Cobalt in PDB 1u8r: Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions

The structure of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions, PDB code: 1u8r was solved by G.Wisedchaisri, R.K.Holmes, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.75 / 2.75
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	107.959, 107.959, 215.124, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 26.5

The structure of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions (pdb code 1u8r). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 24 binding sites of Cobalt where determined in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions, PDB code: 1u8r:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1001 b:65.1 occ:1.00 OE1 A:GLN175 1.9 52.0 1.0 OE2 A:GLU83 1.9 83.1 1.0 NE2 A:HIS79 2.0 63.2 1.0 OE1 A:GLU172 2.0 64.0 1.0 ND1 A:HIS98 2.0 75.2 1.0 CE1 A:HIS79 2.7 62.3 1.0 CD A:GLU83 2.7 81.9 1.0 CE1 A:HIS98 2.8 75.7 1.0 CD A:GLN175 2.9 53.6 1.0 CD A:GLU172 3.0 63.6 1.0 OE1 A:GLU83 3.1 81.2 1.0 CD2 A:HIS79 3.1 64.0 1.0 CG A:HIS98 3.2 76.7 1.0 OE2 A:GLU172 3.3 64.3 1.0 NE2 A:GLN175 3.5 54.9 1.0 CB A:HIS98 3.7 76.4 1.0 ND1 A:HIS79 3.9 63.6 1.0 CA A:HIS98 3.9 67.9 1.0 CG A:GLU83 4.0 79.5 1.0 NE2 A:HIS98 4.0 76.0 1.0 CG A:HIS79 4.1 63.9 1.0 CD2 A:HIS98 4.2 76.1 1.0 CG A:GLN175 4.2 54.6 1.0 CG A:GLU172 4.3 63.1 1.0 CB A:GLN175 4.4 55.9 1.0 O A:HIS98 4.6 67.9 1.0 C A:HIS98 4.7 66.8 1.0 CB A:GLU172 4.8 63.1 1.0 CA A:GLU172 4.9 56.8 1.0

Cobalt binding site 2 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1002 b:60.8 occ:1.00 OE2 A:GLU105 1.9 40.1 1.0 NE2 A:HIS106 2.1 51.8 1.0 O A:CYS102 2.2 65.7 1.0 SD A:MET10 2.2 69.7 1.0 CE1 A:HIS106 2.9 52.0 1.0 CD A:GLU105 3.1 42.1 1.0 C A:CYS102 3.2 64.7 1.0 SG A:CYS102 3.2 42.8 1.0 CD2 A:HIS106 3.2 53.0 1.0 CE A:MET10 3.3 66.2 1.0 CG A:MET10 3.4 67.8 1.0 CA A:CYS102 3.7 62.5 1.0 NH2 A:ARG13 3.7 62.3 1.0 CG A:GLU105 3.7 41.4 1.0 CB A:CYS102 3.8 49.2 1.0 OE1 A:GLU105 4.1 41.4 1.0 ND1 A:HIS106 4.1 50.3 1.0 CG A:HIS106 4.3 50.9 1.0 O A:LEU4 4.3 54.1 1.0 N A:ARG103 4.4 58.5 1.0 CZ A:ARG13 4.8 60.5 1.0 CB A:MET10 4.8 68.0 1.0 CA A:ARG103 4.9 58.6 1.0

Cobalt binding site 3 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1003 b:73.1 occ:1.00 NE2 A:HIS223 2.0 70.8 1.0 NE2 A:HIS219 2.3 60.1 1.0 CE1 A:HIS219 2.7 59.3 1.0 CE1 A:HIS223 2.8 71.5 1.0 CD2 A:HIS223 3.2 70.8 1.0 CD2 A:HIS219 3.6 60.9 1.0 ND1 A:HIS223 4.0 70.5 1.0 ND1 A:HIS219 4.0 59.5 1.0 CG A:HIS223 4.2 69.9 1.0 CG A:HIS219 4.5 60.2 1.0 CG2 A:THR155 5.0 81.1 1.0

Cobalt binding site 4 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2001 b:67.5 occ:1.00 OE2 B:GLU83 1.8 78.5 1.0 NE2 B:HIS79 2.0 67.0 1.0 OE1 B:GLU172 2.0 46.8 1.0 OE1 B:GLN175 2.1 74.0 1.0 ND1 B:HIS98 2.1 74.6 1.0 CD B:GLU83 2.6 77.6 1.0 CE1 B:HIS79 2.7 66.7 1.0 CD B:GLU172 2.9 49.8 1.0 OE1 B:GLU83 3.0 78.0 1.0 CE1 B:HIS98 3.0 76.5 1.0 CD B:GLN175 3.1 73.3 1.0 CD2 B:HIS79 3.2 67.4 1.0 CG B:HIS98 3.2 73.4 1.0 OE2 B:GLU172 3.2 49.2 1.0 CB B:HIS98 3.6 73.6 1.0 NE2 B:GLN175 3.6 71.7 1.0 CA B:HIS98 3.8 73.3 1.0 CG B:GLU83 3.9 76.2 1.0 ND1 B:HIS79 4.0 65.3 1.0 NE2 B:HIS98 4.1 76.0 1.0 CG B:HIS79 4.2 65.6 1.0 CD2 B:HIS98 4.3 74.0 1.0 CG B:GLU172 4.3 51.7 1.0 CG B:GLN175 4.4 72.9 1.0 O B:HIS98 4.5 73.1 1.0 CB B:GLN175 4.6 73.8 1.0 C B:HIS98 4.6 72.7 1.0 CB B:GLU172 4.8 53.1 1.0 CA B:GLU172 4.9 75.6 1.0 N B:HIS98 4.9 75.0 1.0

Cobalt binding site 5 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2002 b:70.7 occ:1.00 OE2 B:GLU105 1.9 66.2 1.0 O B:CYS102 2.0 47.7 1.0 NE2 B:HIS106 2.1 60.8 1.0 SD B:MET10 2.2 84.2 1.0 SG B:CYS102 2.9 53.8 1.0 CE1 B:HIS106 3.0 62.2 1.0 CD B:GLU105 3.1 68.8 1.0 C B:CYS102 3.1 48.0 1.0 CE B:MET10 3.1 80.1 1.0 CD2 B:HIS106 3.1 62.7 1.0 CG B:MET10 3.5 79.5 1.0 CA B:CYS102 3.6 47.4 1.0 CG B:GLU105 3.7 67.6 1.0 CB B:CYS102 3.8 54.3 1.0 NH2 B:ARG13 3.9 73.1 1.0 OE1 B:GLU105 4.1 69.4 1.0 ND1 B:HIS106 4.2 62.9 1.0 O B:LEU4 4.2 64.6 1.0 CG B:HIS106 4.3 61.8 1.0 N B:ARG103 4.3 56.7 1.0 CA B:ARG103 4.8 57.5 1.0 CB B:MET10 4.9 76.4 1.0

Cobalt binding site 6 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2003 b:85.8 occ:1.00 NE2 B:HIS223 1.9 88.3 1.0 O B:HOH2105 2.0 59.5 1.0 NE2 B:HIS219 2.2 84.4 1.0 CE1 B:HIS219 2.6 84.4 1.0 CE1 B:HIS223 2.8 88.5 1.0 CD2 B:HIS223 3.0 88.0 1.0 CD2 B:HIS219 3.4 84.2 1.0 ND1 B:HIS219 3.9 84.3 1.0 ND1 B:HIS223 3.9 87.8 1.0 CG B:HIS223 4.0 87.7 1.0 CG B:HIS219 4.3 84.9 1.0 CG2 B:THR155 4.9 0.1 1.0

Cobalt binding site 7 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ C:Co3001 b:67.6 occ:1.00 OE1 C:GLU172 1.7 60.3 1.0 OE1 C:GLN175 1.8 74.5 1.0 ND1 C:HIS98 2.0 56.7 1.0 NE2 C:HIS79 2.1 64.2 1.0 OE2 C:GLU83 2.1 90.9 1.0 CD C:GLU172 2.7 60.2 1.0 CE1 C:HIS98 2.7 57.2 1.0 CE1 C:HIS79 2.8 64.1 1.0 CD C:GLU83 2.8 92.1 1.0 CD C:GLN175 2.8 73.9 1.0 OE1 C:GLU83 3.0 92.6 1.0 OE2 C:GLU172 3.1 59.2 1.0 CG C:HIS98 3.1 57.6 1.0 CD2 C:HIS79 3.3 63.7 1.0 NE2 C:GLN175 3.4 74.4 1.0 CB C:HIS98 3.7 58.7 1.0 NE2 C:HIS98 3.9 59.1 1.0 ND1 C:HIS79 4.0 65.0 1.0 CA C:HIS98 4.1 85.5 1.0 CG C:GLU83 4.1 90.6 1.0 CG C:GLU172 4.1 60.1 1.0 CG C:GLN175 4.1 73.0 1.0 CD2 C:HIS98 4.1 57.8 1.0 CG C:HIS79 4.2 63.3 1.0 CB C:GLN175 4.3 72.5 1.0 CB C:GLU172 4.6 61.4 1.0 O C:HIS98 4.7 84.9 1.0 CA C:GLU172 4.7 64.5 1.0 C C:HIS98 4.8 84.0 1.0

Cobalt binding site 8 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ C:Co3002 b:61.1 occ:1.00 OE2 C:GLU105 1.9 56.2 1.0 O C:CYS102 2.0 75.0 1.0 NE2 C:HIS106 2.1 46.5 1.0 SD C:MET10 2.3 55.8 1.0 CE1 C:HIS106 3.0 47.9 1.0 SG C:CYS102 3.0 50.6 1.0 CD C:GLU105 3.0 59.3 1.0 C C:CYS102 3.1 72.8 1.0 CD2 C:HIS106 3.1 48.0 1.0 CE C:MET10 3.3 55.0 1.0 CG C:MET10 3.5 57.0 1.0 CA C:CYS102 3.6 70.7 1.0 CG C:GLU105 3.6 59.2 1.0 CB C:CYS102 3.8 57.9 1.0 NH2 C:ARG13 3.8 68.0 1.0 OE1 C:GLU105 4.1 62.7 1.0 ND1 C:HIS106 4.1 47.5 1.0 CG C:HIS106 4.2 48.2 1.0 N C:ARG103 4.3 73.4 1.0 O C:LEU4 4.3 80.2 1.0 CA C:ARG103 4.7 73.8 1.0 CB C:MET10 4.8 58.0 1.0 CZ C:ARG13 4.9 67.2 1.0

Cobalt binding site 9 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ C:Co3003 b:73.1 occ:1.00 NE2 C:HIS219 1.8 83.9 1.0 NE2 C:HIS223 1.9 92.0 1.0 O C:HOH3107 2.2 62.5 1.0 CE1 C:HIS219 2.4 83.8 1.0 CD2 C:HIS223 2.9 91.1 1.0 CE1 C:HIS223 3.0 91.8 1.0 O C:HOH3109 3.0 32.1 1.0 CD2 C:HIS219 3.0 84.2 1.0 ND1 C:HIS219 3.6 83.8 1.0 CG C:HIS219 3.9 84.0 1.0 CG C:HIS223 4.0 90.4 1.0 ND1 C:HIS223 4.0 90.2 1.0 CG2 C:THR155 5.0 0.6 1.0

Cobalt binding site 10 out of 24 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ D:Co4001 b:56.5 occ:1.00 OE1 D:GLN175 1.8 57.9 1.0 OE1 D:GLU172 1.9 60.1 1.0 NE2 D:HIS79 2.0 58.9 1.0 OE2 D:GLU83 2.0 82.0 1.0 ND1 D:HIS98 2.1 59.6 1.0 CE1 D:HIS79 2.7 59.5 1.0 CD D:GLU83 2.7 81.0 1.0 CE1 D:HIS98 2.9 60.8 1.0 CD D:GLN175 2.9 61.0 1.0 CD D:GLU172 2.9 60.7 1.0 OE1 D:GLU83 3.0 81.6 1.0 CD2 D:HIS79 3.2 60.9 1.0 CG D:HIS98 3.2 58.9 1.0 OE2 D:GLU172 3.2 61.2 1.0 NE2 D:GLN175 3.4 63.2 1.0 CB D:HIS98 3.7 60.8 1.0 ND1 D:HIS79 3.9 60.7 1.0 CG D:GLU83 4.0 80.1 1.0 CA D:HIS98 4.0 76.7 1.0 NE2 D:HIS98 4.1 60.0 1.0 CG D:HIS79 4.2 60.5 1.0 CG D:GLN175 4.2 61.6 1.0 CD2 D:HIS98 4.2 59.0 1.0 CG D:GLU172 4.3 60.3 1.0 CB D:GLN175 4.4 62.9 1.0 O D:HIS98 4.5 76.4 1.0 C D:HIS98 4.7 76.2 1.0 CB D:GLU172 4.8 60.9 1.0 CA D:GLU172 4.9 45.6 1.0

G.Wisedchaisri, R.K.Holmes, W.G.J.Hol. Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions. J.Mol.Biol. V. 342 1155 2004.
ISSN: ISSN 0022-2836
PubMed: 15351642
DOI: 10.1016/J.JMB.2004.07.083