Calcium in PDB 2c5u: T4 Rna Ligase (RNL1) Crystal Structure

All present enzymatic activity of T4 Rna Ligase (RNL1) Crystal Structure:
6.5.1.3;

The structure of T4 Rna Ligase (RNL1) Crystal Structure, PDB code: 2c5u was solved by K.El Omari, J.Ren, L.E.Bird, M.K.Bona, G.Klarmann, S.F.J.Legrice, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.78 / 2.21
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.050, 39.870, 108.540, 90.00, 117.27, 90.00
R / Rfree (%)	19.8 / 25.8

The structure of T4 Rna Ligase (RNL1) Crystal Structure also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Calcium atom in the T4 Rna Ligase (RNL1) Crystal Structure (pdb code 2c5u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the T4 Rna Ligase (RNL1) Crystal Structure, PDB code: 2c5u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the T4 Rna Ligase (RNL1) Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of T4 Rna Ligase (RNL1) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1376 b:22.2 occ:1.00 O A:HOH2193 2.3 13.3 1.0 O A:HOH2277 2.4 20.1 1.0 O A:HOH2369 2.5 18.4 1.0 O1A A:APC1375 2.5 16.8 1.0 O A:HOH2147 2.5 19.9 1.0 O A:HOH2276 2.5 14.1 1.0 O A:HOH2047 2.5 22.7 1.0 PA A:APC1375 3.8 17.0 1.0 NZ A:LYS99 4.0 14.7 1.0 O A:GLY102 4.2 19.0 1.0 C3A A:APC1375 4.3 16.3 1.0 OD1 A:ASP101 4.4 16.9 1.0 C4' A:APC1375 4.5 22.1 1.0 O A:HOH2371 4.5 26.0 1.0 OE2 A:GLU227 4.5 18.6 1.0 O A:HOH2139 4.6 48.4 1.0 O4' A:APC1375 4.6 16.4 1.0 OE1 A:GLU227 4.6 22.7 1.0 OE2 A:GLU159 4.7 21.2 1.0 OH A:TYR246 4.7 19.7 1.0 O2A A:APC1375 4.8 13.4 1.0 CL A:CL1378 4.8 24.6 1.0 C1' A:APC1375 4.8 2.6 1.0 O5' A:APC1375 4.9 15.3 1.0 CD A:GLU227 5.0 16.0 1.0

Calcium binding site 2 out of 4 in the T4 Rna Ligase (RNL1) Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of T4 Rna Ligase (RNL1) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1377 b:20.7 occ:1.00 O B:HOH2154 2.3 14.4 1.0 O B:HOH2275 2.5 19.3 1.0 O B:HOH2354 2.5 23.4 1.0 O B:HOH2197 2.5 20.6 1.0 O B:HOH2276 2.5 15.2 1.0 O1A B:APC1375 2.5 12.1 1.0 O B:HOH2058 2.5 23.3 1.0 PA B:APC1375 3.9 15.8 1.0 NZ B:LYS99 3.9 11.1 1.0 OD1 B:ASP101 4.2 16.6 1.0 O B:GLY102 4.3 13.9 1.0 C3A B:APC1375 4.4 21.8 1.0 OE2 B:GLU227 4.4 15.3 1.0 OE1 B:GLU227 4.5 9.9 1.0 C4' B:APC1375 4.5 15.5 1.0 OE2 B:GLU159 4.6 18.9 1.0 O4' B:APC1375 4.6 11.5 1.0 OH B:TYR246 4.6 13.4 1.0 O2A B:APC1375 4.7 14.0 1.0 C1' B:APC1375 4.8 7.9 1.0 CL B:CL1380 4.8 20.3 1.0 CD B:GLU227 4.9 12.0 1.0 NZ B:LYS242 4.9 15.1 1.0 O5' B:APC1375 5.0 13.4 1.0

Calcium binding site 3 out of 4 in the T4 Rna Ligase (RNL1) Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of T4 Rna Ligase (RNL1) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1378 b:25.8 occ:1.00 OD2 A:ASP212 2.3 22.1 1.0 O B:HOH2142 2.3 20.1 1.0 O B:ILE211 2.4 13.5 1.0 O B:HOH2254 2.4 20.4 1.0 OD1 B:ASP212 2.4 25.5 1.0 O A:HOH2250 2.5 25.6 1.0 OD1 A:ASP212 2.5 16.8 1.0 CG A:ASP212 2.7 20.0 1.0 O A:HOH2252 3.4 30.1 1.0 C B:ILE211 3.5 13.5 1.0 CG B:ASP212 3.5 17.6 1.0 CA B:CA1379 3.9 23.5 1.0 CA B:ASP212 3.9 19.1 1.0 N B:ASP212 4.1 10.7 1.0 CB A:ASP212 4.2 23.7 1.0 CB B:ASP212 4.3 12.7 1.0 OD2 B:ASP212 4.4 17.7 1.0 O A:HOH2251 4.5 15.0 1.0 O B:HOH2281 4.6 42.9 1.0 CA B:ILE211 4.7 14.6 1.0 O B:HOH2140 4.7 19.4 1.0 O B:ASP94 4.8 19.1 1.0 N B:ILE211 4.8 18.9 1.0 O B:HOH2255 4.9 31.4 1.0 O B:HOH2143 4.9 41.1 1.0 O B:HOH2258 4.9 27.9 1.0

Calcium binding site 4 out of 4 in the T4 Rna Ligase (RNL1) Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of T4 Rna Ligase (RNL1) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1379 b:23.5 occ:1.00 OD1 A:ASP212 2.3 16.8 1.0 O A:ILE211 2.4 19.8 1.0 O B:HOH2258 2.4 27.9 1.0 OD2 B:ASP212 2.4 17.7 1.0 O A:HOH2135 2.5 19.6 1.0 O A:HOH2252 2.5 30.1 1.0 OD1 B:ASP212 2.6 25.5 1.0 O A:HOH2247 2.7 22.1 1.0 CG B:ASP212 2.8 17.6 1.0 C A:ILE211 3.5 18.2 1.0 CG A:ASP212 3.5 20.0 1.0 CA A:ASP212 3.8 19.6 1.0 CA B:CA1378 3.9 25.8 1.0 N A:ASP212 4.1 8.9 1.0 CB A:ASP212 4.3 23.7 1.0 CB B:ASP212 4.3 12.7 1.0 OD2 A:ASP212 4.4 22.1 1.0 CA A:ILE211 4.7 11.6 1.0 O B:HOH2256 4.7 18.2 1.0 O A:HOH2249 4.8 32.6 1.0 O A:HOH2133 4.8 29.1 1.0 O A:HOH2282 4.8 39.7 1.0 N A:ILE211 4.8 15.2 1.0 O A:ASP94 4.8 27.4 1.0 O A:HOH2250 4.9 25.6 1.0

K.El Omari, J.Ren, L.E.Bird, M.K.Bona, G.Klarmann, S.F.J.Legrice, D.K.Stammers. Molecular Architecture and Ligand Recognition Determinants For T4 Rna Ligase J.Biol.Chem. V. 281 1573 2006.
ISSN: ISSN 0021-9258
PubMed: 16263720
DOI: 10.1074/JBC.M509658200