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Copper 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:

Calcium (Ca) 7 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 9 binding sites of Copper 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 Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 7mmr

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Copper binding site 1 out of 9 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 Copper with other atoms in the Cu 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
A:Cu401

b:33.5
occ:0.80
 ND1 A:HIS213 2.1 18.2 1.0
O A:HOH597 2.3 14.6 1.0
O A:HOH553 2.3 33.6 1.0
CG A:HIS213 3.0 18.3 1.0
CG2 A:VAL116 3.1 17.1 1.0
CE1 A:HIS213 3.1 18.2 1.0
CB A:HIS213 3.3 18.4 1.0
CB A:PRO176 3.7 24.3 1.0
NZ A:LYS210 4.0 21.1 1.0
CG A:PRO176 4.1 24.2 1.0
CG A:LYS210 4.2 19.5 1.0
CD2 A:HIS213 4.2 18.2 1.0
NE2 A:HIS213 4.2 18.3 1.0
OD2 A:ASP93 4.3 21.7 1.0
CA A:LYS210 4.4 18.5 1.0
CB A:VAL116 4.5 16.8 1.0
CG A:GLN88 4.6 20.8 1.0
CB A:LYS210 4.7 19.2 1.0
CD A:PRO176 4.7 24.2 1.0
CD A:LYS210 4.7 20.1 1.0
CA A:PRO176 4.7 24.0 1.0
CA A:HIS213 4.8 18.7 1.0
CG1 A:VAL116 4.8 17.0 1.0
O A:HOH582 4.9 40.4 1.0
CE A:LYS210 5.0 20.5 1.0

Copper binding site 2 out of 9 in 7mmr

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Copper binding site 2 out of 9 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 Copper with other atoms in the Cu 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
A:Cu402

b:56.5
occ:0.57
 OG1 A:THR75 2.5 27.0 1.0
SG A:CYS131 2.8 43.6 1.0
OE1 A:GLN135 2.8 31.5 1.0
CB A:GLN135 2.8 37.0 1.0
CD A:GLN135 2.9 34.2 1.0
CB A:CYS131 3.1 41.1 1.0
CG A:GLN135 3.2 36.0 1.0
O A:HOH609 3.3 40.9 1.0
CB A:THR75 3.5 26.9 1.0
NE2 A:GLN135 3.5 34.4 1.0
CG2 A:THR75 3.6 27.2 1.0
CA A:CYS131 3.9 40.2 1.0
CZ2 A:TRP63 3.9 40.2 1.0
CH2 A:TRP63 4.0 40.1 1.0
O A:GLN71 4.1 30.4 1.0
CA A:GLN135 4.1 37.9 1.0
C A:GLN135 4.3 37.0 1.0
O A:GLN135 4.6 36.9 1.0
N A:THR132 4.7 40.1 1.0
C A:GLN71 4.7 31.3 1.0
N A:ILE136 4.7 36.1 1.0
CA A:THR75 4.8 26.7 1.0
C A:CYS131 4.8 39.9 1.0
N A:CYS131 5.0 39.7 1.0

Copper binding site 3 out of 9 in 7mmr

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Copper binding site 3 out of 9 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 Copper with other atoms in the Cu 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
B:Cu401

b:33.6
occ:0.88
 ND1 B:HIS213 2.0 17.8 1.0
O B:HOH586 2.3 11.9 1.0
O B:HOH550 2.5 33.0 1.0
CG B:HIS213 2.9 17.7 1.0
CE1 B:HIS213 3.0 17.7 1.0
CG2 B:VAL116 3.1 16.9 1.0
CB B:HIS213 3.2 17.8 1.0
CB B:PRO176 3.7 25.6 1.0
NZ B:LYS210 4.0 21.7 1.0
CD2 B:HIS213 4.1 17.6 1.0
NE2 B:HIS213 4.1 17.4 1.0
CG B:LYS210 4.2 20.4 1.0
CG B:PRO176 4.2 25.5 1.0
CA B:LYS210 4.4 19.5 1.0
OD2 B:ASP93 4.4 23.9 1.0
CB B:VAL116 4.6 16.8 1.0
CG B:GLN88 4.6 21.7 1.0
CD B:LYS210 4.6 21.1 1.0
CB B:LYS210 4.7 20.0 1.0
CD B:PRO176 4.7 25.4 1.0
CA B:HIS213 4.7 18.1 1.0
CA B:PRO176 4.7 26.0 1.0
CG1 B:VAL116 4.9 16.9 1.0
CE B:LYS210 5.0 21.3 1.0
O B:HOH529 5.0 36.8 1.0

Copper binding site 4 out of 9 in 7mmr

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Copper binding site 4 out of 9 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 Copper with other atoms in the Cu 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
B:Cu402

b:64.5
occ:0.80
 OG1 B:THR75 2.5 30.0 1.0
SG B:CYS131 2.8 43.1 1.0
OE1 B:GLN135 2.9 33.5 1.0
CD B:GLN135 2.9 36.1 1.0
CB B:GLN135 2.9 37.8 1.0
CB B:CYS131 3.1 39.5 1.0
CG B:GLN135 3.3 37.3 1.0
NE2 B:GLN135 3.3 36.6 1.0
O B:HOH597 3.4 52.7 1.0
CB B:THR75 3.6 29.4 1.0
CG2 B:THR75 3.7 30.1 1.0
CZ2 B:TRP63 3.8 40.0 1.0
CA B:CYS131 4.0 39.0 1.0
CH2 B:TRP63 4.0 39.9 1.0
O B:GLN71 4.1 36.4 1.0
CA B:GLN135 4.2 38.0 1.0
C B:GLN135 4.5 37.0 1.0
C B:GLN71 4.6 36.4 1.0
O B:GLN135 4.7 37.3 1.0
O B:HOH512 4.8 24.7 1.0
N B:THR132 4.8 39.1 1.0
CA B:THR75 4.9 29.0 1.0
O3 B:GOL404 4.9 48.8 0.9
CB B:GLN71 4.9 37.5 1.0
N B:ILE136 4.9 34.7 1.0
C B:CYS131 5.0 38.9 1.0

Copper binding site 5 out of 9 in 7mmr

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Copper binding site 5 out of 9 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 Copper with other atoms in the Cu 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
C:Cu401

b:31.2
occ:0.89
 ND1 C:HIS213 2.1 19.2 1.0
O C:HOH594 2.3 10.4 1.0
O C:HOH571 2.4 31.3 1.0
CG C:HIS213 3.0 18.7 1.0
CG2 C:VAL116 3.1 16.4 1.0
CE1 C:HIS213 3.1 19.0 1.0
CB C:HIS213 3.3 18.6 1.0
CB C:PRO176 3.7 24.1 1.0
NZ C:LYS210 4.1 20.0 1.0
CD2 C:HIS213 4.2 18.9 1.0
NE2 C:HIS213 4.2 18.5 1.0
CG C:LYS210 4.2 19.3 1.0
CG C:PRO176 4.3 23.9 1.0
CA C:LYS210 4.3 18.4 1.0
OD2 C:ASP93 4.4 21.0 1.0
CB C:VAL116 4.5 16.3 1.0
CG C:GLN88 4.5 20.7 1.0
CD C:LYS210 4.6 19.7 1.0
CB C:LYS210 4.6 19.0 1.0
CG1 C:VAL116 4.7 16.5 1.0
CD C:PRO176 4.8 23.9 1.0
CA C:PRO176 4.8 23.9 1.0
CA C:HIS213 4.8 18.8 1.0
O C:HOH570 5.0 34.1 1.0
CE C:LYS210 5.0 19.8 1.0
CE1 C:HIS119 5.0 16.8 1.0

Copper binding site 6 out of 9 in 7mmr

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Copper binding site 6 out of 9 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 Copper with other atoms in the Cu 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
C:Cu402

b:33.9
occ:0.77
 ND1 C:HIS256 1.9 24.9 1.0
CE1 C:HIS256 2.8 25.0 1.0
CG C:HIS256 3.0 25.0 1.0
CB C:HIS256 3.3 24.6 1.0
O C:HOH549 3.8 20.9 1.0
CB C:ALA265 3.9 28.6 1.0
CA C:HIS256 3.9 24.3 1.0
NE2 C:HIS256 4.0 24.8 1.0
CD2 C:HIS256 4.1 24.5 1.0
O C:HOH537 4.1 34.2 1.0
CD1 C:ILE269 4.9 24.6 1.0
C C:HIS256 5.0 24.6 1.0
O C:HIS256 5.0 25.4 1.0
N C:HIS256 5.0 23.2 1.0

Copper binding site 7 out of 9 in 7mmr

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Copper binding site 7 out of 9 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 Copper with other atoms in the Cu 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
C:Cu405

b:56.6
occ:0.71
 OE1 C:GLN135 2.5 29.7 1.0
CD C:GLN135 2.7 32.6 1.0
SG C:CYS131 2.7 35.5 1.0
OG1 C:THR75 2.8 24.6 1.0
CB C:GLN135 3.0 33.0 1.0
CB C:CYS131 3.1 33.6 1.0
O C:HOH596 3.1 24.9 1.0
NE2 C:GLN135 3.2 33.2 1.0
CG C:GLN135 3.3 32.9 1.0
CZ2 C:TRP63 3.5 27.6 1.0
CA C:CYS131 3.7 33.2 1.0
CH2 C:TRP63 3.9 27.6 1.0
CB C:THR75 3.9 23.9 1.0
CG2 C:THR75 4.1 24.5 1.0
O C:GLN71 4.3 26.9 1.0
CA C:GLN135 4.4 32.5 1.0
N C:THR132 4.6 34.4 1.0
C C:GLN135 4.6 31.1 1.0
O2 C:TRS404 4.6 50.0 0.9
N C:CYS131 4.7 32.5 1.0
C C:CYS131 4.7 33.6 1.0
CE2 C:TRP63 4.7 27.6 1.0
C C:GLN71 4.8 27.5 1.0
CB C:GLN71 4.9 27.7 1.0
O C:GLN135 5.0 30.1 1.0

Copper binding site 8 out of 9 in 7mmr

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Copper binding site 8 out of 9 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 Copper with other atoms in the Cu binding site number 8 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
D:Cu401

b:38.2
occ:0.85
 ND1 D:HIS213 2.2 18.6 1.0
O D:HOH597 2.2 14.7 1.0
O D:HOH563 2.4 38.1 1.0
CG D:HIS213 3.1 18.8 1.0
CG2 D:VAL116 3.2 18.1 1.0
CE1 D:HIS213 3.2 18.7 1.0
CB D:HIS213 3.3 19.3 1.0
CB D:PRO176 3.6 27.6 1.0
NZ D:LYS210 4.1 24.1 1.0
CG D:PRO176 4.1 27.6 1.0
CG D:LYS210 4.2 22.5 1.0
CD2 D:HIS213 4.3 18.7 1.0
OD2 D:ASP93 4.3 23.9 1.0
NE2 D:HIS213 4.3 18.7 1.0
CD D:LYS210 4.4 23.4 1.0
CA D:LYS210 4.4 21.3 1.0
CG D:GLN88 4.5 22.9 1.0
CB D:VAL116 4.6 17.8 1.0
CB D:LYS210 4.6 22.0 1.0
CD D:PRO176 4.6 27.6 1.0
CA D:PRO176 4.7 27.8 1.0
CG1 D:VAL116 4.8 18.1 1.0
O D:HOH548 4.8 40.9 1.0
CE D:LYS210 4.9 23.7 1.0
CA D:HIS213 4.9 19.9 1.0

Copper binding site 9 out of 9 in 7mmr

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Copper binding site 9 out of 9 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 Copper with other atoms in the Cu binding site number 9 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
D:Cu402

b:57.0
occ:0.70
 OG1 D:THR75 2.6 28.5 1.0
SG D:CYS131 2.7 42.1 1.0
CD D:GLN135 2.8 34.2 1.0
OE1 D:GLN135 2.8 31.0 1.0
CB D:GLN135 3.0 36.5 1.0
CB D:CYS131 3.1 38.6 1.0
NE2 D:GLN135 3.2 34.5 1.0
CG D:GLN135 3.2 35.6 1.0
O D:HOH602 3.5 55.0 1.0
CB D:THR75 3.6 28.7 1.0
CG2 D:THR75 3.7 28.8 1.0
CZ2 D:TRP63 3.8 36.0 1.0
CA D:CYS131 3.9 37.6 1.0
CH2 D:TRP63 4.0 36.1 1.0
O D:GLN71 4.1 32.7 1.0
CA D:GLN135 4.3 37.0 1.0
O1 D:GOL404 4.4 47.0 0.9
C D:GLN135 4.5 35.6 1.0
C D:GLN71 4.7 33.4 1.0
O D:HOH519 4.7 31.9 1.0
N D:THR132 4.8 37.2 1.0
O D:GLN135 4.8 35.6 1.0
CA D:THR75 4.9 28.1 1.0
N D:ILE136 4.9 34.3 1.0
C D:CYS131 4.9 37.3 1.0
N D:CYS131 5.0 36.2 1.0
CB D:GLN71 5.0 34.3 1.0

Reference:

G.M.Palowitch, A.K.Boal. Ribonucleotide Reductase To Be Published.
Page generated: Wed Jul 31 08:37:43 2024

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