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Zinc in PDB 4u3e: Anaerobic Ribonucleotide Reductase

Enzymatic activity of Anaerobic Ribonucleotide Reductase

All present enzymatic activity of Anaerobic Ribonucleotide Reductase:
1.17.4.2;

Protein crystallography data

The structure of Anaerobic Ribonucleotide Reductase, PDB code: 4u3e was solved by M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.38 / 1.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.313, 98.768, 86.556, 90.00, 111.72, 90.00
R / Rfree (%) 17.1 / 20

Other elements in 4u3e:

The structure of Anaerobic Ribonucleotide Reductase also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Anaerobic Ribonucleotide Reductase (pdb code 4u3e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Anaerobic Ribonucleotide Reductase, PDB code: 4u3e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4u3e

Go back to Zinc Binding Sites List in 4u3e
Zinc binding site 1 out of 2 in the Anaerobic Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Anaerobic Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:27.5
occ:1.00
ND1 A:HIS598 2.1 24.1 1.0
SG A:CYS605 2.3 26.4 1.0
SG A:CYS594 2.3 23.6 1.0
SG A:CYS608 2.3 29.4 1.0
CG A:HIS598 3.1 25.5 1.0
CE1 A:HIS598 3.1 25.5 1.0
CB A:CYS605 3.2 27.0 1.0
CB A:HIS598 3.3 24.4 1.0
CB A:CYS608 3.5 32.5 1.0
CB A:CYS594 3.5 23.7 1.0
N A:CYS608 3.8 34.3 1.0
CA A:CYS608 4.2 32.4 1.0
NE2 A:HIS598 4.2 26.5 1.0
CD2 A:HIS598 4.2 26.6 1.0
CB A:VAL607 4.4 30.7 1.0
CB A:ASP596 4.4 33.9 1.0
N A:HIS598 4.5 18.7 1.0
CA A:HIS598 4.5 22.1 1.0
CA A:CYS605 4.6 29.7 1.0
C A:CYS608 4.8 34.2 1.0
C A:VAL607 4.8 37.0 1.0
CA A:CYS594 4.8 24.1 1.0
OD2 A:ASP596 4.9 45.1 1.0
N A:GLY609 4.9 32.1 1.0
CE2 A:PHE600 4.9 26.8 1.0
CG1 A:VAL607 4.9 28.4 1.0

Zinc binding site 2 out of 2 in 4u3e

Go back to Zinc Binding Sites List in 4u3e
Zinc binding site 2 out of 2 in the Anaerobic Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Anaerobic Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:29.0
occ:1.00
ND1 B:HIS598 2.2 28.4 1.0
SG B:CYS605 2.2 29.8 1.0
SG B:CYS594 2.3 25.1 1.0
SG B:CYS608 2.3 32.6 1.0
CE1 B:HIS598 3.1 28.3 1.0
CB B:CYS605 3.1 26.0 1.0
CG B:HIS598 3.1 23.9 1.0
CB B:HIS598 3.4 22.9 1.0
CB B:CYS594 3.4 26.6 1.0
CB B:CYS608 3.5 31.5 1.0
N B:CYS608 3.7 33.7 1.0
CA B:CYS608 4.2 33.5 1.0
NE2 B:HIS598 4.2 28.4 1.0
CD2 B:HIS598 4.3 27.1 1.0
CB B:VAL607 4.3 37.2 1.0
N B:HIS598 4.5 22.8 1.0
CB B:ASP596 4.6 33.4 1.0
CA B:HIS598 4.6 22.0 1.0
CA B:CYS605 4.6 30.3 1.0
C B:VAL607 4.7 37.2 1.0
C B:CYS608 4.8 35.0 1.0
CA B:CYS594 4.8 24.5 1.0
CE2 B:PHE600 4.8 24.1 1.0
CG1 B:VAL607 4.8 37.5 1.0
N B:GLY609 4.8 31.2 1.0
CA B:VAL607 4.9 36.3 1.0
CB B:LYS610 4.9 33.6 1.0
N B:LYS610 5.0 33.1 1.0
N B:VAL607 5.0 36.5 1.0

Reference:

Y.Wei, M.A.Funk, L.A.Rosado, J.Baek, C.L.Drennan, J.Stubbe. The Class III Ribonucleotide Reductase From Neisseria Bacilliformis Can Utilize Thioredoxin As A Reductant. Proc.Natl.Acad.Sci.Usa V. 111 E3756 2014.
ISSN: ESSN 1091-6490
PubMed: 25157154
DOI: 10.1073/PNAS.1414396111
Page generated: Wed Dec 16 05:47:47 2020

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