Cobalt in PDB 7jnh: Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna

The structure of Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna, PDB code: 7jnh was solved by S.F.Torabi, A.T.Vaidya, K.T.Tycowski, S.J.Degregorio, J.Wang, M.D.Shu, T.A.Steitz, J.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.03 / 2.89
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.973, 93.973, 202.171, 90, 90, 120
R / Rfree (%)	18.4 / 22.5

The structure of Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna also contains other interesting chemical elements:

Strontium	(Sr)	6 atoms
Magnesium	(Mg)	3 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna (pdb code 7jnh). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna, PDB code: 7jnh:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:207.7 occ:1.00 CO A:NCO104 0.0 207.7 1.0 N4 A:NCO104 2.0 226.5 1.0 N1 A:NCO104 2.0 193.1 1.0 N3 A:NCO104 2.0 203.7 1.0 N2 A:NCO104 2.0 220.8 1.0 N6 A:NCO104 2.0 218.3 1.0 N5 A:NCO104 2.0 217.5 1.0 O5' A:A21 3.8 135.3 1.0 OP1 A:A21 3.8 140.7 1.0 P A:A21 4.1 154.2 1.0 OP2 A:A21 4.1 156.6 1.0 C8 A:A22 4.3 129.6 1.0 N9 A:A22 4.4 128.8 1.0 O2' B:U66 4.5 116.9 1.0 N7 A:A22 4.7 120.5 1.0 C1' A:A22 4.7 127.0 1.0 C5' A:A21 4.7 134.6 1.0 C4 A:A22 4.8 117.2 1.0 O4' A:A22 4.9 135.5 1.0 C5 A:A22 4.9 112.5 1.0

Cobalt binding site 2 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


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 A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co104 b:111.3 occ:1.00 CO B:NCO104 0.0 111.3 1.0 N1 B:NCO104 2.0 128.9 1.0 N4 B:NCO104 2.0 113.1 1.0 N6 B:NCO104 2.0 110.8 1.0 N2 B:NCO104 2.0 123.7 1.0 N3 B:NCO104 2.0 96.3 1.0 N5 B:NCO104 2.0 112.8 1.0 O6 B:G41 4.0 101.5 1.0 O4 B:U49 4.1 120.9 1.0 O6 B:G48 4.3 92.1 1.0 O6 B:G42 4.4 112.4 1.0 N7 B:G41 4.4 93.1 1.0 O6 B:G44 4.6 114.5 1.0 C6 B:G41 4.8 83.5 1.0 N4 B:C43 4.8 108.5 1.0 C5 B:G41 5.0 85.5 1.0

Cobalt binding site 3 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


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 A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co105 b:220.8 occ:1.00 CO B:NCO105 0.0 220.8 1.0 N4 B:NCO105 2.0 224.2 1.0 N3 B:NCO105 2.0 218.7 1.0 N6 B:NCO105 2.0 204.8 1.0 N5 B:NCO105 2.0 220.3 1.0 N2 B:NCO105 2.0 188.6 1.0 N1 B:NCO105 2.0 224.7 1.0 N7 B:G2 3.9 133.6 1.0 O6 B:G2 4.1 137.8 1.0 O6 B:G3 4.4 122.2 1.0 C5 B:G2 4.7 130.6 1.0 N7 B:G3 4.7 105.5 1.0 C6 B:G2 4.7 136.9 1.0 C8 B:G2 4.9 137.5 1.0

Cobalt binding site 4 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


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 A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co106 b:135.0 occ:1.00 CO B:NCO106 0.0 135.0 1.0 N6 B:NCO106 2.0 148.8 1.0 N4 B:NCO106 2.0 155.4 1.0 N2 B:NCO106 2.0 131.9 1.0 N1 B:NCO106 2.0 150.1 1.0 N5 B:NCO106 2.0 97.2 1.0 N3 B:NCO106 2.0 106.6 1.0 O6 B:G74 4.0 113.9 1.0 O4 B:U75 4.7 115.2 1.0 C6 B:G74 4.9 96.7 1.0 O4 B:U13 4.9 101.2 1.0

Cobalt binding site 5 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


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 A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co107 b:125.2 occ:1.00 CO B:NCO107 0.0 125.2 1.0 N1 B:NCO107 2.0 133.5 1.0 N4 B:NCO107 2.0 130.5 1.0 N6 B:NCO107 2.0 125.0 1.0 N3 B:NCO107 2.0 118.4 1.0 N2 B:NCO107 2.0 120.3 1.0 N5 B:NCO107 2.0 123.9 1.0 OP1 B:G73 4.2 109.1 1.0 OP1 B:G74 4.2 102.9 1.0

Cobalt binding site 6 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


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 A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co108 b:133.3 occ:1.00 CO B:NCO108 0.0 133.3 1.0 N2 B:NCO108 2.0 128.8 1.0 N5 B:NCO108 2.0 128.0 1.0 N4 B:NCO108 2.0 120.5 1.0 N6 B:NCO108 2.0 129.6 1.0 N1 B:NCO108 2.0 125.5 1.0 N3 B:NCO108 2.0 128.6 1.0 OP2 B:U77 3.9 85.5 1.0 N7 B:G8 4.2 90.2 1.0 O6 B:G8 4.5 80.8 1.0 OP1 B:U76 4.5 99.8 1.0 OP2 B:U76 4.7 104.7 1.0 P B:U76 4.9 100.7 1.0 O5' B:U76 5.0 85.8 1.0

Cobalt binding site 7 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co109 b:119.8 occ:1.00 CO B:NCO109 0.0 119.8 1.0 N4 B:NCO109 2.0 103.6 1.0 N2 B:NCO109 2.0 135.0 1.0 N5 B:NCO109 2.0 137.7 1.0 N3 B:NCO109 2.0 122.0 1.0 N1 B:NCO109 2.0 131.0 1.0 N6 B:NCO109 2.0 105.5 1.0 OP2 B:A56 3.9 99.3 1.0 OP1 B:U55 4.4 108.7 1.0 O5' B:U55 4.5 94.8 1.0 N7 B:A31 4.6 127.8 1.0 P B:U55 4.7 100.4 1.0 OP2 B:U55 4.7 86.4 1.0 OP2 B:A30 4.9 96.8 1.0

Cobalt binding site 8 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co110 b:136.8 occ:1.00 CO B:NCO110 0.0 136.8 1.0 N2 B:NCO110 2.0 145.5 1.0 N4 B:NCO110 2.0 117.4 1.0 N3 B:NCO110 2.0 132.9 1.0 N6 B:NCO110 2.0 139.7 1.0 N5 B:NCO110 2.0 132.8 1.0 N1 B:NCO110 2.0 123.5 1.0 O4 B:U60 4.1 96.4 1.0 O4 B:U29 4.4 95.2 1.0 O4 B:U28 4.7 107.6 1.0

Cobalt binding site 9 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co111 b:128.3 occ:1.00 CO B:NCO111 0.0 128.3 1.0 N1 B:NCO111 2.0 140.6 1.0 N4 B:NCO111 2.0 122.8 1.0 N3 B:NCO111 2.0 135.0 1.0 N5 B:NCO111 2.0 132.5 1.0 N2 B:NCO111 2.0 154.9 1.0 N6 B:NCO111 2.0 120.8 1.0 N7 B:G24 4.2 102.6 1.0 OP2 B:U62 4.2 100.8 1.0 O6 B:G24 4.5 112.0 1.0 OP2 B:U61 4.5 103.6 1.0 C5 B:G24 5.0 103.9 1.0

Cobalt binding site 10 out of 12 in the Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of A Double-Ene Rna Stability Element in Complex with A 28-Mer Poly(A) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Co112 b:133.1 occ:1.00 CO B:NCO112 0.0 133.1 1.0 N5 B:NCO112 2.0 120.0 1.0 N1 B:NCO112 2.0 155.7 1.0 N3 B:NCO112 2.0 132.5 1.0 N2 B:NCO112 2.0 144.7 1.0 N4 B:NCO112 2.0 137.3 1.0 N6 B:NCO112 2.0 129.1 1.0 N7 B:G68 4.3 106.6 1.0 O4 B:U69 4.5 101.5 1.0 O6 B:G68 4.9 93.5 1.0 O6 B:G18 4.9 107.3 1.0

S.F.Torabi, A.T.Vaidya, K.T.Tycowski, S.J.Degregorio, J.Wang, M.D.Shu, T.A.Steitz, J.A.Steitz. Rna Stabilization By A Poly(A) Tail 3'-End Binding Pocket and Other Modes of Poly(A)-Rna Interaction. Science 2021.
ISSN: ESSN 1095-9203
PubMed: 33414189
DOI: 10.1126/SCIENCE.ABE6523