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Cadmium in PDB 1jre: Dna Protection and Binding By E. Coli Dps Protein

Protein crystallography data

The structure of Dna Protection and Binding By E. Coli Dps Protein, PDB code: 1jre was solved by J.Luo, D.Liu, M.A.White, R.O.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.92 / 2.65
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 90.585, 90.585, 226.507, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 26.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Dna Protection and Binding By E. Coli Dps Protein (pdb code 1jre). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Dna Protection and Binding By E. Coli Dps Protein, PDB code: 1jre:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13;

Cadmium binding site 1 out of 13 in 1jre

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Cadmium binding site 1 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:61.4
occ:1.00
OE2 A:GLU82 2.1 45.7 1.0
NE2 B:HIS51 2.4 50.6 1.0
O A:HOH590 2.5 14.5 1.0
O B:HOH575 2.7 15.9 1.0
O A:HOH603 2.8 38.4 1.0
O B:HOH579 3.2 44.4 1.0
CE1 B:HIS51 3.3 53.3 1.0
CD A:GLU82 3.3 46.4 1.0
CD2 B:HIS51 3.4 51.3 1.0
O B:HOH595 3.4 60.9 1.0
OD2 B:ASP67 3.7 63.0 1.0
NE2 B:HIS63 3.9 44.6 1.0
OE1 A:GLU82 3.9 49.7 1.0
CE1 B:HIS63 4.2 44.5 1.0
ND1 B:HIS51 4.5 52.0 1.0
CG A:GLU82 4.5 44.3 1.0
CG B:HIS51 4.5 51.3 1.0
NE1 B:TRP52 4.7 55.4 1.0
CD1 B:TRP52 4.8 55.1 1.0
CG B:ASP67 4.9 58.1 1.0
CB A:ALA78 4.9 40.5 1.0
CD2 B:HIS63 5.0 44.6 1.0

Cadmium binding site 2 out of 13 in 1jre

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Cadmium binding site 2 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:61.5
occ:1.00
OE2 B:GLU82 2.2 60.0 1.0
NE2 A:HIS51 2.3 51.3 1.0
O A:HOH568 2.5 17.4 1.0
O A:HOH557 2.6 13.7 1.0
O A:HOH570 2.8 45.3 1.0
CE1 A:HIS51 3.2 51.0 1.0
CD B:GLU82 3.4 57.4 1.0
CD2 A:HIS51 3.4 51.0 1.0
OD2 A:ASP67 3.7 61.6 1.0
NE2 A:HIS63 3.9 46.3 1.0
OE1 B:GLU82 4.0 58.7 1.0
CE1 A:HIS63 4.3 45.0 1.0
O A:HOH569 4.3 46.9 1.0
ND1 A:HIS51 4.4 52.4 1.0
CG A:HIS51 4.5 51.6 1.0
CG B:GLU82 4.5 55.5 1.0
NE1 A:TRP52 4.8 56.0 1.0
CD1 A:TRP52 4.8 57.1 1.0
CG A:ASP67 4.9 60.8 1.0
CD2 A:HIS63 4.9 45.9 1.0
CB B:ALA78 5.0 46.0 1.0

Cadmium binding site 3 out of 13 in 1jre

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Cadmium binding site 3 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd201

b:90.3
occ:1.00
OE2 C:GLU82 2.1 71.5 1.0
NE2 D:HIS51 2.4 79.7 1.0
O C:HOH693 2.5 39.2 1.0
O C:HOH681 3.1 56.9 1.0
CD C:GLU82 3.2 71.1 1.0
CE1 D:HIS51 3.3 79.2 1.0
CD2 D:HIS51 3.4 79.6 1.0
OD2 D:ASP67 3.6 71.8 1.0
NE2 D:HIS63 3.8 69.3 1.0
OE1 C:GLU82 3.9 74.2 1.0
CE1 D:HIS63 4.2 69.8 1.0
CG C:GLU82 4.4 70.2 1.0
ND1 D:HIS51 4.5 78.8 1.0
CG D:HIS51 4.5 78.9 1.0
CG D:ASP67 4.8 73.2 1.0
CD2 D:HIS63 4.9 70.2 1.0
NE1 D:TRP52 4.9 80.4 1.0
CD1 D:TRP52 4.9 79.8 1.0
CB C:ALA78 4.9 61.8 1.0

Cadmium binding site 4 out of 13 in 1jre

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Cadmium binding site 4 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd201

b:71.5
occ:1.00
OE2 D:GLU82 2.1 60.9 1.0
O C:HOH662 2.4 20.9 1.0
NE2 C:HIS51 2.4 64.0 1.0
O D:HOH651 2.7 21.4 1.0
O C:HOH656 3.1 57.7 1.0
CE1 C:HIS51 3.3 65.3 1.0
CD D:GLU82 3.3 58.1 1.0
CD2 C:HIS51 3.5 61.8 1.0
OD2 C:ASP67 3.7 63.2 1.0
NE2 C:HIS63 3.8 50.9 1.0
OE1 D:GLU82 3.9 58.6 1.0
CE1 C:HIS63 4.1 51.5 1.0
O C:HOH664 4.3 46.6 1.0
CG D:GLU82 4.4 55.3 1.0
ND1 C:HIS51 4.4 63.9 1.0
CG C:HIS51 4.6 61.0 1.0
NE1 C:TRP52 4.8 60.0 1.0
CD1 C:TRP52 4.9 59.4 1.0
CD2 C:HIS63 4.9 52.5 1.0
CG C:ASP67 4.9 61.3 1.0

Cadmium binding site 5 out of 13 in 1jre

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Cadmium binding site 5 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd201

b:73.8
occ:1.00
OE2 E:GLU82 2.1 65.8 1.0
O F:HOH683 2.4 22.7 1.0
NE2 F:HIS51 2.4 75.5 1.0
O F:HOH694 2.4 17.3 1.0
CD E:GLU82 3.3 66.6 1.0
CE1 F:HIS51 3.3 75.0 1.0
CD2 F:HIS51 3.3 73.5 1.0
OD2 F:ASP67 3.7 71.4 1.0
OE1 E:GLU82 3.9 67.6 1.0
NE2 F:HIS63 4.0 67.2 1.0
O F:HOH692 4.1 56.2 1.0
CE1 F:HIS63 4.3 65.9 1.0
ND1 F:HIS51 4.5 74.3 1.0
CG E:GLU82 4.5 65.5 1.0
CG F:HIS51 4.5 73.4 1.0
NE1 F:TRP52 4.7 71.5 1.0
CD1 F:TRP52 4.7 71.8 1.0
CG F:ASP67 4.9 69.8 1.0
CB E:ALA78 4.9 54.1 1.0

Cadmium binding site 6 out of 13 in 1jre

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Cadmium binding site 6 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd201

b:65.8
occ:1.00
OE2 F:GLU82 2.1 72.3 1.0
O E:HOH612 2.4 18.5 1.0
NE2 E:HIS51 2.5 71.3 1.0
O E:HOH628 2.5 13.5 1.0
O F:HOH624 2.8 46.8 1.0
CD F:GLU82 3.3 71.6 1.0
CE1 E:HIS51 3.4 71.3 1.0
CD2 E:HIS51 3.5 68.3 1.0
OD2 E:ASP67 3.6 65.4 1.0
OE1 F:GLU82 4.0 72.5 1.0
NE2 E:HIS63 4.1 60.7 1.0
CE1 E:HIS63 4.4 60.1 1.0
CG F:GLU82 4.5 69.0 1.0
ND1 E:HIS51 4.5 70.5 1.0
CG E:HIS51 4.6 67.7 1.0
NE1 E:TRP52 4.8 61.1 1.0
CG E:ASP67 4.8 61.6 1.0
CD1 E:TRP52 4.9 61.0 1.0
CB F:ALA78 4.9 53.1 1.0

Cadmium binding site 7 out of 13 in 1jre

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Cadmium binding site 7 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cd202

b:87.8
occ:1.00
O G:HOH585 2.7 37.1 1.0
O G:HOH573 2.9 28.4 1.0
OE2 G:GLU120 3.0 64.1 1.0
OE1 G:GLU120 3.0 68.9 1.0
CD G:GLU120 3.2 65.2 1.0
O G:HOH566 4.4 54.2 1.0
CG G:GLU120 4.6 63.0 1.0
NZ G:LYS105 4.6 45.7 1.0
NH2 G:ARG124 4.8 53.9 1.0
CE G:LYS105 4.9 46.6 1.0

Cadmium binding site 8 out of 13 in 1jre

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Cadmium binding site 8 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cd201

b:67.5
occ:1.00
OE2 G:GLU82 2.2 60.1 1.0
O H:HOH643 2.2 18.1 1.0
NE2 H:HIS51 2.5 50.6 1.0
O H:HOH631 2.5 30.3 1.0
O G:HOH642 3.0 55.9 1.0
O G:HOH648 3.2 25.8 1.0
CD G:GLU82 3.4 57.7 1.0
CD2 H:HIS51 3.4 52.0 1.0
CE1 H:HIS51 3.4 51.7 1.0
OD2 H:ASP67 3.6 63.2 1.0
OE1 G:GLU82 4.0 56.9 1.0
NE2 H:HIS63 4.1 51.7 1.0
CE1 H:HIS63 4.4 51.7 1.0
CG G:GLU82 4.5 56.8 1.0
ND1 H:HIS51 4.5 50.5 1.0
CG H:HIS51 4.6 51.3 1.0
NE1 H:TRP52 4.7 60.5 1.0
CD1 H:TRP52 4.8 58.5 1.0
CG H:ASP67 4.9 62.0 1.0
CB G:ALA78 4.9 48.8 1.0

Cadmium binding site 9 out of 13 in 1jre

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Cadmium binding site 9 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd201

b:57.4
occ:1.00
OE2 H:GLU82 2.0 58.7 1.0
O G:HOH559 2.4 16.0 1.0
O G:HOH565 2.4 31.2 1.0
NE2 G:HIS51 2.5 43.9 1.0
O H:HOH558 3.1 49.5 1.0
CD H:GLU82 3.2 59.7 1.0
O G:HOH572 3.4 58.1 1.0
CE1 G:HIS51 3.4 45.5 1.0
CD2 G:HIS51 3.5 44.2 1.0
OD2 G:ASP67 3.8 53.7 1.0
OE1 H:GLU82 3.9 62.6 1.0
NE2 G:HIS63 4.0 46.2 1.0
CE1 G:HIS63 4.3 46.7 1.0
O G:HOH580 4.3 50.9 1.0
CG H:GLU82 4.4 57.8 1.0
ND1 G:HIS51 4.6 44.6 1.0
CG G:HIS51 4.6 45.5 1.0
NE1 G:TRP52 4.7 45.9 1.0
CD1 G:TRP52 4.8 44.3 1.0
CB H:ALA78 4.8 40.3 1.0
CG G:ASP67 5.0 49.7 1.0

Cadmium binding site 10 out of 13 in 1jre

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Cadmium binding site 10 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cd201

b:72.8
occ:1.00
O J:HOH660 2.1 29.3 1.0
OE2 I:GLU82 2.2 75.1 1.0
NE2 J:HIS51 2.4 66.8 1.0
O I:HOH677 2.5 36.3 1.0
O J:HOH670 2.9 48.0 1.0
CE1 J:HIS51 3.4 67.0 1.0
CD I:GLU82 3.4 73.0 1.0
CD2 J:HIS51 3.4 67.5 1.0
OD2 J:ASP67 3.6 72.0 1.0
NE2 J:HIS63 4.0 60.2 1.0
OE1 I:GLU82 4.0 73.1 1.0
CE1 J:HIS63 4.3 60.9 1.0
CG I:GLU82 4.5 70.8 1.0
ND1 J:HIS51 4.5 67.9 1.0
CG J:HIS51 4.6 68.2 1.0
NE1 J:TRP52 4.8 62.0 1.0
CG J:ASP67 4.8 67.8 1.0
CD1 J:TRP52 4.9 59.7 1.0
CB I:ALA78 4.9 53.0 1.0

Cadmium binding site 11 out of 13 in 1jre

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Cadmium binding site 11 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cd201

b:75.6
occ:1.00
OE2 J:GLU82 2.1 83.6 1.0
O I:HOH701 2.2 10.7 1.0
NE2 I:HIS51 2.4 77.2 1.0
O I:HOH697 2.7 49.3 1.0
O I:HOH699 2.7 39.2 1.0
CE1 I:HIS51 3.3 77.4 1.0
CD J:GLU82 3.3 81.5 1.0
CD2 I:HIS51 3.4 75.7 1.0
OD2 I:ASP67 3.6 74.2 1.0
NE2 I:HIS63 3.9 68.2 1.0
OE1 J:GLU82 3.9 81.7 1.0
O I:HOH695 4.2 50.9 1.0
CE1 I:HIS63 4.2 68.2 1.0
ND1 I:HIS51 4.4 76.2 1.0
CG J:GLU82 4.5 77.9 1.0
CG I:HIS51 4.5 75.9 1.0
NE1 I:TRP52 4.8 66.3 1.0
CD1 I:TRP52 4.8 66.8 1.0
CG I:ASP67 4.9 71.8 1.0
CB J:ALA78 4.9 63.7 1.0
CD2 I:HIS63 5.0 67.9 1.0

Cadmium binding site 12 out of 13 in 1jre

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Cadmium binding site 12 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cd201

b:67.9
occ:1.00
OE2 K:GLU82 2.0 53.6 1.0
O L:HOH531 2.4 20.8 1.0
NE2 L:HIS51 2.4 62.5 1.0
O L:HOH526 2.6 22.7 1.0
O L:HOH540 2.9 53.2 1.0
CD K:GLU82 3.2 54.9 1.0
CE1 L:HIS51 3.3 61.1 1.0
CD2 L:HIS51 3.4 61.9 1.0
O K:HOH532 3.4 34.4 1.0
OD2 L:ASP67 3.6 62.5 1.0
OE1 K:GLU82 3.8 53.4 1.0
NE2 L:HIS63 3.9 50.4 1.0
CE1 L:HIS63 4.2 53.5 1.0
CG K:GLU82 4.4 54.2 1.0
ND1 L:HIS51 4.5 61.6 1.0
CG L:HIS51 4.6 63.0 1.0
NE1 L:TRP52 4.8 64.7 1.0
CD1 L:TRP52 4.8 63.1 1.0
CG L:ASP67 4.8 61.0 1.0
CD2 L:HIS63 4.9 52.2 1.0
CB K:ALA78 5.0 47.9 1.0

Cadmium binding site 13 out of 13 in 1jre

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Cadmium binding site 13 out of 13 in the Dna Protection and Binding By E. Coli Dps Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Dna Protection and Binding By E. Coli Dps Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd201

b:74.6
occ:1.00
OE2 L:GLU82 2.1 62.3 1.0
NE2 K:HIS51 2.4 67.7 1.0
O L:HOH583 2.4 61.2 1.0
O K:HOH586 2.5 26.2 1.0
O K:HOH564 2.7 28.8 1.0
CD L:GLU82 3.3 61.8 1.0
CE1 K:HIS51 3.3 67.7 1.0
CD2 K:HIS51 3.4 66.3 1.0
OD2 K:ASP67 3.6 63.5 1.0
O L:HOH601 3.7 43.0 1.0
OE1 L:GLU82 3.9 61.7 1.0
NE2 K:HIS63 3.9 49.4 1.0
O L:HOH576 4.3 56.1 1.0
CE1 K:HIS63 4.3 49.7 1.0
CG L:GLU82 4.4 62.7 1.0
ND1 K:HIS51 4.5 67.3 1.0
CG K:HIS51 4.5 64.6 1.0
NE1 K:TRP52 4.7 66.8 1.0
CD1 K:TRP52 4.7 67.0 1.0
CG K:ASP67 4.9 60.9 1.0
CB L:ALA78 4.9 55.6 1.0
CD2 K:HIS63 5.0 51.2 1.0

Reference:

J.Luo, D.Liu, M.A.White, R.O.Fox. Dna Protection and Binding By E. Coli Dps Protein To Be Published.
Page generated: Fri Aug 28 12:02:44 2020
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