Cobalt in PDB 7k9d: Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I)

The structure of Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I), PDB code: 7k9d was solved by Y.Yang, R.R.Breaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.83 / 2.10
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	98.817, 98.817, 198.897, 90, 90, 120
R / Rfree (%)	16.2 / 19.8

The binding sites of Cobalt atom in the Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I) (pdb code 7k9d). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I), PDB code: 7k9d:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in the Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I)


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 Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co602 b:79.8 occ:1.00 CO B:NCO602 0.0 79.8 1.0 N2 B:NCO602 2.0 81.4 1.0 N5 B:NCO602 2.0 79.2 1.0 N4 B:NCO602 2.0 82.9 1.0 N3 B:NCO602 2.0 76.1 1.0 N6 B:NCO602 2.0 79.5 1.0 N1 B:NCO602 2.0 81.2 1.0 O B:HOH765 3.9 69.2 1.0 O B:HOH783 4.2 69.5 1.0 O B:HOH719 4.3 64.7 1.0 N7 B:G489 4.3 54.2 1.0 O6 B:G489 4.3 57.2 1.0 O B:HOH789 4.5 71.2 1.0 O4 B:U490 4.9 58.5 1.0 O B:HOH882 4.9 81.5 1.0

Cobalt binding site 2 out of 6 in the Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I)


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 Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co603 b:120.7 occ:1.00 CO B:NCO603 0.0 120.7 1.0 N5 B:NCO603 2.0 126.6 1.0 N1 B:NCO603 2.0 120.1 1.0 N6 B:NCO603 2.0 122.1 1.0 N3 B:NCO603 2.0 119.7 1.0 N4 B:NCO603 2.0 118.4 1.0 N2 B:NCO603 2.0 123.8 1.0 O B:HOH704 3.5 69.3 1.0 O B:HOH739 3.8 58.7 1.0 O B:HOH745 3.9 75.3 1.0 O6 B:G493 4.0 57.4 1.0 O B:HOH717 4.2 116.2 1.0 N7 B:G493 4.5 62.5 1.0 O B:HOH868 4.5 82.7 1.0 O6 B:G494 4.8 55.7 1.0 C6 B:G493 4.8 58.8 1.0 O4 B:U492 4.9 61.4 1.0 O B:HOH859 5.0 62.8 1.0

Cobalt binding site 3 out of 6 in the Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I)


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 Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co604 b:79.1 occ:0.91 CO B:NCO604 0.0 79.1 0.9 N2 B:NCO604 2.0 76.8 0.9 N3 B:NCO604 2.0 78.9 0.9 N1 B:NCO604 2.0 82.0 0.9 N6 B:NCO604 2.0 78.0 0.9 N5 B:NCO604 2.0 77.2 0.9 N4 B:NCO604 2.0 79.3 0.9 O B:HOH736 3.9 68.7 1.0 O B:HOH747 4.0 88.3 1.0 O B:HOH808 4.2 60.9 1.0 O6 B:G540 4.2 53.0 1.0 O6 B:G541 4.4 52.1 1.0 N7 B:G540 4.4 53.4 1.0 O B:HOH866 4.6 76.6 1.0 N7 B:G541 4.8 53.2 1.0 C6 B:G540 4.8 55.2 1.0 C5 B:G540 4.9 59.4 1.0

Cobalt binding site 4 out of 6 in the Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I)


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 Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co605 b:102.4 occ:0.79 CO B:NCO605 0.0 102.4 0.8 N4 B:NCO605 2.0 103.4 0.8 N3 B:NCO605 2.0 104.0 0.8 N6 B:NCO605 2.0 97.5 0.8 N1 B:NCO605 2.0 106.9 0.8 N5 B:NCO605 2.0 96.5 0.8 N2 B:NCO605 2.0 101.0 0.8 O2S B:EPE601 3.8 59.3 1.0 O B:HOH709 3.9 71.7 1.0 O B:HOH727 4.0 67.9 1.0 O4 B:U497 4.2 54.6 1.0 O B:HOH764 4.2 68.0 1.0 OP2 B:A506 4.2 53.2 1.0 O1S B:EPE601 4.4 61.4 1.0 O6 B:G496 4.5 53.4 1.0 N7 B:A506 4.6 49.1 1.0 S B:EPE601 4.7 63.0 1.0 O6 B:G507 4.9 49.4 1.0 O B:HOH704 4.9 69.3 1.0

Cobalt binding site 5 out of 6 in the Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co606 b:138.3 occ:0.93 CO B:NCO606 0.0 138.3 0.9 N4 B:NCO606 2.0 139.1 0.9 N3 B:NCO606 2.0 137.5 0.9 N5 B:NCO606 2.0 137.3 0.9 N6 B:NCO606 2.0 138.6 0.9 N1 B:NCO606 2.0 137.7 0.9 N2 B:NCO606 2.0 136.9 0.9 OP1 B:C534 4.0 110.6 1.0 OP2 B:C487 4.2 67.0 1.0 OP1 B:C486 4.2 68.0 1.0 OP2 B:C486 5.0 64.0 1.0

Cobalt binding site 6 out of 6 in the Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Bacillus Halodurans Oapb in Complex with Its Ole Rna Target (Crystal Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co607 b:116.2 occ:0.79 CO B:NCO607 0.0 116.2 0.8 N2 B:NCO607 2.0 118.6 0.8 N3 B:NCO607 2.0 114.6 0.8 N4 B:NCO607 2.0 116.2 0.8 N6 B:NCO607 2.0 115.3 0.8 N1 B:NCO607 2.0 116.2 0.8 N5 B:NCO607 2.0 115.5 0.8 OP1 B:G527 4.1 74.5 1.0 O6 B:G529 4.3 103.6 1.0 N7 B:G527 4.7 64.2 1.0 O6 B:G528 4.7 83.0 1.0 O6 B:G527 4.9 68.4 1.0

Y.Yang, K.A.Harris, D.L.Widner, R.R.Breaker. Structure of A Bacterial Oapb Protein with Its Ole Rna Target Gives Insights Into the Architecture of the Ole Ribonucleoprotein Complex Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490