Chlorine in PDB 8vhu: Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit

Enzymatic activity of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit

All present enzymatic activity of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit, PDB code: 8vhu was solved by M.A.Funk, C.M.Zimanyi, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.15 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.214, 111.207, 209.701, 90, 90, 90
R / Rfree (%) 15.9 / 19.2

Other elements in 8vhu:

The structure of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit also contains other interesting chemical elements:

Sodium (Na) 1 atom
Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit (pdb code 8vhu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit, PDB code: 8vhu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8vhu

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Chlorine binding site 1 out of 6 in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1406

b:41.9
occ:1.00
 O A:HOH1876 3.0 62.4 1.0
O A:HOH1699 3.2 48.9 1.0
N A:ARG331 3.2 32.3 1.0
O A:HOH2039 3.3 63.4 1.0
NE2 A:GLN286 3.3 36.0 1.0
O A:ARG329 3.8 37.8 1.0
CA A:VAL330 3.9 32.1 1.0
CD2 A:HIS332 3.9 47.5 1.0
CG A:ARG331 3.9 50.2 1.0
C A:VAL330 4.0 33.5 1.0
CB A:ARG331 4.0 40.7 1.0
CA A:ARG331 4.2 34.1 1.0
CD A:GLN286 4.2 42.6 1.0
OE1 A:GLN286 4.3 37.8 1.0
C A:ARG329 4.3 40.4 1.0
N A:VAL330 4.4 35.2 1.0
NE2 A:HIS332 4.4 51.0 1.0
N A:HIS332 4.5 29.2 1.0
CD A:ARG331 4.6 60.9 1.0
NE A:ARG331 4.7 66.7 1.0
CG A:HIS332 4.8 38.7 1.0
OE1 A:GLU326 4.8 96.2 1.0
C A:ARG331 4.8 40.5 1.0
NZ A:LYS283 4.8 45.0 1.0

Chlorine binding site 2 out of 6 in 8vhu

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Chlorine binding site 2 out of 6 in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1407

b:105.3
occ:1.00
 O A:HOH1927 3.2 42.9 1.0
N A:THR624 3.2 55.5 1.0
N A:SER625 3.3 47.0 1.0
N A:GLU623 3.5 57.9 0.5
CB A:THR624 3.5 56.8 1.0
CA A:SER622 3.5 60.0 0.5
CA A:THR624 3.7 53.9 1.0
CA A:SER622 3.7 61.0 0.5
N A:GLU623 3.7 59.0 0.5
O A:HOH1885 3.8 55.7 1.0
C A:SER622 3.8 62.0 0.5
C A:SER622 3.8 60.4 0.5
O A:HOH2050 4.0 53.4 1.0
C A:THR624 4.0 50.7 1.0
O A:HOH1502 4.0 43.6 1.0
OG A:SER625 4.0 67.2 1.0
CB A:SER625 4.0 58.7 1.0
O A:HOH1772 4.1 51.0 1.0
OG1 A:THR624 4.2 61.0 1.0
CA A:SER625 4.3 52.3 1.0
C A:GLU623 4.3 59.3 0.5
C A:GLU623 4.3 58.9 0.5
CB A:SER622 4.3 72.2 0.5
O A:PRO621 4.4 41.4 0.5
O A:SER622 4.4 68.7 0.5
CA A:GLU623 4.4 61.8 0.5
N A:SER622 4.5 50.4 0.5
OG A:SER622 4.5 75.8 0.5
CB A:SER622 4.5 70.7 0.5
CA A:GLU623 4.6 62.7 0.5
CG2 A:THR624 4.6 54.5 1.0
O A:SER622 4.8 65.1 0.5
N A:SER622 4.8 52.7 0.5
OG A:SER622 4.9 74.8 0.5

Chlorine binding site 3 out of 6 in 8vhu

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Chlorine binding site 3 out of 6 in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1408

b:54.5
occ:1.00
 O A:HOH2168 2.8 54.6 1.0
O A:HOH1585 3.1 70.1 1.0
N A:LYS585 3.2 39.8 1.0
CB A:LYS585 3.8 62.6 1.0
CD A:LYS584 3.8 43.6 1.0
O A:HOH1880 3.8 79.4 1.0
CA A:LYS584 3.9 38.3 1.0
O A:HOH2139 4.0 65.5 1.0
C A:LYS584 4.1 41.4 1.0
CA A:LYS585 4.1 48.0 1.0
CG A:LYS585 4.1 79.7 1.0
O A:TYR583 4.2 37.2 1.0
CG A:LYS584 4.5 44.4 1.0
O A:HOH2190 4.7 78.9 1.0
CE A:LYS584 4.7 37.6 1.0
CB A:LYS584 4.8 41.8 1.0
N A:LYS584 4.9 38.5 1.0
O A:HOH1780 4.9 32.8 1.0
C A:TYR583 4.9 36.8 1.0

Chlorine binding site 4 out of 6 in 8vhu

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Chlorine binding site 4 out of 6 in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1403

b:42.3
occ:1.00
 O B:HOH1799 3.0 54.9 1.0
N B:ARG331 3.2 35.0 1.0
NE2 B:GLN286 3.4 32.8 1.0
O B:ARG329 3.8 39.8 1.0
CA B:VAL330 3.9 33.5 1.0
CG B:ARG331 3.9 42.0 1.0
CB B:ARG331 4.0 39.0 1.0
C B:VAL330 4.0 39.1 1.0
CD2 B:HIS332 4.1 48.7 1.0
CA B:ARG331 4.2 38.2 1.0
C B:ARG329 4.3 37.0 1.0
OE1 B:GLN286 4.3 31.5 1.0
CD B:GLN286 4.3 37.5 1.0
N B:VAL330 4.4 36.2 1.0
NE2 B:HIS332 4.5 56.7 1.0
N B:HIS332 4.6 32.5 1.0
CD B:ARG331 4.6 49.2 1.0
NE B:ARG331 4.7 54.1 1.0
NZ B:LYS283 4.8 52.5 1.0
OE1 B:GLU326 4.8 98.6 1.0
C B:ARG331 4.9 38.3 1.0
CG B:HIS332 4.9 43.6 1.0

Chlorine binding site 5 out of 6 in 8vhu

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Chlorine binding site 5 out of 6 in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1404

b:76.6
occ:1.00
 N B:SER625 3.3 55.1 1.0
N B:THR624 3.4 58.1 1.0
O B:HOH1817 3.4 46.7 1.0
OG B:SER625 3.4 68.2 1.0
CB B:THR624 3.6 61.0 1.0
N B:GLU623 3.7 65.4 1.0
CA B:SER622 3.7 63.2 1.0
CA B:THR624 3.9 52.5 1.0
C B:SER622 4.0 74.4 1.0
CB B:SER625 4.0 62.0 1.0
OG1 B:THR624 4.1 75.5 1.0
C B:THR624 4.1 51.1 1.0
O B:HOH2094 4.2 48.4 1.0
O B:PRO621 4.3 48.0 1.0
CA B:SER625 4.3 54.3 1.0
O B:HOH1552 4.3 54.8 1.0
CB B:SER622 4.4 72.0 1.0
C B:GLU623 4.5 68.7 1.0
OG B:SER622 4.6 83.9 1.0
O B:HOH1725 4.6 55.4 1.0
CA B:GLU623 4.6 71.5 1.0
N B:SER622 4.7 41.4 1.0
CG2 B:THR624 4.8 56.0 1.0
C B:PRO621 4.9 33.2 1.0
O B:SER622 4.9 91.2 1.0

Chlorine binding site 6 out of 6 in 8vhu

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Chlorine binding site 6 out of 6 in the Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Datp Bound E. Coli Class Ia Ribonucleotide Reductase Alpha Construct Fused with the C-Terminal Tail of E. Coli Class Ia Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1405

b:65.3
occ:1.00
 O B:HOH2082 3.1 56.4 1.0
N B:LYS585 3.3 45.7 1.0
CB B:LYS585 3.8 57.1 1.0
CD B:LYS584 4.0 40.3 1.0
CA B:LYS584 4.0 38.6 1.0
CA B:LYS585 4.1 47.4 1.0
C B:LYS584 4.1 41.8 1.0
CD B:LYS585 4.1 80.7 1.0
O B:TYR583 4.2 39.5 1.0
CG B:LYS585 4.4 74.5 1.0
O B:HOH2076 4.6 61.2 1.0
CG B:LYS584 4.7 42.1 1.0
O B:HOH2129 4.8 71.4 1.0
CE B:LYS584 4.8 37.8 1.0
CB B:LYS584 4.9 38.6 1.0
N B:LYS584 5.0 38.6 1.0
C B:TYR583 5.0 39.2 1.0

Reference:

M.A.Funk, C.M.Zimanyi, G.A.Andree, A.E.Hamilos, C.L.Drennan. How Atp and Datp Act As Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39164005
DOI: 10.1021/ACS.BIOCHEM.4C00329
Page generated: Sat Sep 28 19:34:57 2024

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