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Cadmium in PDB 3ip1: Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima

Protein crystallography data

The structure of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima, PDB code: 3ip1 was solved by U.A.Ramagopal, R.Toro, S.K.Burley, S.C.Almo, New York Sgx Research Centerfor Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.365, 131.555, 161.559, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima (pdb code 3ip1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima, PDB code: 3ip1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12;

Cadmium binding site 1 out of 12 in 3ip1

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Cadmium binding site 1 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd500

b:31.1
occ:1.00
SG A:CYS137 2.5 26.9 1.0
SG A:CYS145 2.5 26.5 1.0
SG A:CYS134 2.5 28.3 1.0
SG A:CYS131 2.5 30.0 1.0
CB A:CYS145 3.3 24.3 1.0
CB A:CYS137 3.4 26.5 1.0
N A:CYS131 3.4 29.1 1.0
CB A:CYS134 3.5 28.1 1.0
CA A:CYS145 3.5 25.1 1.0
CB A:CYS131 3.6 29.4 1.0
N A:GLY132 3.7 30.7 1.0
N A:CYS134 3.8 29.7 1.0
N A:GLU146 3.8 26.1 1.0
CA A:CYS131 3.9 29.4 1.0
C A:CYS145 4.1 25.5 1.0
CA A:CYS134 4.2 28.7 1.0
C A:CYS131 4.3 30.3 1.0
N A:HIS133 4.4 31.9 1.0
N A:ASN147 4.4 28.5 1.0
N A:CYS137 4.4 26.6 1.0
CA A:CYS137 4.5 26.7 1.0
C A:TRP130 4.5 28.2 1.0
CA A:GLY132 4.7 31.4 1.0
CB A:TRP130 4.8 27.5 1.0
CA A:TRP130 4.8 27.7 1.0
N A:CYS145 4.8 24.2 1.0
C A:CYS134 4.9 28.1 1.0
C A:GLY132 4.9 31.9 1.0
CA A:GLU146 5.0 27.0 1.0
C A:HIS133 5.0 31.2 1.0
O A:CYS134 5.0 27.3 1.0

Cadmium binding site 2 out of 12 in 3ip1

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Cadmium binding site 2 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:33.5
occ:0.50
CD A:CD501 0.0 33.5 0.5
CD A:CD501 1.7 26.5 0.5
O A:HOH680 2.4 41.8 1.0
NE2 A:HIS95 2.5 27.7 1.0
OE2 A:GLU96 2.6 28.3 1.0
OE1 A:GLU193 2.7 29.9 1.0
SG A:CYS66 3.1 31.1 1.0
CD2 A:HIS95 3.2 29.3 1.0
O A:HOH679 3.2 39.0 1.0
O A:HOH684 3.4 55.4 1.0
CD A:GLU96 3.4 29.4 1.0
CD A:GLU193 3.5 29.0 1.0
CG A:GLU96 3.5 27.4 1.0
OE2 A:GLU193 3.5 32.2 1.0
CB A:CYS66 3.6 27.9 1.0
CE1 A:HIS95 3.7 27.8 1.0
O A:HOH475 4.4 30.4 1.0
CG A:HIS95 4.5 26.5 1.0
OE1 A:GLU96 4.6 29.9 1.0
ND1 A:HIS95 4.7 26.9 1.0
CA A:CYS66 4.8 28.1 1.0
CG A:GLU193 4.9 26.0 1.0
CB A:PRO194 4.9 23.0 1.0
CD A:PRO194 5.0 23.6 1.0
CB A:GLU96 5.0 26.1 1.0

Cadmium binding site 3 out of 12 in 3ip1

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Cadmium binding site 3 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:26.5
occ:0.50
CD A:CD501 0.0 26.5 0.5
CD A:CD501 1.7 33.5 0.5
NE2 A:HIS95 2.3 27.7 1.0
SG A:CYS66 2.3 31.1 1.0
O A:HOH679 2.5 39.0 1.0
O A:HOH684 2.7 55.4 1.0
CE1 A:HIS95 3.0 27.8 1.0
O A:HOH680 3.2 41.8 1.0
CB A:CYS66 3.3 27.9 1.0
CD2 A:HIS95 3.4 29.3 1.0
OG A:SER68 3.7 25.2 0.5
OE2 A:GLU96 3.8 28.3 1.0
OE1 A:GLU193 4.1 29.9 1.0
OE2 A:GLU193 4.2 32.2 1.0
ND1 A:HIS95 4.2 26.9 1.0
CG A:HIS95 4.4 26.5 1.0
OG A:SER68 4.5 25.9 0.5
CB A:SER68 4.6 26.3 0.5
CD A:GLU193 4.6 29.0 1.0
CB A:SER68 4.6 26.2 0.5
CD A:GLU96 4.7 29.4 1.0
CA A:CYS66 4.8 28.1 1.0
CG A:GLU96 4.9 27.4 1.0
CZ A:PHE153 5.0 26.6 1.0

Cadmium binding site 4 out of 12 in 3ip1

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Cadmium binding site 4 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd500

b:28.9
occ:1.00
SG B:CYS134 2.4 24.3 1.0
SG B:CYS131 2.5 27.3 1.0
SG B:CYS145 2.5 27.4 1.0
SG B:CYS137 2.5 27.8 1.0
CB B:CYS145 3.3 24.7 1.0
CB B:CYS137 3.4 27.4 1.0
CB B:CYS134 3.4 27.1 1.0
N B:CYS131 3.5 28.5 1.0
CA B:CYS145 3.6 24.8 1.0
CB B:CYS131 3.6 28.0 1.0
N B:GLY132 3.7 29.9 1.0
N B:CYS134 3.8 28.6 1.0
N B:GLU146 3.9 26.4 1.0
CA B:CYS131 4.0 28.7 1.0
CA B:CYS134 4.2 27.1 1.0
C B:CYS145 4.2 25.2 1.0
C B:CYS131 4.3 29.4 1.0
N B:CYS137 4.4 26.9 1.0
CA B:CYS137 4.5 27.5 1.0
N B:HIS133 4.5 31.3 1.0
N B:ASN147 4.5 29.5 1.0
C B:TRP130 4.6 27.9 1.0
CA B:GLY132 4.7 30.5 1.0
N B:CYS145 4.9 23.7 1.0
C B:CYS134 4.9 27.1 1.0
ND2 B:ASN147 4.9 31.9 1.0
CB B:TRP130 4.9 27.1 1.0
CA B:TRP130 4.9 27.8 1.0
C B:GLY132 4.9 31.1 1.0
C B:HIS133 5.0 30.4 1.0

Cadmium binding site 5 out of 12 in 3ip1

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Cadmium binding site 5 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd501

b:31.9
occ:0.50
CD B:CD501 0.0 31.9 0.5
CD B:CD501 1.7 27.9 0.5
O B:HOH514 2.4 33.0 1.0
OE2 B:GLU96 2.6 28.8 1.0
NE2 B:HIS95 2.6 26.0 1.0
OE1 B:GLU193 2.7 29.3 1.0
O B:HOH645 2.7 27.0 1.0
SG B:CYS66 3.0 30.3 1.0
CD2 B:HIS95 3.3 26.1 1.0
CD B:GLU193 3.4 29.4 1.0
CD B:GLU96 3.4 30.9 1.0
OE2 B:GLU193 3.5 33.1 1.0
CG B:GLU96 3.5 28.7 1.0
CB B:CYS66 3.6 27.5 1.0
CE1 B:HIS95 3.7 25.0 1.0
O B:HOH685 4.0 47.2 1.0
O B:HOH465 4.4 36.7 1.0
CG B:HIS95 4.6 26.3 1.0
OE1 B:GLU96 4.7 31.2 1.0
ND1 B:HIS95 4.7 26.3 1.0
CA B:CYS66 4.8 27.6 1.0
CB B:PRO194 4.8 23.1 1.0
CG B:GLU193 4.9 24.9 1.0

Cadmium binding site 6 out of 12 in 3ip1

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Cadmium binding site 6 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd501

b:27.9
occ:0.50
CD B:CD501 0.0 27.9 0.5
CD B:CD501 1.7 31.9 0.5
SG B:CYS66 2.3 30.3 1.0
NE2 B:HIS95 2.3 26.0 1.0
O B:HOH645 2.3 27.0 1.0
O B:HOH685 2.5 47.2 1.0
CE1 B:HIS95 3.0 25.0 1.0
O B:HOH514 3.2 33.0 1.0
CB B:CYS66 3.3 27.5 1.0
CD2 B:HIS95 3.5 26.1 1.0
OG B:SER68 3.8 26.7 0.5
OE2 B:GLU96 3.8 28.8 1.0
OE1 B:GLU193 4.1 29.3 1.0
OE2 B:GLU193 4.2 33.1 1.0
ND1 B:HIS95 4.2 26.3 1.0
CG B:HIS95 4.5 26.3 1.0
CD B:GLU193 4.5 29.4 1.0
OG B:SER68 4.5 26.0 0.5
CB B:SER68 4.6 26.5 0.5
CA B:CYS66 4.7 27.6 1.0
CD B:GLU96 4.7 30.9 1.0
CB B:SER68 4.7 26.3 0.5
CG B:GLU96 4.8 28.7 1.0
CZ B:PHE153 4.9 29.2 1.0

Cadmium binding site 7 out of 12 in 3ip1

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Cadmium binding site 7 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd500

b:29.7
occ:1.00
SG C:CYS134 2.3 27.2 1.0
SG C:CYS137 2.5 29.1 1.0
SG C:CYS145 2.5 29.8 1.0
SG C:CYS131 2.6 29.5 1.0
CB C:CYS145 3.2 27.1 1.0
CB C:CYS137 3.4 28.7 1.0
N C:CYS131 3.5 31.0 1.0
CB C:CYS134 3.5 29.5 1.0
CB C:CYS131 3.5 30.9 1.0
CA C:CYS145 3.6 27.1 1.0
N C:GLY132 3.8 32.1 1.0
N C:CYS134 3.9 30.2 1.0
CA C:CYS131 3.9 31.3 1.0
N C:GLU146 3.9 28.4 1.0
C C:CYS145 4.2 27.5 1.0
C C:CYS131 4.2 32.0 1.0
CA C:CYS134 4.3 28.9 1.0
N C:HIS133 4.4 32.7 1.0
N C:CYS137 4.5 29.2 1.0
N C:ASN147 4.5 30.5 1.0
CA C:CYS137 4.5 28.9 1.0
C C:TRP130 4.6 30.3 1.0
CA C:GLY132 4.8 32.3 1.0
N C:CYS145 4.8 25.3 1.0
ND2 C:ASN147 4.9 32.2 1.0
C C:GLY132 4.9 32.8 1.0
C C:CYS134 4.9 29.0 1.0
CA C:TRP130 5.0 30.1 1.0
C C:HIS133 5.0 31.6 1.0
CB C:TRP130 5.0 29.7 1.0

Cadmium binding site 8 out of 12 in 3ip1

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Cadmium binding site 8 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd501

b:31.6
occ:0.50
CD C:CD501 0.0 31.6 0.5
CD C:CD501 1.6 29.9 0.5
OE2 C:GLU96 2.5 32.6 1.0
O C:HOH516 2.5 40.7 1.0
NE2 C:HIS95 2.6 29.9 1.0
OE1 C:GLU193 2.7 31.4 1.0
O C:HOH681 2.7 30.0 1.0
SG C:CYS66 3.0 34.7 1.0
CD2 C:HIS95 3.3 29.6 1.0
CD C:GLU96 3.4 32.7 1.0
CD C:GLU193 3.4 31.1 1.0
OE2 C:GLU193 3.5 35.5 1.0
CG C:GLU96 3.5 29.8 1.0
CB C:CYS66 3.6 30.8 1.0
CE1 C:HIS95 3.7 29.0 1.0
O C:HOH686 4.0 43.8 1.0
CG C:HIS95 4.5 28.6 1.0
OE1 C:GLU96 4.6 33.2 1.0
ND1 C:HIS95 4.7 30.4 1.0
CA C:CYS66 4.8 31.2 1.0
CG C:GLU193 4.9 30.1 1.0
CB C:PRO194 5.0 27.6 1.0

Cadmium binding site 9 out of 12 in 3ip1

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Cadmium binding site 9 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd501

b:29.9
occ:0.50
CD C:CD501 0.0 29.9 0.5
CD C:CD501 1.6 31.6 0.5
O C:HOH681 2.3 30.0 1.0
SG C:CYS66 2.3 34.7 1.0
NE2 C:HIS95 2.3 29.9 1.0
O C:HOH686 2.5 43.8 1.0
CE1 C:HIS95 3.0 29.0 1.0
CB C:CYS66 3.3 30.8 1.0
O C:HOH516 3.3 40.7 1.0
CD2 C:HIS95 3.5 29.6 1.0
OE2 C:GLU96 3.7 32.6 1.0
OE1 C:GLU193 4.1 31.4 1.0
OG C:SER68 4.2 34.0 1.0
OE2 C:GLU193 4.2 35.5 1.0
ND1 C:HIS95 4.2 30.4 1.0
CB C:SER68 4.4 31.4 1.0
CG C:HIS95 4.5 28.6 1.0
CD C:GLU193 4.6 31.1 1.0
CD C:GLU96 4.6 32.7 1.0
CA C:CYS66 4.7 31.2 1.0
CG C:GLU96 4.8 29.8 1.0
CZ C:PHE153 5.0 28.3 1.0

Cadmium binding site 10 out of 12 in 3ip1

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Cadmium binding site 10 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd500

b:31.6
occ:1.00
SG D:CYS134 2.4 27.8 1.0
SG D:CYS137 2.5 30.2 1.0
SG D:CYS145 2.5 28.6 1.0
SG D:CYS131 2.5 29.8 1.0
CB D:CYS137 3.3 29.9 1.0
CB D:CYS145 3.4 28.2 1.0
N D:CYS131 3.5 29.6 1.0
CB D:CYS131 3.6 29.6 1.0
CB D:CYS134 3.6 29.6 1.0
CA D:CYS145 3.6 28.6 1.0
N D:GLY132 3.6 32.1 1.0
N D:CYS134 3.9 30.6 1.0
CA D:CYS131 3.9 30.4 1.0
N D:GLU146 3.9 29.1 1.0
C D:CYS131 4.2 31.5 1.0
C D:CYS145 4.2 28.7 1.0
CA D:CYS134 4.3 29.5 1.0
N D:HIS133 4.3 32.3 1.0
N D:CYS137 4.4 29.8 1.0
CA D:CYS137 4.4 30.1 1.0
N D:ASN147 4.5 30.6 1.0
C D:TRP130 4.6 28.7 1.0
CA D:GLY132 4.6 32.4 1.0
ND2 D:ASN147 4.9 27.3 1.0
O D:CYS134 4.9 30.0 1.0
C D:CYS134 4.9 30.0 1.0
N D:CYS145 4.9 27.5 1.0
CB D:TRP130 4.9 28.0 1.0
CA D:TRP130 4.9 28.2 1.0
C D:GLY132 4.9 32.8 1.0
C D:HIS133 5.0 31.9 1.0

Cadmium binding site 11 out of 12 in 3ip1

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Cadmium binding site 11 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd501

b:25.2
occ:0.50
CD D:CD501 0.0 25.2 0.5
CD D:CD501 1.7 37.6 0.5
OE2 D:GLU96 2.3 26.1 1.0
NE2 D:HIS95 2.6 28.4 1.0
OE1 D:GLU193 2.6 26.6 1.0
O D:HOH682 2.7 32.3 1.0
O D:HOH683 2.7 29.8 1.0
SG D:CYS66 2.9 33.5 1.0
CD D:GLU96 3.2 29.4 1.0
CD2 D:HIS95 3.4 28.2 1.0
CD D:GLU193 3.4 27.1 1.0
OE2 D:GLU193 3.4 29.9 1.0
CG D:GLU96 3.5 27.2 1.0
CB D:CYS66 3.5 30.2 1.0
CE1 D:HIS95 3.6 28.3 1.0
O D:HOH513 4.1 30.2 1.0
OE1 D:GLU96 4.4 29.1 1.0
CG D:HIS95 4.6 27.7 1.0
ND1 D:HIS95 4.7 28.1 1.0
CG D:GLU193 4.8 25.8 1.0
CA D:CYS66 4.8 30.8 1.0
CD D:PRO194 4.9 22.2 1.0
CB D:GLU96 4.9 26.7 1.0

Cadmium binding site 12 out of 12 in 3ip1

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Cadmium binding site 12 out of 12 in the Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd501

b:37.6
occ:0.50
CD D:CD501 0.0 37.6 0.5
CD D:CD501 1.7 25.2 0.5
O D:HOH683 2.2 29.8 1.0
SG D:CYS66 2.3 33.5 1.0
NE2 D:HIS95 2.3 28.4 1.0
CE1 D:HIS95 3.0 28.3 1.0
O D:HOH682 3.3 32.3 1.0
CB D:CYS66 3.4 30.2 1.0
CD2 D:HIS95 3.6 28.2 1.0
OE2 D:GLU96 3.6 26.1 1.0
OE1 D:GLU193 4.0 26.6 1.0
OE2 D:GLU193 4.1 29.9 1.0
ND1 D:HIS95 4.2 28.1 1.0
OG D:SER68 4.3 34.9 1.0
CB D:SER68 4.3 32.2 1.0
CD D:GLU193 4.4 27.1 1.0
CG D:HIS95 4.5 27.7 1.0
CD D:GLU96 4.5 29.4 1.0
CG D:GLU96 4.7 27.2 1.0
CA D:CYS66 4.8 30.8 1.0
CZ D:PHE153 4.9 28.2 1.0
O D:HOH513 5.0 30.2 1.0

Reference:

U.A.Ramagopal, R.Toro, S.K.Burley, S.C.Almo. Structure of Putative Alcohol Dehydrogenase (TM_042) From Thermotoga Maritima To Be Published.
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