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Cadmium in PDB 1tq5: Crystal Structure of Yhhw From Escherichia Coli

Protein crystallography data

The structure of Crystal Structure of Yhhw From Escherichia Coli, PDB code: 1tq5 was solved by M.Adams, Z.Jia, Montreal-Kingston Bacterial Structural Genomicsinitiative (Bsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.23 / 1.76
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.769, 62.769, 98.053, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 25

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Yhhw From Escherichia Coli (pdb code 1tq5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Yhhw From Escherichia Coli, PDB code: 1tq5:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1tq5

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Cadmium binding site 1 out of 6 in the Crystal Structure of Yhhw From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Yhhw From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1000

b:38.7
occ:1.00
NE2 A:HIS59 2.3 31.3 1.0
O A:HOH1052 2.5 21.6 1.0
NE2 A:HIS101 2.6 34.8 1.0
O A:HOH1059 2.7 30.9 1.0
CE1 A:HIS57 2.8 44.9 1.0
CD2 A:HIS59 3.1 30.4 1.0
ND1 A:HIS57 3.3 43.9 1.0
CE1 A:HIS59 3.4 35.1 1.0
O A:HOH1107 3.4 57.8 1.0
CE1 A:HIS101 3.5 32.2 1.0
CD2 A:HIS101 3.6 32.6 1.0
NE2 A:HIS57 3.7 45.6 1.0
CG A:HIS59 4.3 31.1 1.0
CG A:HIS57 4.4 37.7 1.0
ND1 A:HIS59 4.4 34.1 1.0
CZ2 A:TRP118 4.6 37.8 1.0
CD2 A:HIS57 4.6 43.4 1.0
ND1 A:HIS101 4.6 30.2 1.0
CG A:HIS101 4.7 30.0 1.0
OE1 A:GLU103 4.9 50.8 1.0
O A:HOH1093 5.0 49.8 1.0

Cadmium binding site 2 out of 6 in 1tq5

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Cadmium binding site 2 out of 6 in the Crystal Structure of Yhhw From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Yhhw From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:47.2
occ:1.00
O A:HOH1145 2.3 28.4 1.0
NZ A:LYS198 3.2 42.3 1.0
CE A:LYS198 3.5 47.5 1.0
OG1 A:THR193 4.2 27.7 1.0
OD1 A:ASP218 4.3 46.5 1.0
CG A:ASP218 4.8 43.6 1.0
OD2 A:ASP218 4.9 46.4 1.0
CD A:LYS198 5.0 43.4 1.0

Cadmium binding site 3 out of 6 in 1tq5

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Cadmium binding site 3 out of 6 in the Crystal Structure of Yhhw From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Yhhw From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:34.3
occ:1.00
OD2 A:ASP203 2.5 22.3 1.0
O A:HOH1094 2.5 29.8 1.0
OD1 A:ASP203 2.6 17.4 1.0
O A:HOH1041 2.6 28.0 1.0
O A:HOH1006 2.6 12.5 1.0
O A:HOH1008 2.6 22.7 1.0
CG A:ASP203 2.8 21.9 1.0
OG A:SER200 3.2 38.7 1.0
N A:ALA7 4.2 18.0 1.0
CB A:ASP203 4.3 17.1 1.0
CB A:ALA7 4.4 22.7 1.0
CB A:SER200 4.6 29.0 1.0
N A:SER200 4.7 24.1 1.0
O A:THR201 4.7 18.8 1.0
CA A:LYS6 4.8 19.8 1.0
O A:SER200 4.9 24.9 1.0
CG A:LYS6 4.9 29.4 1.0
CB A:LYS6 4.9 22.3 1.0
OD1 A:ASN8 5.0 44.8 1.0
CA A:ALA7 5.0 20.2 1.0

Cadmium binding site 4 out of 6 in 1tq5

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Cadmium binding site 4 out of 6 in the Crystal Structure of Yhhw From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Yhhw From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:34.2
occ:1.00
OE1 A:GLU89 2.5 29.5 1.0
OE2 A:GLU89 2.6 37.8 1.0
O A:HOH1019 2.6 34.0 1.0
CD A:GLU89 2.9 32.8 1.0
OE1 A:GLN132 3.9 30.2 1.0
CD A:PRO86 4.0 30.7 1.0
CG A:PRO86 4.4 29.3 1.0
CD A:ARG134 4.4 36.6 1.0
CG A:GLU89 4.4 26.8 1.0
NE2 A:GLN132 4.4 37.1 1.0
CB A:ARG134 4.5 32.3 1.0
CD A:GLN132 4.5 29.7 1.0
O A:GLN84 4.6 34.0 1.0
NH1 A:ARG134 4.7 38.1 1.0
OE1 A:GLU83 4.8 29.7 1.0
CG A:ARG134 4.9 32.4 1.0

Cadmium binding site 5 out of 6 in 1tq5

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Cadmium binding site 5 out of 6 in the Crystal Structure of Yhhw From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Yhhw From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:35.5
occ:1.00
ND1 A:HIS237 2.5 28.9 1.0
O A:HOH1085 2.5 10.0 1.0
O A:HOH1086 2.6 26.1 1.0
CE1 A:HIS239 2.6 24.7 1.0
NE2 A:HIS239 3.0 25.4 1.0
O A:ASN33 3.1 30.1 1.0
CG A:HIS237 3.3 35.0 1.0
CB A:HIS237 3.4 41.7 1.0
CE1 A:HIS237 3.5 35.1 1.0
ND1 A:HIS239 3.9 26.7 1.0
C A:ASN33 4.1 29.6 1.0
O A:GLY36 4.3 32.1 1.0
CD2 A:HIS239 4.4 21.5 1.0
CA A:PHE34 4.4 29.8 1.0
CD1 A:PHE37 4.5 24.4 1.0
CD2 A:HIS237 4.5 36.2 1.0
NE2 A:HIS237 4.6 38.2 1.0
N A:MSE35 4.7 31.4 1.0
N A:PHE34 4.7 29.6 1.0
CG A:HIS239 4.8 25.3 1.0
C A:GLY36 4.9 29.2 1.0
CA A:HIS237 4.9 40.0 1.0
O A:HOH1024 5.0 29.0 1.0

Cadmium binding site 6 out of 6 in 1tq5

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Cadmium binding site 6 out of 6 in the Crystal Structure of Yhhw From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Yhhw From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:72.5
occ:1.00
OD1 A:ASP136 2.8 44.4 1.0
O A:HOH1087 3.0 43.8 1.0
OD2 A:ASP136 3.2 54.9 1.0
CG A:ASP136 3.3 50.6 1.0
O A:ALA137 4.7 60.0 1.0
CB A:ASP136 4.7 49.6 1.0
N A:ALA137 4.9 55.8 1.0

Reference:

M.Adams, Z.Jia. Structural and Biochemical Analysis Reveal Pirins to Possess Quercetinase Activity. J.Biol.Chem. V. 280 28675 2005.
ISSN: ISSN 0021-9258
PubMed: 15951572
DOI: 10.1074/JBC.M501034200
Page generated: Fri Aug 28 12:27:06 2020
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