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Cobalt in PDB 1c0w: Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain

Protein crystallography data

The structure of Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain, PDB code: 1c0w was solved by E.Pohl, R.K.Holmes, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.20
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 180.200, 180.200, 151.000, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 27.9

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain (pdb code 1c0w). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain, PDB code: 1c0w:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 1c0w

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Cobalt binding site 1 out of 8 in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain


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 the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co601

b:39.0
occ:1.00
 OE1 A:GLN173 2.0 71.1 1.0
NE2 A:HIS79 2.2 54.9 1.0
OE1 A:GLU83 2.2 42.3 1.0
OE1 A:GLU170 2.2 37.8 1.0
ND1 A:HIS98 2.3 41.9 1.0
OE2 A:GLU170 2.4 37.8 1.0
CD A:GLU170 2.6 37.8 1.0
CD A:GLU83 2.8 42.3 1.0
CD A:GLN173 3.0 71.1 1.0
CD2 A:HIS79 3.0 54.9 1.0
OE2 A:GLU83 3.1 42.3 1.0
CE1 A:HIS98 3.1 41.9 1.0
CE1 A:HIS79 3.3 54.9 1.0
CG A:HIS98 3.5 41.9 1.0
NE2 A:GLN173 3.5 71.1 1.0
CB A:HIS98 3.9 41.9 1.0
CG A:GLU83 4.1 42.3 1.0
CG A:GLU170 4.1 37.8 1.0
CG A:HIS79 4.3 54.9 1.0
NE2 A:HIS98 4.3 41.9 1.0
CD2 A:PHE128 4.3 62.2 1.0
CG A:GLN173 4.3 71.1 1.0
ND1 A:HIS79 4.4 54.9 1.0
CA A:HIS98 4.4 31.6 1.0
CE2 A:PHE128 4.4 62.2 1.0
CD2 A:HIS98 4.5 41.9 1.0
CB A:GLN173 4.6 71.1 1.0
CB A:GLU170 4.8 37.8 1.0
CA A:GLU170 4.9 96.7 1.0
O A:HIS98 4.9 41.9 1.0
OD1 A:ASN130 5.0 74.7 1.0

Cobalt binding site 2 out of 8 in 1c0w

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Cobalt binding site 2 out of 8 in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain


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 the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co602

b:37.3
occ:1.00
 OE1 B:GLU83 1.8 27.6 1.0
ND1 B:HIS98 1.9 35.9 1.0
OE1 B:GLU170 1.9 33.2 1.0
NE2 B:HIS79 2.1 46.0 1.0
OE1 B:GLN173 2.4 28.7 1.0
CE1 B:HIS98 2.7 35.9 1.0
CD B:GLU170 2.8 33.2 1.0
CD B:GLU83 2.9 27.6 1.0
CG B:HIS98 3.0 35.9 1.0
CE1 B:HIS79 3.1 46.0 1.0
OE2 B:GLU170 3.1 33.2 1.0
CD2 B:HIS79 3.1 46.0 1.0
OE2 B:GLU83 3.4 27.6 1.0
CB B:HIS98 3.5 35.9 1.0
CD B:GLN173 3.5 28.7 1.0
CA B:HIS98 3.9 39.3 1.0
NE2 B:HIS98 3.9 35.9 1.0
CG B:GLU83 4.0 27.6 1.0
CD2 B:HIS98 4.1 35.9 1.0
CG B:GLU170 4.2 33.2 1.0
ND1 B:HIS79 4.2 46.0 1.0
CG B:HIS79 4.3 46.0 1.0
NE2 B:GLN173 4.3 28.7 1.0
O B:HIS98 4.5 35.9 1.0
CB B:GLN173 4.6 28.7 1.0
CG B:GLN173 4.6 28.7 1.0
CB B:GLU170 4.6 33.2 1.0
C B:HIS98 4.7 39.3 1.0
CA B:GLU170 4.8 49.0 1.0

Cobalt binding site 3 out of 8 in 1c0w

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Cobalt binding site 3 out of 8 in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain


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 the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co603

b:50.8
occ:1.00
 ND1 C:HIS98 1.8 50.6 1.0
OE1 C:GLU170 2.0 41.3 1.0
OE1 C:GLN173 2.0 40.4 1.0
NE2 C:HIS79 2.2 67.5 1.0
OE1 C:GLU83 2.2 67.2 1.0
CE1 C:HIS98 2.5 50.6 1.0
CD C:GLU170 2.8 41.3 1.0
OE2 C:GLU170 3.0 41.3 1.0
CG C:HIS98 3.1 50.6 1.0
CE1 C:HIS79 3.1 67.5 1.0
CD C:GLU83 3.1 67.2 1.0
CD C:GLN173 3.2 40.4 1.0
CD2 C:HIS79 3.2 67.5 1.0
OE2 C:GLU83 3.6 67.2 1.0
CB C:HIS98 3.7 50.6 1.0
NE2 C:HIS98 3.8 50.6 1.0
NE2 C:GLN173 3.9 40.4 1.0
CD2 C:HIS98 4.0 50.6 1.0
CA C:HIS98 4.1 93.5 1.0
CG C:GLU170 4.2 41.3 1.0
ND1 C:HIS79 4.3 67.5 1.0
CB C:GLN173 4.3 40.4 1.0
CG C:GLU83 4.3 67.2 1.0
CG C:GLN173 4.3 40.4 1.0
CG C:HIS79 4.4 67.5 1.0
O C:HIS98 4.6 50.6 1.0
CB C:GLU170 4.6 41.3 1.0
C C:HIS98 4.8 93.5 1.0
CA C:GLU170 4.8 65.1 1.0
O C:GLU170 5.0 41.3 1.0

Cobalt binding site 4 out of 8 in 1c0w

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Cobalt binding site 4 out of 8 in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain


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 the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co604

b:54.1
occ:1.00
 OE1 D:GLN173 1.9 81.9 1.0
OE1 D:GLU83 2.1 99.5 1.0
ND1 D:HIS98 2.2 67.9 1.0
NE2 D:HIS79 2.2 62.7 1.0
OE1 D:GLU170 2.3 56.8 1.0
CD D:GLU83 2.8 99.5 1.0
OE2 D:GLU170 2.9 56.8 1.0
CD D:GLU170 2.9 56.8 1.0
CD D:GLN173 3.0 81.9 1.0
OE2 D:GLU83 3.0 99.5 1.0
CE1 D:HIS98 3.1 67.9 1.0
CD2 D:HIS79 3.2 62.7 1.0
CE1 D:HIS79 3.3 62.7 1.0
CG D:HIS98 3.3 67.9 1.0
NE2 D:GLN173 3.5 81.9 1.0
CB D:HIS98 3.7 67.9 1.0
CG D:GLU83 4.0 99.5 1.0
CA D:HIS98 4.1 86.5 1.0
CG D:GLN173 4.2 81.9 1.0
NE2 D:HIS98 4.3 67.9 1.0
CG D:GLU170 4.3 56.8 1.0
CG D:HIS79 4.4 62.7 1.0
CD2 D:PHE128 4.4 74.1 1.0
ND1 D:HIS79 4.4 62.7 1.0
CB D:GLN173 4.4 81.9 1.0
CD2 D:HIS98 4.4 67.9 1.0
CE2 D:PHE128 4.5 74.1 1.0
O D:HIS98 4.8 67.9 1.0
CB D:GLU170 4.8 56.8 1.0
CA D:GLU170 4.9 0.0 1.0
C D:HIS98 5.0 86.5 1.0

Cobalt binding site 5 out of 8 in 1c0w

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Cobalt binding site 5 out of 8 in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain


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 the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co701

b:39.0
occ:1.00
 O A:CYS102 1.9 23.8 1.0
OE1 A:GLU105 2.0 49.8 1.0
NE2 A:HIS106 2.1 34.4 1.0
SD A:MET10 2.2 26.2 1.0
SG A:CYS102 2.7 23.8 1.0
C A:CYS102 2.9 31.0 1.0
CE1 A:HIS106 3.0 34.4 1.0
CD A:GLU105 3.1 49.8 1.0
CD2 A:HIS106 3.2 34.4 1.0
CE A:MET10 3.4 26.2 1.0
CA A:CYS102 3.4 31.0 1.0
CG A:MET10 3.4 26.2 1.0
CB A:CYS102 3.6 23.8 1.0
CG A:GLU105 3.7 49.8 1.0
NH2 A:ARG13 4.0 37.9 1.0
N A:ARG103 4.1 23.9 1.0
OE2 A:GLU105 4.2 49.8 1.0
ND1 A:HIS106 4.2 34.4 1.0
O A:LEU4 4.3 25.9 1.0
CG A:HIS106 4.3 34.4 1.0
CA A:ARG103 4.7 23.9 1.0
CB A:MET10 4.8 26.2 1.0
NE A:ARG13 4.8 37.9 1.0
CZ A:ARG13 4.8 37.9 1.0
N A:CYS102 4.8 31.0 1.0

Cobalt binding site 6 out of 8 in 1c0w

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Cobalt binding site 6 out of 8 in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain


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 the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co702

b:37.3
occ:1.00
 O B:CYS102 1.9 18.8 1.0
NE2 B:HIS106 2.0 30.4 1.0
OE1 B:GLU105 2.1 24.7 1.0
SD B:MET10 2.3 33.7 1.0
SG B:CYS102 2.9 18.8 1.0
CE1 B:HIS106 2.9 30.4 1.0
C B:CYS102 3.0 27.7 1.0
CD2 B:HIS106 3.1 30.4 1.0
CG B:MET10 3.2 33.7 1.0
CD B:GLU105 3.3 24.7 1.0
CA B:CYS102 3.5 27.7 1.0
CB B:CYS102 3.6 18.8 1.0
CE B:MET10 3.7 33.7 1.0
CG B:GLU105 3.9 24.7 1.0
O B:LEU4 3.9 30.7 1.0
ND1 B:HIS106 4.1 30.4 1.0
N B:ARG103 4.2 10.4 1.0
CG B:HIS106 4.2 30.4 1.0
NH2 B:ARG13 4.3 39.5 1.0
OE2 B:GLU105 4.3 24.7 1.0
CA B:ARG103 4.6 10.4 1.0
CB B:MET10 4.7 33.7 1.0
C B:LEU4 4.8 36.5 1.0
N B:CYS102 4.9 27.7 1.0

Cobalt binding site 7 out of 8 in 1c0w

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Cobalt binding site 7 out of 8 in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain


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 the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co703

b:50.8
occ:1.00
 O C:CYS102 1.9 51.6 1.0
OE1 C:GLU105 2.0 51.0 1.0
NE2 C:HIS106 2.2 41.3 1.0
SD C:MET10 2.3 59.2 1.0
SG C:CYS102 2.8 51.6 1.0
C C:CYS102 2.9 0.0 1.0
CE1 C:HIS106 3.1 41.3 1.0
CD C:GLU105 3.2 51.0 1.0
CD2 C:HIS106 3.2 41.3 1.0
CG C:MET10 3.4 59.2 1.0
CE C:MET10 3.4 59.2 1.0
CA C:CYS102 3.5 0.0 1.0
CB C:CYS102 3.6 51.6 1.0
CG C:GLU105 3.9 51.0 1.0
N C:ARG103 4.1 28.5 1.0
NH2 C:ARG13 4.1 52.4 1.0
O C:LEU4 4.1 50.6 1.0
OE2 C:GLU105 4.2 51.0 1.0
ND1 C:HIS106 4.3 41.3 1.0
CG C:HIS106 4.4 41.3 1.0
CA C:ARG103 4.6 28.5 1.0
CB C:MET10 4.9 59.2 1.0
N C:CYS102 4.9 0.0 1.0
C C:LEU4 5.0 32.5 1.0
NE C:ARG13 5.0 52.4 1.0
CZ C:ARG13 5.0 52.4 1.0

Cobalt binding site 8 out of 8 in 1c0w

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Cobalt binding site 8 out of 8 in the Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain


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 the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co704

b:54.1
occ:1.00
 O D:CYS102 1.9 40.6 1.0
OE1 D:GLU105 2.0 54.4 1.0
SD D:MET10 2.2 41.9 1.0
NE2 D:HIS106 2.3 31.4 1.0
SG D:CYS102 2.7 40.6 1.0
C D:CYS102 2.9 66.1 1.0
CD D:GLU105 3.2 54.4 1.0
CE1 D:HIS106 3.2 31.4 1.0
CE D:MET10 3.3 41.9 1.0
CA D:CYS102 3.3 66.1 1.0
CD2 D:HIS106 3.4 31.4 1.0
CG D:MET10 3.4 41.9 1.0
CB D:CYS102 3.5 40.6 1.0
CG D:GLU105 3.9 54.4 1.0
NH2 D:ARG13 3.9 34.6 1.0
N D:ARG103 4.1 52.7 1.0
OE2 D:GLU105 4.2 54.4 1.0
O D:LEU4 4.4 34.2 1.0
ND1 D:HIS106 4.4 31.4 1.0
CG D:HIS106 4.5 31.4 1.0
CZ D:ARG13 4.7 34.6 1.0
CA D:ARG103 4.7 52.7 1.0
CB D:MET10 4.7 41.9 1.0
N D:CYS102 4.7 66.1 1.0
NE D:ARG13 4.7 34.6 1.0

Reference:

E.Pohl, R.K.Holmes, W.G.Hol. Crystal Structure of A Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal-Binding SH3-Like Domain. J.Mol.Biol. V. 292 653 1999.
ISSN: ISSN 0022-2836
PubMed: 10497029
DOI: 10.1006/JMBI.1999.3073
Page generated: Tue Jul 30 14:08:24 2024

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