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

Enzymatic activity of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone 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 Semiquinone 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 Semiquinone Form with Cu(I) Bound, PDB code: 7mms 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) 49.25 / 1.91
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.354, 104.787, 137.412, 90, 100.29, 90
R / Rfree (%) 20.1 / 22.6

Other elements in 7mms:

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

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

Copper binding site 1 out of 4 in 7mms

Go back to Copper Binding Sites List in 7mms
Copper binding site 1 out of 4 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone 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 Semiquinone Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:36.6
occ:0.55
 O A:HOH545 1.9 27.9 1.0
ND1 A:HIS213 2.2 12.1 1.0
O A:HOH590 2.3 13.2 1.0
CG2 A:VAL116 3.1 9.9 1.0
CG A:HIS213 3.1 12.1 1.0
CE1 A:HIS213 3.3 11.9 1.0
CB A:HIS213 3.3 12.1 1.0
CB A:PRO176 3.6 16.1 1.0
NZ A:LYS210 4.0 13.5 1.0
CG A:PRO176 4.0 16.0 1.0
OD2 A:ASP93 4.2 14.2 1.0
CG A:LYS210 4.3 13.0 1.0
CD2 A:HIS213 4.3 11.9 1.0
NE2 A:HIS213 4.4 11.9 1.0
CD A:PRO176 4.5 16.1 1.0
CG A:GLN88 4.5 13.3 1.0
CA A:LYS210 4.5 12.6 1.0
CB A:VAL116 4.5 9.8 1.0
CD A:LYS210 4.6 13.3 1.0
CA A:PRO176 4.6 16.2 1.0
CB A:LYS210 4.8 12.9 1.0
CA A:HIS213 4.8 12.3 1.0
CG1 A:VAL116 4.9 10.0 1.0
CE A:LYS210 4.9 13.3 1.0
N A:PRO176 5.0 16.2 1.0
O A:HOH528 5.0 40.5 1.0

Copper binding site 2 out of 4 in 7mms

Go back to Copper Binding Sites List in 7mms
Copper binding site 2 out of 4 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone 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 Semiquinone Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:36.5
occ:0.61
 ND1 B:HIS213 2.1 12.1 1.0
O B:HOH555 2.4 30.2 1.0
O B:HOH578 2.4 9.7 1.0
CG B:HIS213 3.0 12.1 1.0
CG2 B:VAL116 3.1 10.3 1.0
CE1 B:HIS213 3.1 11.9 1.0
CB B:HIS213 3.2 12.4 1.0
CB B:PRO176 3.7 16.7 1.0
CG B:PRO176 4.1 16.7 1.0
NZ B:LYS210 4.1 13.8 1.0
CD2 B:HIS213 4.2 11.9 1.0
NE2 B:HIS213 4.2 11.9 1.0
OD2 B:ASP93 4.2 15.7 1.0
CG B:LYS210 4.4 13.4 1.0
CG B:GLN88 4.5 14.0 1.0
CB B:VAL116 4.5 10.2 1.0
CA B:LYS210 4.5 12.8 1.0
CD B:PRO176 4.6 16.6 1.0
CD B:LYS210 4.7 13.6 1.0
CA B:PRO176 4.7 16.8 1.0
CA B:HIS213 4.8 12.7 1.0
O B:HOH582 4.8 34.3 1.0
CB B:LYS210 4.8 13.2 1.0
CG1 B:VAL116 4.9 10.3 1.0
OD1 B:ASP93 4.9 15.3 1.0

Copper binding site 3 out of 4 in 7mms

Go back to Copper Binding Sites List in 7mms
Copper binding site 3 out of 4 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone 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 Semiquinone Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:42.0
occ:0.70
 ND1 C:HIS213 2.2 13.4 1.0
O C:HOH598 2.3 12.9 1.0
O C:HOH527 2.7 33.4 1.0
CG C:HIS213 3.1 13.2 1.0
CG2 C:VAL116 3.1 10.9 1.0
CE1 C:HIS213 3.2 13.3 1.0
CB C:HIS213 3.3 13.2 1.0
CB C:PRO176 3.6 15.2 1.0
CG C:PRO176 4.0 15.3 1.0
NZ C:LYS210 4.1 14.8 1.0
CD2 C:HIS213 4.2 13.2 1.0
OD2 C:ASP93 4.3 13.9 1.0
NE2 C:HIS213 4.3 13.0 1.0
CG C:LYS210 4.4 14.5 1.0
CG C:GLN88 4.5 12.3 1.0
CB C:VAL116 4.5 10.7 1.0
CD C:PRO176 4.5 15.1 1.0
CA C:LYS210 4.6 13.9 1.0
CD C:LYS210 4.7 14.8 1.0
CA C:PRO176 4.7 15.0 1.0
CG1 C:VAL116 4.7 10.9 1.0
CB C:LYS210 4.9 14.4 1.0
CA C:HIS213 4.9 13.2 1.0
O C:HOH575 4.9 29.9 1.0
CE C:LYS210 5.0 14.7 1.0
OD1 C:ASP93 5.0 13.9 1.0

Copper binding site 4 out of 4 in 7mms

Go back to Copper Binding Sites List in 7mms
Copper binding site 4 out of 4 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone 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 Semiquinone Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu403

b:42.0
occ:0.74
 ND1 C:HIS256 1.9 21.7 1.0
CE1 C:HIS256 2.9 21.5 1.0
CG C:HIS256 2.9 21.7 1.0
CB C:HIS256 3.3 20.8 1.0
O C:HOH567 3.8 22.8 1.0
CB C:ALA265 3.8 24.0 1.0
CA C:HIS256 3.8 20.2 1.0
NE2 C:HIS256 4.0 21.8 1.0
CD2 C:HIS256 4.0 22.0 1.0
O C:HOH528 4.4 31.4 1.0
C C:HIS256 4.9 20.5 1.0
N C:HIS256 4.9 18.8 1.0
O C:HIS256 4.9 21.0 1.0
CD1 C:ILE269 4.9 19.2 1.0

Reference:

G.M.Palowitch, A.K.Boal. Ribonucleotide Reductase To Be Published.
Page generated: Wed Jul 31 08:37:40 2024

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