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Cobalt in PDB 5cki: Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals)

Protein crystallography data

The structure of Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals), PDB code: 5cki was solved by A.Ponce-Salvatierra, C.Hoebartner, V.Pena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.93 / 2.99
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.845, 80.845, 55.814, 90.00, 90.00, 90.00
R / Rfree (%) 25.6 / 31.1

Other elements in 5cki:

The structure of Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals) (pdb code 5cki). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals), PDB code: 5cki:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 5cki

Go back to Cobalt Binding Sites List in 5cki
Cobalt binding site 1 out of 4 in the Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co101

b:0.2
occ:1.00
N7 D:A-1 2.2 0.1 1.0
N6 D:A-1 2.8 0.3 1.0
C5 D:A-1 3.0 0.8 1.0
C6 D:A-1 3.2 0.3 1.0
C8 D:A-1 3.4 0.3 1.0
O6 D:G1 3.5 0.2 1.0
N6 Y:DA15 3.7 0.2 1.0
C6 D:G1 4.0 0.4 1.0
C4 D:A-1 4.3 88.2 1.0
OP2 D:U-2 4.3 0.9 1.0
N1 D:G1 4.4 0.2 1.0
N9 D:A-1 4.4 92.0 1.0
OP2 D:A-1 4.5 0.1 1.0
N1 D:A-1 4.6 0.9 1.0
C5 D:G1 4.8 0.5 1.0
O4 Y:DT29 4.8 0.1 1.0
C6 Y:DA15 4.9 0.1 1.0

Cobalt binding site 2 out of 4 in 5cki

Go back to Cobalt Binding Sites List in 5cki
Cobalt binding site 2 out of 4 in the Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co102

b:1.0
occ:1.00
O6 D:G9 2.8 0.1 1.0
O4 D:U8 3.4 0.8 1.0
C6 D:G9 3.8 0.6 1.0
C4 D:U8 4.0 0.7 1.0
N7 D:G9 4.1 0.6 1.0
C5 D:G9 4.3 0.3 1.0
C5 D:U8 4.4 0.8 1.0
N3 D:U8 4.9 0.4 1.0
N1 D:G9 4.9 1.0 1.0

Cobalt binding site 3 out of 4 in 5cki

Go back to Cobalt Binding Sites List in 5cki
Cobalt binding site 3 out of 4 in the Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Co101

b:1.0
occ:1.00
N7 Y:DA39 2.2 0.8 1.0
C8 Y:DA39 2.8 0.6 1.0
C5 Y:DA39 3.4 95.3 1.0
OP2 Y:DA39 3.6 0.1 1.0
N6 Y:DA39 4.1 0.5 1.0
OP2 Y:DC16 4.1 0.7 1.0
N9 Y:DA39 4.1 0.5 1.0
C6 Y:DA39 4.2 97.0 1.0
C4 Y:DA39 4.4 96.2 1.0
O3' Y:DA15 4.5 98.8 1.0
C1' Y:DA15 4.9 93.9 1.0
P Y:DC16 4.9 1.0 1.0
P Y:DA39 5.0 0.3 1.0

Cobalt binding site 4 out of 4 in 5cki

Go back to Cobalt Binding Sites List in 5cki
Cobalt binding site 4 out of 4 in the Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of 9DB1* Deoxyribozyme (Cobalt Hexammine Soaked Crystals) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Co102

b:0.6
occ:1.00
OP2 Y:DG25 2.2 0.9 1.0
N7 Y:DG8 2.7 0.0 1.0
O6 Y:DG8 3.1 0.8 1.0
C5 Y:DG8 3.4 0.2 1.0
C6 Y:DG8 3.6 0.8 1.0
P Y:DG25 3.6 0.3 1.0
C2' Y:DT7 3.8 0.7 1.0
C8 Y:DG8 3.8 0.2 1.0
O5' Y:DG25 4.0 0.1 1.0
C6 Y:DT7 4.4 1.0 1.0
OP1 Y:DG25 4.5 0.4 1.0
O3' Y:DG24 4.7 0.2 1.0
C4 Y:DG8 4.7 0.9 1.0
C3' Y:DT7 4.8 0.1 1.0
N9 Y:DG8 4.9 0.7 1.0
N1 Y:DG8 4.9 0.6 1.0
C7 Y:DT7 4.9 1.0 1.0
C5 Y:DT7 5.0 0.6 1.0
C1' Y:DT7 5.0 0.5 1.0
C3' Y:DG24 5.0 0.5 1.0
N1 Y:DT7 5.0 0.4 1.0

Reference:

A.Ponce-Salvatierra, K.Wawrzyniak-Turek, U.Steuerwald, C.Hobartner, V.Pena. Crystal Structure of A Dna Catalyst. Nature V. 529 231 2016.
ISSN: ESSN 1476-4687
PubMed: 26735012
DOI: 10.1038/NATURE16471
Page generated: Tue Jul 30 17:47:19 2024

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