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Calcium in PDB 7mmr: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound

Enzymatic activity of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound

All present enzymatic activity of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound, PDB code: 7mmr 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) 34.32 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.398, 104.958, 138.067, 90, 100.01, 90
R / Rfree (%) 20.9 / 23.4

Other elements in 7mmr:

The structure of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound also contains other interesting chemical elements:

Copper (Cu) 9 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound (pdb code 7mmr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound, PDB code: 7mmr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 7mmr

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Calcium binding site 1 out of 7 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound


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 Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca406

b:38.8
occ:1.00
 OE2 C:GLU299 2.5 41.5 1.0
CD C:GLU299 3.3 40.0 1.0
OE1 C:GLU299 3.4 40.6 1.0
CG C:GLU299 4.8 38.4 1.0
CG C:PRO298 4.9 32.9 1.0
CB C:PRO298 5.0 32.9 1.0
CD C:PRO298 5.0 33.1 1.0

Calcium binding site 2 out of 7 in 7mmr

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Calcium binding site 2 out of 7 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound


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 Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca407

b:51.5
occ:1.00
 O C:GLY263 2.4 32.0 1.0
OE1 C:GLU267 2.6 33.3 1.0
OD1 C:ASP266 2.9 34.3 1.0
OD2 C:ASP266 3.0 36.6 1.0
OE2 C:GLU267 3.1 35.8 1.0
CD C:GLU267 3.2 33.7 1.0
CG C:ASP266 3.3 33.3 1.0
C C:GLY263 3.6 31.4 1.0
CA C:GLY263 4.3 31.6 1.0
N C:LEU264 4.6 31.0 1.0
CG C:GLU267 4.7 32.7 1.0
CA C:LEU264 4.8 30.3 1.0
CB C:ASP266 4.8 31.4 1.0
O C:HOH537 4.9 34.2 1.0

Calcium binding site 3 out of 7 in 7mmr

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Calcium binding site 3 out of 7 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound


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 Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca408

b:47.7
occ:1.00
 OE2 C:GLU52 2.6 36.4 1.0
O D:HOH546 2.7 22.5 1.0
OE1 C:GLU52 3.0 36.5 1.0
CD C:GLU52 3.1 36.6 1.0
O D:HOH540 3.3 21.9 1.0
NE1 D:TRP41 3.4 17.5 1.0
NE C:ARG121 3.6 20.0 1.0
CD C:ARG121 3.7 19.6 1.0
CD C:PRO51 4.1 24.8 1.0
CD1 D:TRP41 4.2 17.5 1.0
CG C:PRO51 4.3 25.2 1.0
CB C:LEU50 4.3 21.2 1.0
CE2 D:TRP41 4.3 17.6 1.0
CD2 C:LEU50 4.3 21.2 1.0
CG C:GLU52 4.5 35.8 1.0
OD1 D:ASN42 4.6 20.1 1.0
CD1 C:LEU50 4.6 21.4 1.0
CG C:LEU50 4.6 21.2 1.0
CZ2 D:TRP41 4.6 17.6 1.0
OG1 D:THR45 4.7 18.7 1.0
CZ C:ARG121 4.7 19.9 1.0
CG C:ARG121 4.8 19.3 1.0
N C:PRO51 4.9 24.6 1.0

Calcium binding site 4 out of 7 in 7mmr

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Calcium binding site 4 out of 7 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound


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 Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:32.7
occ:1.00
 O3' E:FMN201 3.1 17.4 1.0
ND2 E:ASN92 3.4 21.4 1.0
O A:HOH539 3.5 23.0 1.0
ND2 A:ASN282 3.5 26.2 1.0
CD2 E:LEU120 3.5 23.7 1.0
C1' E:FMN201 3.6 17.6 1.0
CB E:ASN92 3.8 22.1 1.0
CB A:PHE215 3.9 19.1 1.0
C3' E:FMN201 3.9 17.5 1.0
CG2 A:VAL211 4.0 18.4 1.0
CG E:ASN92 4.1 22.1 1.0
O A:VAL211 4.2 18.2 1.0
CD1 A:PHE215 4.3 20.2 1.0
C2' E:FMN201 4.3 17.5 1.0
CG A:PHE215 4.4 19.6 1.0
CG A:ASN282 4.5 25.9 1.0
OD1 A:ASN282 4.5 27.1 1.0
N10 E:FMN201 4.7 17.8 1.0
CE2 E:PHE95 4.8 21.6 1.0
CA A:PHE215 4.8 18.6 1.0
C9 E:FMN201 4.8 17.9 1.0
CG E:LEU120 4.9 23.8 1.0

Calcium binding site 5 out of 7 in 7mmr

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Calcium binding site 5 out of 7 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound


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 Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca202

b:36.8
occ:1.00
 O3' G:FMN201 3.1 19.8 1.0
ND2 G:ASN92 3.2 22.2 1.0
O C:HOH523 3.5 33.4 1.0
CD2 G:LEU120 3.5 25.6 1.0
C1' G:FMN201 3.6 21.2 1.0
ND2 C:ASN282 3.6 27.0 1.0
CB G:ASN92 3.7 22.5 1.0
CG G:ASN92 3.9 22.7 1.0
C3' G:FMN201 3.9 20.2 1.0
CG2 C:VAL211 3.9 18.1 1.0
CB C:PHE215 4.0 20.6 1.0
O C:VAL211 4.3 18.1 1.0
C2' G:FMN201 4.4 20.9 1.0
CD1 C:PHE215 4.4 21.8 1.0
OD1 C:ASN282 4.5 28.0 1.0
CG C:ASN282 4.5 26.5 1.0
CG C:PHE215 4.5 21.3 1.0
N10 G:FMN201 4.7 21.3 1.0
CG G:LEU120 4.8 25.7 1.0
CE2 G:PHE95 4.8 24.9 1.0
C9 G:FMN201 4.9 21.8 1.0
CA C:PHE215 4.9 19.7 1.0

Calcium binding site 6 out of 7 in 7mmr

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Calcium binding site 6 out of 7 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound


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 Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca202

b:32.1
occ:1.00
 O3' F:FMN201 3.1 17.2 1.0
O B:HOH595 3.2 33.1 1.0
O B:HOH562 3.3 24.5 1.0
ND2 F:ASN92 3.4 21.2 1.0
CD2 F:LEU120 3.4 25.0 1.0
ND2 B:ASN282 3.5 27.0 1.0
C1' F:FMN201 3.6 17.8 1.0
CB F:ASN92 3.8 20.7 1.0
C3' F:FMN201 3.9 17.7 1.0
CB B:PHE215 4.0 18.5 1.0
CG F:ASN92 4.0 20.9 1.0
CG2 B:VAL211 4.0 18.6 1.0
O B:VAL211 4.3 17.6 1.0
C2' F:FMN201 4.4 17.9 1.0
CD1 B:PHE215 4.4 19.4 1.0
CG B:ASN282 4.4 26.5 1.0
OD1 B:ASN282 4.5 27.0 1.0
CG B:PHE215 4.5 18.9 1.0
CE2 F:PHE95 4.7 20.8 1.0
N10 F:FMN201 4.7 18.0 1.0
CG F:LEU120 4.8 24.9 1.0
CA B:PHE215 4.9 18.1 1.0
C9 F:FMN201 4.9 18.2 1.0

Calcium binding site 7 out of 7 in 7mmr

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Calcium binding site 7 out of 7 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Oxidized Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca202

b:41.7
occ:1.00
 O3' H:FMN201 3.2 21.2 1.0
O D:HOH532 3.2 28.5 1.0
ND2 H:ASN92 3.3 24.9 1.0
CD2 H:LEU120 3.6 29.0 1.0
C1' H:FMN201 3.6 21.4 1.0
ND2 D:ASN282 3.7 28.7 1.0
CB H:ASN92 3.8 25.3 1.0
CG2 D:VAL211 3.8 20.2 1.0
C3' H:FMN201 3.9 21.1 1.0
CB D:PHE215 4.0 20.5 1.0
CG H:ASN92 4.0 25.1 1.0
O D:VAL211 4.3 19.2 1.0
C2' H:FMN201 4.3 21.3 1.0
OD1 D:ASN282 4.5 30.5 1.0
CD1 D:PHE215 4.5 21.3 1.0
CG D:PHE215 4.5 20.9 1.0
CG D:ASN282 4.6 29.2 1.0
N10 H:FMN201 4.7 21.5 1.0
CE2 H:PHE95 4.8 26.6 1.0
C9 H:FMN201 4.8 21.6 1.0
CA D:PHE215 4.9 20.3 1.0
CG H:LEU120 4.9 29.0 1.0

Reference:

G.M.Palowitch, A.K.Boal. Ribonucleotide Reductase To Be Published.
Page generated: Fri Jul 19 02:04:26 2024

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