Calcium in PDB 4udm: Crystal Structure of IM3 in Complex with Y52A Mutant of E3RNASE

The structure of Crystal Structure of IM3 in Complex with Y52A Mutant of E3RNASE, PDB code: 4udm was solved by A.Sharma, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.47 / 2.96
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.854, 92.854, 76.942, 90.00, 90.00, 120.00
R / Rfree (%)	18.425 / 21.378

The structure of Crystal Structure of IM3 in Complex with Y52A Mutant of E3RNASE also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of IM3 in Complex with Y52A Mutant of E3RNASE (pdb code 4udm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of IM3 in Complex with Y52A Mutant of E3RNASE, PDB code: 4udm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of IM3 in Complex with Y52A Mutant of E3RNASE


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 IM3 in Complex with Y52A Mutant of E3RNASE within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1086 b:0.3 occ:1.00 OD1 A:ASP71 3.1 67.4 1.0 OG A:SER70 3.4 60.1 1.0 OD2 A:ASP68 3.8 61.6 1.0 CG A:ASP71 4.0 63.6 1.0 OD2 A:ASP71 4.2 65.5 1.0 OD1 A:ASP68 4.6 59.3 1.0 CG A:ASP68 4.6 57.8 1.0 CB A:SER70 4.7 57.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of IM3 in Complex with Y52A Mutant of E3RNASE


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 IM3 in Complex with Y52A Mutant of E3RNASE within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1097 b:35.2 occ:0.50 OE2 B:GLU62 2.4 62.2 1.0 OE2 B:GLU60 2.5 56.4 1.0 OD2 B:ASP55 2.6 58.1 1.0 CD2 B:HIS58 2.7 58.9 1.0 NE2 B:HIS58 3.2 59.2 1.0 CD B:GLU62 3.5 59.2 1.0 CG B:HIS58 3.7 57.5 1.0 CD B:GLU60 3.7 57.8 1.0 CG B:ASP55 3.9 56.7 1.0 NH1 B:ARG90 3.9 54.5 1.0 NZ B:LYS84 3.9 68.6 1.0 OE1 B:GLU62 4.1 60.5 1.0 CE1 B:HIS58 4.2 59.5 1.0 CB B:HIS58 4.4 55.6 1.0 ND1 B:HIS58 4.5 59.7 1.0 CG B:GLU60 4.5 55.1 1.0 NH2 B:ARG90 4.6 57.9 1.0 CG B:GLU62 4.6 54.6 1.0 OE1 B:GLU60 4.7 56.5 1.0 CB B:ASP55 4.7 53.8 1.0 CZ B:ARG90 4.7 56.1 1.0 OD1 B:ASP55 4.8 57.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of IM3 in Complex with Y52A Mutant of E3RNASE


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 IM3 in Complex with Y52A Mutant of E3RNASE within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1098 b:46.6 occ:0.50 O B:ARG40 2.7 51.6 1.0 OE2 B:GLU53 2.8 52.3 1.0 N B:LYS30 2.9 52.1 1.0 N B:THR31 2.9 56.9 1.0 OG1 B:THR31 3.5 57.5 1.0 CB B:THR31 3.5 58.8 1.0 CA B:PRO29 3.5 49.9 1.0 NH2 B:ARG42 3.6 49.1 1.0 C B:PRO29 3.6 51.3 1.0 N B:ARG40 3.6 52.7 1.0 NE B:ARG42 3.6 46.0 1.0 C B:ARG40 3.6 50.8 1.0 CB B:ARG40 3.6 51.3 1.0 CA B:THR31 3.7 59.0 1.0 CD B:GLU53 3.7 51.9 1.0 C B:LYS30 3.8 54.5 1.0 CA B:LYS30 3.8 52.7 1.0 CA B:ARG40 3.8 51.8 1.0 CB B:PRO29 3.9 49.4 1.0 CZ B:ARG42 3.9 48.4 1.0 CB B:ARG42 4.0 45.0 1.0 O B:THR31 4.2 62.0 1.0 OE1 B:GLU53 4.3 51.9 1.0 C B:THR31 4.4 61.7 1.0 C B:LYS39 4.5 54.6 1.0 CD B:ARG42 4.6 41.7 1.0 CG B:GLU53 4.6 48.7 1.0 CB B:LYS30 4.6 51.7 1.0 CG B:ARG42 4.8 43.6 1.0 O B:PRO29 4.8 51.5 1.0 N B:PRO29 4.8 49.0 1.0 CB B:LYS39 4.8 57.0 1.0 N B:LYS41 4.8 48.8 1.0 N B:ARG42 4.9 45.6 1.0 CG2 B:THR31 4.9 59.1 1.0 C B:LYS41 4.9 46.0 1.0 O B:ILE28 4.9 48.9 1.0 CA B:ARG42 4.9 45.8 1.0 NH1 B:ARG42 4.9 48.9 1.0 O B:LYS30 5.0 55.0 1.0 O B:LYS41 5.0 45.3 1.0

G.Papadakos, A.Sharma, L.E.Lancaster, R.Bowen, R.Kaminska, A.P.Leech, D.Walker, C.Redfield, C.Kleanthous. Consequences of Inducing Intrinsic Disorder in A High- Affinity Protein-Protein Interaction. J.Am.Chem.Soc. V. 137 5252 2015.
ISSN: ISSN 0002-7863
PubMed: 25856265
DOI: 10.1021/JA512607R