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Calcium in PDB 6ebp: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form

Enzymatic activity of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form

All present enzymatic activity of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form, PDB code: 6ebp 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) 35.18 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.004, 109.417, 83.861, 90.00, 90.06, 90.00
R / Rfree (%) 16.3 / 17.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form (pdb code 6ebp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form, PDB code: 6ebp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6ebp

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Calcium binding site 1 out of 6 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:12.4
occ:1.00
 O A:HOH654 2.4 17.1 1.0
O A:GLY263 2.4 12.0 1.0
O2 A:GOL404 2.5 19.9 1.0
OE2 A:GLU267 2.5 12.5 1.0
OE1 A:GLU267 2.5 12.4 1.0
OD1 A:ASP266 2.6 13.6 1.0
O3 A:GOL404 2.6 20.2 1.0
CD A:GLU267 2.9 12.3 1.0
C A:GLY263 3.5 11.6 1.0
CG A:ASP266 3.5 13.5 1.0
C2 A:GOL404 3.5 20.4 1.0
C3 A:GOL404 3.6 20.3 1.0
OD2 A:ASP266 3.7 13.9 1.0
CA A:GLY263 4.2 11.4 1.0
CG A:GLU267 4.4 12.1 1.0
O A:HOH660 4.4 16.6 1.0
N A:LEU264 4.5 11.5 1.0
CA A:LEU264 4.6 11.6 1.0
O A:HOH682 4.7 15.4 1.0
C1 A:GOL404 4.8 20.6 1.0
N A:GLU267 4.9 11.9 1.0
CB A:ASP266 4.9 13.0 1.0
C A:LEU264 4.9 11.6 1.0
O A:HOH630 5.0 24.7 1.0

Calcium binding site 2 out of 6 in 6ebp

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Calcium binding site 2 out of 6 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:16.4
occ:1.00
 O A:HOH612 2.4 19.1 1.0
O A:HOH628 2.4 19.1 1.0
OD2 A:ASP245 4.3 13.4 1.0
OD1 A:ASP242 4.5 10.9 1.0
O A:HOH696 4.5 22.3 1.0

Calcium binding site 3 out of 6 in 6ebp

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Calcium binding site 3 out of 6 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:20.6
occ:1.00
 O A:HOH679 2.4 22.8 1.0
O A:HOH635 2.4 20.9 1.0
O C:HOH583 2.4 17.8 1.0
O A:HOH573 2.4 13.7 1.0
O A:HOH604 2.5 19.8 1.0
O A:SER128 2.5 11.2 1.0
C A:SER128 3.7 11.0 1.0
OD2 C:ASP245 4.3 13.6 1.0
O A:THR129 4.3 10.7 1.0
OD1 C:ASP242 4.4 12.5 1.0
C A:THR129 4.5 10.7 1.0
CA A:THR129 4.6 11.0 1.0
N A:THR129 4.6 11.0 1.0
O A:HOH648 4.7 24.5 1.0
CA A:SER128 4.7 11.1 1.0
OG A:SER128 4.8 12.1 1.0
O A:CYS131 4.8 10.5 1.0
CE C:LYS246 4.9 10.5 1.0

Calcium binding site 4 out of 6 in 6ebp

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Calcium binding site 4 out of 6 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:11.8
occ:1.00
 O B:GLY263 2.3 13.8 1.0
OE1 B:GLU267 2.4 13.4 1.0
OE2 B:GLU267 2.6 13.5 1.0
OD1 B:ASP266 2.6 15.4 1.0
CD B:GLU267 2.9 13.4 1.0
CG B:ASP266 3.4 15.1 1.0
OD2 B:ASP266 3.5 16.4 1.0
C B:GLY263 3.5 13.2 1.0
CA B:GLY263 4.3 12.8 1.0
CG B:GLU267 4.4 13.2 1.0
N B:LEU264 4.5 13.1 1.0
CA B:LEU264 4.6 13.2 1.0
O B:HOH505 4.6 21.7 1.0
O B:HOH555 4.7 16.4 1.0
N B:GLU267 4.8 13.3 1.0
CB B:ASP266 4.9 14.6 1.0
C B:LEU264 4.9 13.2 1.0

Calcium binding site 5 out of 6 in 6ebp

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Calcium binding site 5 out of 6 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:11.4
occ:1.00
 O C:GLY263 2.3 14.5 1.0
O D:GLY261 2.3 15.1 1.0
O2 C:GOL402 2.4 18.5 1.0
O C:HOH624 2.5 18.5 1.0
OE1 C:GLU267 2.5 13.6 1.0
OD1 C:ASP266 2.6 15.5 1.0
O3 C:GOL402 2.6 19.3 1.0
OE2 C:GLU267 2.7 14.2 1.0
CD C:GLU267 3.0 13.5 1.0
CG C:ASP266 3.4 15.3 1.0
C2 C:GOL402 3.4 19.1 1.0
C D:GLY261 3.4 15.1 1.0
C C:GLY263 3.5 13.6 1.0
C3 C:GOL402 3.5 19.1 1.0
OD2 C:ASP266 3.5 16.6 1.0
CA D:GLY261 3.9 15.6 1.0
CA C:GLY263 4.3 13.4 1.0
N C:LEU264 4.4 13.4 1.0
CG C:GLU267 4.5 13.3 1.0
CA C:LEU264 4.5 13.3 1.0
N D:PHE262 4.6 14.6 1.0
O C:HOH502 4.6 14.7 1.0
C1 C:GOL402 4.7 19.2 1.0
O C:HOH547 4.8 19.2 1.0
CB C:ASP266 4.8 14.8 1.0
N C:GLU267 4.9 13.2 1.0
C C:LEU264 4.9 13.1 1.0

Calcium binding site 6 out of 6 in 6ebp

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Calcium binding site 6 out of 6 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit From Aerococcus Urinae in Activated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:13.3
occ:1.00
 O C:GLY261 2.3 12.4 1.0
O D:GLY263 2.4 15.2 1.0
OE1 D:GLU267 2.4 15.3 1.0
O1 C:GOL403 2.5 21.1 1.0
O D:HOH609 2.5 15.7 1.0
OE2 D:GLU267 2.6 15.6 1.0
OD1 D:ASP266 2.6 17.2 1.0
O2 C:GOL403 2.6 21.0 1.0
CD D:GLU267 2.9 15.4 1.0
OD2 D:ASP266 3.2 18.2 1.0
CG D:ASP266 3.3 16.9 1.0
C2 C:GOL403 3.3 21.3 1.0
C1 C:GOL403 3.4 21.1 1.0
C C:GLY261 3.5 12.7 1.0
C D:GLY263 3.5 14.9 1.0
CA C:GLY261 4.0 12.8 1.0
CA D:GLY263 4.3 14.6 1.0
CG D:GLU267 4.4 15.3 1.0
O D:HOH601 4.5 15.3 1.0
N D:LEU264 4.5 14.8 1.0
O D:HOH502 4.6 17.5 1.0
N C:PHE262 4.6 12.5 1.0
CA D:LEU264 4.6 15.0 1.0
CB D:ASP266 4.7 16.6 1.0
C3 C:GOL403 4.8 21.6 1.0
N D:GLU267 4.8 15.2 1.0
O D:HOH540 4.9 22.0 1.0
CA C:PHE262 5.0 12.7 1.0
C D:LEU264 5.0 14.9 1.0

Reference:

E.J.Blaesi, G.M.Palowitch, K.Hu, A.J.Kim, H.R.Rose, R.Alapati, M.G.Lougee, H.J.Kim, A.T.Taguchi, K.O.Tan, T.N.Laremore, R.G.Griffin, C.Krebs, M.L.Matthews, A.Silakov, J.M.Bollinger Jr., B.D.Allen, A.K.Boal. Metal-Free Class Ie Ribonucleotide Reductase From Pathogens Initiates Catalysis with A Tyrosine-Derived Dihydroxyphenylalanine Radical. Proc. Natl. Acad. Sci. V. 115 10022 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30224458
DOI: 10.1073/PNAS.1811993115
Page generated: Wed Jul 9 13:39:33 2025

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