Calcium in PDB 7mmp: Crystal Structure of the Class Ie Ribonucleotide Reductase

All present enzymatic activity of Crystal Structure of the Class Ie Ribonucleotide Reductase:
1.17.4.1;

The structure of Crystal Structure of the Class Ie Ribonucleotide Reductase, PDB code: 7mmp was solved by G.M.Palowitch, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.65 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.656, 105.331, 138.894, 90, 100.46, 90
R / Rfree (%)	19.5 / 22.4

The binding sites of Calcium atom in the Crystal Structure of the Class Ie Ribonucleotide Reductase (pdb code 7mmp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Class Ie Ribonucleotide Reductase, PDB code: 7mmp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of the Class Ie Ribonucleotide Reductase


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 Class Ie Ribonucleotide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:27.9 occ:1.00 O3' E:FMN201 3.1 19.3 1.0 O A:HOH599 3.3 35.5 1.0 ND2 A:ASN282 3.4 22.9 1.0 O A:HOH546 3.4 23.2 1.0 ND2 E:ASN92 3.5 21.5 1.0 CD2 E:LEU120 3.6 23.5 1.0 C1' E:FMN201 3.6 19.5 1.0 CB A:PHE215 3.8 18.9 1.0 CB E:ASN92 3.9 21.2 1.0 C3' E:FMN201 3.9 19.9 1.0 CG2 A:VAL211 4.0 18.8 1.0 CG E:ASN92 4.1 21.5 1.0 CD1 A:PHE215 4.2 19.9 1.0 O A:VAL211 4.2 18.3 1.0 CG A:PHE215 4.3 19.4 1.0 C2' E:FMN201 4.3 19.9 1.0 CG A:ASN282 4.5 23.5 1.0 OD1 A:ASN282 4.6 24.2 1.0 N10 E:FMN201 4.7 19.5 1.0 CA A:PHE215 4.8 18.7 1.0 CE2 E:PHE95 4.8 22.3 1.0 C9 E:FMN201 4.8 19.5 1.0 CG E:LEU120 4.9 24.0 1.0 C A:VAL211 5.0 18.3 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of the Class Ie Ribonucleotide Reductase


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 Class Ie Ribonucleotide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:33.8 occ:1.00 OE2 C:GLU299 2.4 42.2 1.0 OE1 C:GLU299 3.0 40.9 1.0 CD C:GLU299 3.1 40.7 1.0 CG C:GLU299 4.5 39.5 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of the Class Ie Ribonucleotide Reductase


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 Class Ie Ribonucleotide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca202 b:31.1 occ:1.00 O3' G:FMN201 3.1 22.0 1.0 O C:HOH582 3.2 34.9 1.0 ND2 G:ASN92 3.3 25.0 1.0 O C:HOH526 3.5 24.4 1.0 CD2 G:LEU120 3.5 27.5 1.0 ND2 C:ASN282 3.6 26.9 1.0 C1' G:FMN201 3.6 22.3 1.0 CB G:ASN92 3.7 24.7 1.0 C3' G:FMN201 3.9 22.1 1.0 CG2 C:VAL211 3.9 21.0 1.0 CG G:ASN92 3.9 25.2 1.0 CB C:PHE215 3.9 20.9 1.0 O C:VAL211 4.3 20.2 1.0 C2' G:FMN201 4.3 22.4 1.0 CD1 C:PHE215 4.5 21.5 1.0 CG C:ASN282 4.5 26.9 1.0 CG C:PHE215 4.5 21.1 1.0 OD1 C:ASN282 4.6 27.2 1.0 N10 G:FMN201 4.7 22.6 1.0 CE2 G:PHE95 4.8 24.1 1.0 CA C:PHE215 4.9 20.7 1.0 C9 G:FMN201 4.9 23.0 1.0 CG G:LEU120 4.9 28.2 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of the Class Ie Ribonucleotide Reductase


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 Class Ie Ribonucleotide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca202 b:34.1 occ:1.00 O3' F:FMN201 3.1 21.0 1.0 O B:HOH485 3.1 37.6 1.0 ND2 F:ASN92 3.3 24.5 1.0 O B:HOH454 3.3 36.8 1.0 CD2 F:LEU120 3.5 26.9 1.0 ND2 B:ASN282 3.5 27.1 1.0 C1' F:FMN201 3.6 21.1 1.0 CB F:ASN92 3.8 24.3 1.0 C3' F:FMN201 3.9 21.2 1.0 CG2 B:VAL211 3.9 20.3 1.0 CB B:PHE215 3.9 19.8 1.0 CG F:ASN92 4.0 24.6 1.0 O B:VAL211 4.2 19.9 1.0 C2' F:FMN201 4.4 21.5 1.0 CD1 B:PHE215 4.4 20.2 1.0 CG B:PHE215 4.5 19.8 1.0 CG B:ASN282 4.5 27.0 1.0 OD1 B:ASN282 4.6 27.0 1.0 CE2 F:PHE95 4.7 23.1 1.0 N10 F:FMN201 4.7 21.1 1.0 CA B:PHE215 4.8 19.8 1.0 C9 F:FMN201 4.8 21.1 1.0 CG F:LEU120 4.9 27.5 1.0 C B:VAL211 5.0 19.6 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of the Class Ie Ribonucleotide Reductase


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 Class Ie Ribonucleotide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca202 b:38.4 occ:1.00 O D:HOH483 3.0 38.2 1.0 O3' H:FMN201 3.1 22.5 1.0 ND2 H:ASN92 3.4 26.4 1.0 O D:HOH442 3.5 27.7 1.0 CD2 H:LEU120 3.6 29.4 1.0 C1' H:FMN201 3.6 23.4 1.0 ND2 D:ASN282 3.7 29.2 1.0 CB H:ASN92 3.8 26.2 1.0 CG2 D:VAL211 3.9 22.0 1.0 CB D:PHE215 3.9 22.3 1.0 C3' H:FMN201 3.9 22.8 1.0 CG H:ASN92 4.1 26.7 1.0 CD1 D:PHE215 4.3 23.0 1.0 O D:VAL211 4.3 21.6 1.0 C2' H:FMN201 4.3 22.9 1.0 CG D:PHE215 4.4 22.6 1.0 OD1 D:ASN282 4.5 30.5 1.0 CG D:ASN282 4.5 29.8 1.0 N10 H:FMN201 4.7 23.4 1.0 CE2 H:PHE95 4.8 28.5 1.0 C9 H:FMN201 4.9 23.8 1.0 CA D:PHE215 4.9 22.3 1.0 CG H:LEU120 4.9 30.1 1.0

G.M.Palowitch, A.K.Boal. Ribonucleotide Reductase To Be Published.