Atomistry » Copper » PDB 7ev9-7o3c » 7mmr
Atomistry »
  Copper »
    PDB 7ev9-7o3c »
      7mmr »

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

Go back to Copper Binding Sites List in 7mmr
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

Go back to Copper Binding Sites List in 7mmr
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

Go back to Copper Binding Sites List in 7mmr
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

Go back to Copper Binding Sites List in 7mmr
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

Go back to Copper Binding Sites List in 7mmr
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

Go back to Copper Binding Sites List in 7mmr
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

Go back to Copper Binding Sites List in 7mmr
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

Go back to Copper Binding Sites List in 7mmr
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

Go back to Copper Binding Sites List in 7mmr
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy