17.6 1.0 OG1 B:THR128 4.4 16.6 1.0 O B:ASP16 4.4 19.9 1.0 CB B:THR128 4.4 17.0 1.0 O B:HOH642 4.5 26.6 1.0 N B:ASP16 4.5 15.5 1.0 CA B:THR128 4.5 16.2 1.0 OD1 B:ASN170 4.6 16.3 1.0 N B:ASP21 4.6 18.3 1.0 ND2 B:ASN170 4.7 17.2 1.0 C B:ASP16 4.7 17.9 1.0 CB B:ASP16 4.7 16.7 1.0 CB B:ASP238 4.8 16.0 1.0 CA B:ASP16 4.9 16.1 1.0 CA B:ASP21 4.9 17.2 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:17.8 occ:1.00 OE1 D:GLU111 2.3 16.6 1.0 OE1 B:GLU111 2.3 19.3 1.0 OE1 B:GLU140 2.4 16.7 1.0 OE1 D:GLU140 2.4 17.2 1.0 OE2 B:GLU140 2.5 16.9 1.0 OE2 D:GLU140 2.5 15.7 1.0 CD B:GLU140 2.8 19.9 1.0 CD D:GLU140 2.8 18.1 1.0 CD D:GLU111 3.3 21.7 1.0 CD B:GLU111 3.3 20.6 1.0 CG D:GLU111 3.9 18.6 1.0 CG B:GLU111 3.9 17.9 1.0 CG1 D:VAL110 3.9 16.0 1.0 CG1 B:VAL110 4.0 15.8 1.0 CE2 D:TYR141 4.3 17.7 1.0 O D:HOH605 4.3 17.8 1.0 CG D:GLU140 4.3 17.4 1.0 CG B:GLU140 4.3 16.7 1.0 OE2 D:GLU111 4.3 18.7 1.0 OH D:TYR141 4.3 16.9 1.0 CE2 B:TYR141 4.3 18.4 1.0 OH B:TYR141 4.3 17.2 1.0 OE2 B:GLU111 4.4 19.0 1.0 CB D:VAL110 4.5 16.4 1.0 CB B:VAL110 4.6 15.7 1.0 CZ D:TYR141 4.7 18.7 1.0 OG1 B:THR108 4.7 15.5 1.0 OG1 D:THR108 4.8 17.0 1.0 CZ B:TYR141 4.8 17.0 1.0 N D:GLU111 5.0 14.5 1.0 N B:GLU111 5.0 14.6 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:16.1 occ:1.00 O C:HOH568 2.3 27.5 1.0 OD1 C:ASP16 2.3 13.8 1.0 O C:HOH583 2.4 22.9 1.0 O C:THR128 2.4 14.2 1.0 OD1 C:ASP21 2.5 15.7 1.0 OD2 C:ASP238 2.5 15.5 1.0 O C:HOH513 2.5 13.6 1.0 OD2 C:ASP21 2.7 18.3 1.0 CG C:ASP21 2.9 16.0 1.0 CG C:ASP238 3.5 16.0 1.0 C C:THR128 3.5 15.4 1.0 CG C:ASP16 3.5 14.0 1.0 OD1 C:ASP238 3.8 16.9 1.0 OD2 C:ASP16 4.0 16.9 1.0 N C:GLY129 4.2 16.3 1.0 CA C:GLY129 4.2 14.2 1.0 OG1 C:THR128 4.3 16.0 1.0 O C:ASP16 4.4 15.9 1.0 CB C:ASP21 4.4 13.8 1.0 CB C:THR128 4.4 16.4 1.0 CA C:THR128 4.5 16.2 1.0 N C:ASP16 4.5 14.6 1.0 O C:HOH620 4.5 21.3 1.0 OD1 C:ASN170 4.6 16.0 1.0 ND2 C:ASN170 4.6 15.2 1.0 N C:ASP21 4.6 15.5 1.0 C C:ASP16 4.7 14.9 1.0 CB C:ASP16 4.7 13.9 1.0 CB C:ASP238 4.8 13.7 1.0 CA C:ASP16 4.9 15.5 1.0 CA C:ASP21 4.9 15.1 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Ribonucleoside Hydrolase C From Lactobacillus Reuteri within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:18.5 occ:1.00 OD1 D:ASP16 2.3 20.6 1.0 O D:HOH507 2.3 39.8 1.0 O D:THR128 2.4 17.6 1.0 O D:HOH530 2.4 26.6 1.0 OD1 D:ASP21 2.5 19.1 1.0 OD2 D:ASP238 2.5 18.1 1.0 O D:HOH539 2.5 18.2 1.0 OD2 D:ASP21 2.7 22.8 1.0 CG D:ASP21 2.9 20.6 1.0 CG D:ASP238 3.5 17.8 1.0 C D:THR128 3.5 15.8 1.0 CG D:ASP16 3.5 21.5 1.0 OD1 D:ASP238 3.8 18.6 1.0 OD2 D:ASP16 4.0 22.6 1.0 N D:GLY129 4.2 17.7 1.0 CA D:GLY129 4.2 15.8 1.0 OG1 D:THR128 4.3 17.8 1.0 O D:ASP16 4.3 20.2 1.0 CB D:ASP21 4.4 19.3 1.0 CB D:THR128 4.4 18.3 1.0 CA D:THR128 4.5 15.8 1.0 N D:ASP16 4.5 20.2 1.0 OD1 D:ASN170 4.6 19.9 1.0 ND2 D:ASN170 4.6 18.7 1.0 N D:ASP21 4.7 17.6 1.0 C D:ASP16 4.7 20.6 1.0 CB D:ASP16 4.8 20.5 1.0 CB D:ASP238 4.8 19.2 1.0 CA D:ASP16 4.9 20.3 1.0 CA D:ASP21 4.9 20.1 1.0

L.A.Shaposhnikov, N.Y.Chikurova, D.L.Atroshenko, S.S.Savin, A.A.Loginova, S.Y.Kleymenov, E.V.Pometun, M.E.Minyaev, I.O.Matyuta, K.M.Boyko, V.I.Tishkov, A.A.Pometun. Cloning of Ribonucleoside Hydrolase C (Rihc) From Limosilactobacillus Reuteri LR1 and Study of Its Structural and Functional Characteristics To Be Published.