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Cadmium in PDB 1ihf: Integration Host Factor/Dna Complex

Protein crystallography data

The structure of Integration Host Factor/Dna Complex, PDB code: 1ihf was solved by P.A.Rice, S.-W.Yang, K.Mizuuchi, H.A.Nash, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.360, 59.920, 180.800, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 25.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Integration Host Factor/Dna Complex (pdb code 1ihf). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Integration Host Factor/Dna Complex, PDB code: 1ihf:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15;

Cadmium binding site 1 out of 15 in 1ihf

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Cadmium binding site 1 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd303

b:57.3
occ:0.50
O C:HOH710 2.1 30.5 1.0
N7 C:DG-49 2.4 54.8 1.0
C8 C:DG-49 3.2 56.4 1.0
C5 C:DG-49 3.6 54.3 1.0
O6 C:DG-49 4.0 53.4 1.0
C6 C:DG-49 4.2 53.8 1.0
O A:HOH707 4.3 55.0 1.0
N9 C:DG-49 4.4 58.6 1.0
C5 C:DC-50 4.6 55.5 1.0
C4 C:DG-49 4.6 55.3 1.0
C6 C:DC-50 4.7 57.1 1.0
HO5' C:DC-50 4.8 30.0 1.0
C2' C:DC-50 4.8 65.6 1.0
C4 C:DC-50 4.8 56.5 1.0
N1 C:DC-50 4.9 58.9 1.0
O6 C:DG-48 5.0 44.0 1.0

Cadmium binding site 2 out of 15 in 1ihf

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Cadmium binding site 2 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd306

b:32.5
occ:0.25
O C:HOH519 2.2 41.0 1.0
CD C:CD315 2.3 59.9 0.2
N7 C:DG-18 2.5 40.5 1.0
O C:HOH525 2.6 53.7 1.0
O C:HOH520 3.1 43.1 1.0
C8 C:DG-18 3.3 42.2 1.0
C5 C:DG-18 3.6 39.8 1.0
O B:HOH523 3.9 45.8 1.0
O6 C:DG-18 4.0 42.2 1.0
C6 C:DG-18 4.2 40.4 1.0
C7 C:DT-19 4.5 33.9 1.0
O6 C:DG-17 4.5 39.8 1.0
C6 C:DT-19 4.5 35.3 1.0
C5 C:DT-19 4.6 34.7 1.0
N9 C:DG-18 4.6 43.5 1.0
C4 C:DG-18 4.8 40.7 1.0
H42 D:DC17 4.9 30.0 1.0
C2' C:DT-19 4.9 44.0 1.0

Cadmium binding site 3 out of 15 in 1ihf

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Cadmium binding site 3 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd313

b:53.8
occ:0.35
N7 C:DA-41 2.4 42.6 1.0
C8 C:DA-41 3.1 43.0 1.0
H61 C:DA-41 3.4 30.0 1.0
HZ3 B:LYS81 3.5 30.0 1.0
C5 C:DA-41 3.6 43.5 1.0
H61 C:DA-40 3.6 30.0 1.0
HZ2 B:LYS81 3.8 30.0 1.0
NZ B:LYS81 4.1 59.5 1.0
N6 C:DA-41 4.1 45.5 1.0
C6 C:DA-41 4.3 43.7 1.0
N9 C:DA-41 4.3 44.3 1.0
N7 C:DA-40 4.4 53.8 1.0
OP2 C:DA-41 4.5 33.8 1.0
N6 C:DA-40 4.5 53.4 1.0
C4 C:DA-41 4.5 43.4 1.0
HZ1 B:LYS81 4.6 30.0 1.0
C5 C:DC-42 4.6 38.0 1.0
C6 C:DC-42 4.7 37.7 1.0
H62 C:DA-40 5.0 30.0 1.0

Cadmium binding site 4 out of 15 in 1ihf

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Cadmium binding site 4 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd314

b:48.2
occ:0.25
N7 C:DG-36 2.1 47.0 1.0
O C:HOH574 2.4 46.7 1.0
O C:HOH573 2.6 57.5 1.0
C8 C:DG-36 2.9 47.8 1.0
C5 C:DG-36 3.2 46.5 1.0
O C:HOH575 3.5 57.4 1.0
O6 C:DG-36 3.6 42.6 1.0
C6 C:DG-36 3.7 44.4 1.0
O E:HOH570 4.1 43.5 1.0
N9 C:DG-36 4.1 50.5 1.0
C4 C:DG-36 4.3 47.9 1.0
H61 C:DA-35 4.3 30.0 1.0
C5 C:DT-37 4.3 55.3 1.0
C6 C:DT-37 4.4 55.8 1.0
C7 C:DT-37 4.5 53.9 1.0
C4 C:DT-37 4.7 55.1 1.0
H62 C:DA-35 4.8 30.0 1.0
N6 C:DA-35 4.8 46.9 1.0
N1 C:DT-37 4.8 57.1 1.0
O C:HOH576 4.9 60.3 1.0

Cadmium binding site 5 out of 15 in 1ihf

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Cadmium binding site 5 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd315

b:59.9
occ:0.25
CD C:CD306 2.3 32.5 0.2
O C:HOH520 2.5 43.1 1.0
N7 C:DG-18 3.2 40.5 1.0
C8 C:DG-18 3.5 42.2 1.0
O C:HOH519 3.7 41.0 1.0
N7 C:DG-17 3.8 42.1 1.0
O C:HOH525 3.9 53.7 1.0
O D:HOH521 4.0 41.5 1.0
O B:HOH523 4.1 45.8 1.0
O6 C:DG-17 4.1 39.8 1.0
C5 C:DG-18 4.2 39.8 1.0
H41 C:DC-16 4.3 30.0 1.0
N9 C:DG-18 4.5 43.5 1.0
H42 C:DC-16 4.7 30.0 1.0
C5 C:DG-17 4.7 41.1 1.0
C6 C:DG-17 4.8 40.9 1.0
N4 C:DC-16 4.8 46.4 1.0
C8 C:DG-17 4.8 43.5 1.0
C4 C:DG-18 4.9 40.7 1.0
C6 C:DG-18 5.0 40.4 1.0

Cadmium binding site 6 out of 15 in 1ihf

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Cadmium binding site 6 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd304

b:33.1
occ:0.35
OP2 D:DT28 2.0 32.6 1.0
O D:HOH642 2.1 47.9 1.0
O D:HOH641 2.1 63.8 1.0
P D:DT28 3.4 32.8 1.0
OP1 D:DT28 4.1 34.0 1.0
O5' D:DT28 4.1 31.6 1.0
C5' D:DT28 4.4 29.6 1.0
O3' D:DA27 4.5 31.9 1.0
O D:HOH643 4.6 46.3 1.0
OP2 D:DT29 4.7 30.0 1.0
O5' D:DA27 4.7 36.9 1.0
OP2 D:DA27 4.7 37.0 1.0
C3' D:DT28 4.8 29.7 1.0

Cadmium binding site 7 out of 15 in 1ihf

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Cadmium binding site 7 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd305

b:49.8
occ:0.35
N7 D:DG15 2.2 55.5 1.0
O D:HOH522 2.2 50.1 1.0
O D:HOH521 2.2 41.5 1.0
C8 D:DG15 3.0 56.2 1.0
C5 D:DG15 3.3 54.4 1.0
O6 D:DG15 3.8 53.9 1.0
C6 D:DG15 3.9 53.8 1.0
O C:HOH520 4.1 43.1 1.0
HO5' D:DG15 4.2 30.0 1.0
N9 D:DG15 4.2 57.2 1.0
C4 D:DG15 4.4 54.6 1.0
O6 D:DG16 4.7 54.8 1.0
N7 D:DG16 4.9 56.0 1.0
O5' D:DG15 4.9 65.5 1.0

Cadmium binding site 8 out of 15 in 1ihf

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Cadmium binding site 8 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd309

b:47.1
occ:1.00
N7 D:DA24 2.3 30.7 1.0
O D:HOH450 2.4 44.3 1.0
O D:HOH456 2.5 34.1 1.0
O D:HOH457 2.5 18.2 1.0
H61 D:DA24 3.0 30.0 1.0
C8 D:DA24 3.1 29.9 1.0
C5 D:DA24 3.5 27.9 1.0
N6 D:DA24 3.9 26.7 1.0
C6 D:DA24 4.1 26.8 1.0
O D:HOH449 4.2 25.9 1.0
O D:HOH451 4.2 40.9 1.0
O C:HOH453 4.3 45.0 1.0
N9 D:DA24 4.4 28.4 1.0
O6 D:DG25 4.5 28.9 1.0
C4 D:DA24 4.6 28.2 1.0
C8 D:DA23 4.6 32.4 1.0
O C:HOH455 4.6 43.5 1.0
N7 D:DA23 4.6 32.3 1.0
H62 D:DA24 4.7 30.0 1.0
H42 C:DC-25 4.8 30.0 1.0
O D:HOH458 4.8 41.5 1.0

Cadmium binding site 9 out of 15 in 1ihf

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Cadmium binding site 9 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd301

b:40.4
occ:1.00
O E:HOH662 2.2 47.3 1.0
O E:HOH425 2.2 27.1 1.0
N7 E:DG30 2.3 33.5 1.0
O C:HOH424 2.4 31.2 1.0
C8 E:DG30 3.2 35.3 1.0
C5 E:DG30 3.4 33.6 1.0
O C:HOH423 3.4 49.7 1.0
O6 E:DG30 3.6 33.3 1.0
C6 E:DG30 3.9 33.4 1.0
H41 E:DC31 4.3 30.0 1.0
HO5' E:DG30 4.4 30.0 1.0
N9 E:DG30 4.5 37.3 1.0
C4 E:DG30 4.5 34.6 1.0
O D:HOH426 4.7 45.9 1.0
N4 E:DC31 4.7 32.3 1.0
H42 E:DC31 4.7 30.0 1.0
O5' E:DG30 4.9 46.6 1.0

Cadmium binding site 10 out of 15 in 1ihf

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Cadmium binding site 10 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:48.5
occ:0.25
OE2 A:GLU10 2.1 56.0 1.0
OD2 A:ASP14 2.7 56.1 1.0
OD1 A:ASP14 2.9 55.0 1.0
CD A:GLU10 3.1 56.5 1.0
CG A:ASP14 3.2 55.3 1.0
CG A:GLU10 3.5 54.2 1.0
OE1 A:GLU10 4.2 57.2 1.0
CB A:ASP14 4.7 53.6 1.0

Cadmium binding site 11 out of 15 in 1ihf

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Cadmium binding site 11 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd311

b:44.7
occ:0.25
OE2 A:GLU7 2.1 52.8 1.0
O A:HOH555 2.6 42.5 1.0
O A:ALA2 2.6 37.9 1.0
CD B:CD310 2.8 44.7 0.2
CD A:GLU7 3.0 51.7 1.0
OE2 B:GLU41 3.1 54.3 1.0
OE1 A:GLU7 3.3 53.4 1.0
C A:ALA2 3.4 34.4 1.0
N A:ALA2 3.5 33.9 1.0
O A:HOH556 3.8 38.1 1.0
CA A:ALA2 4.1 33.6 1.0
CD B:GLU41 4.2 53.2 1.0
N A:LEU3 4.3 33.7 1.0
CG A:GLU7 4.4 46.6 1.0
CA A:LEU3 4.6 32.2 1.0
OE1 B:GLU41 4.7 57.0 1.0
O A:HOH735 4.8 54.9 1.0
HG1 A:THR4 4.9 30.0 1.0

Cadmium binding site 12 out of 15 in 1ihf

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Cadmium binding site 12 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd312

b:62.5
occ:0.25
HH11 A:ARG21 2.4 30.0 1.0
NH1 A:ARG21 3.2 74.0 1.0
CD A:ARG21 3.2 66.2 1.0
O B:HOH532 3.3 46.7 1.0
OD1 A:ASP22 3.6 56.7 1.0
OD2 A:ASP22 3.7 57.0 1.0
HH12 A:ARG21 3.7 30.0 1.0
CG A:ASP22 3.9 56.9 1.0
NE A:ARG21 3.9 70.0 1.0
CZ A:ARG21 3.9 73.0 1.0
HD1 B:HIS16 4.2 30.0 1.0
CG A:ARG21 4.4 62.0 1.0
OG A:SER19 4.4 53.8 1.0
HG A:SER19 4.7 30.0 1.0
CB A:ARG21 4.7 57.5 1.0
HE A:ARG21 4.8 30.0 1.0
ND1 B:HIS16 4.8 63.5 1.0
H A:ASP22 4.8 30.0 1.0
CE1 B:HIS16 5.0 63.2 1.0

Cadmium binding site 13 out of 15 in 1ihf

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Cadmium binding site 13 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:44.6
occ:0.50
HE2 B:HIS54 1.5 30.0 1.0
O B:HOH565 2.0 42.0 1.0
O B:HOH564 2.1 34.2 1.0
HD1 B:HIS79 2.2 30.0 1.0
NE2 B:HIS54 2.4 27.1 1.0
OG B:SER52 2.7 37.6 1.0
ND1 B:HIS79 2.8 31.1 1.0
HG B:SER52 3.2 30.0 1.0
CE1 B:HIS54 3.2 26.4 1.0
CE1 B:HIS79 3.4 31.1 1.0
O B:HOH741 3.5 36.0 1.0
CD2 B:HIS54 3.5 27.0 1.0
CG B:HIS79 3.8 29.6 1.0
O E:HOH566 3.9 31.3 1.0
CB B:SER52 3.9 35.0 1.0
O C:HOH740 4.2 50.8 1.0
CB B:HIS79 4.4 27.6 1.0
ND1 B:HIS54 4.4 25.8 1.0
NE2 B:HIS79 4.5 31.2 1.0
CG B:HIS54 4.6 27.6 1.0
CD2 B:HIS79 4.7 29.4 1.0
O B:HOH563 4.9 48.8 1.0
O B:HIS79 4.9 31.0 1.0

Cadmium binding site 14 out of 15 in 1ihf

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Cadmium binding site 14 out of 15 in the Integration Host Factor/Dna Complex


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd308

b:63.4
occ:0.63
HE2 B:HIS16 1.4 30.0 1.0
NE2 B:HIS16 2.2 63.6 1.0
OE1 B:GLN14 2.2 65.7 1.0
OE2 A:GLU25 2.3 59.0 1.0
O B:HOH533 2.3 43.1 1.0
OE1 A:GLU25 2.4 56.9 1.0
CD A:GLU25 2.7 55.5 1.0
CE1 B:HIS16 3.1 63.2 1.0
CD2 B:HIS16 3.1 63.3 1.0
CD B:GLN14 3.3 64.2 1.0
HE21 B:GLN14 3.4 30.0 1.0
NE2 B:GLN14 3.8 64.8 1.0
CG A:GLU25 4.1 52.4 1.0
ND1 B:HIS16 4.2 63.5 1.0
CG B:HIS16 4.3 63.0 1.0
CG B:GLN14 4.6 62.8 1.0
HE22 B:GLN14 4.8 30.0 1.0

Cadmium binding site 15 out of 15 in 1ihf

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Cadmium binding site 15 out of 15 in the Integration Host Factor/Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 15 of Integration Host Factor/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd310

b:44.7
occ:0.25
OE2 B:GLU41 2.6 54.3 1.0
OE1 B:GLU41 2.7 57.0 1.0
CD A:CD311 2.8 44.7 0.2
OE1 A:GLU7 3.0 53.4 1.0
CD B:GLU41 3.0 53.2 1.0
CD A:GLU7 3.7 51.7 1.0
OE2 A:GLU7 3.8 52.8 1.0
O B:HOH734 4.1 49.8 1.0
O A:HOH733 4.2 56.0 1.0
CG B:GLU41 4.6 49.1 1.0
O A:ALA2 4.6 37.9 1.0
C A:ALA2 4.9 34.4 1.0

Reference:

P.A.Rice, S.Yang, K.Mizuuchi, H.A.Nash. Crystal Structure of An Ihf-Dna Complex: A Protein-Induced Dna U-Turn. Cell(Cambridge,Mass.) V. 87 1295 1996.
ISSN: ISSN 0092-8674
PubMed: 8980235
DOI: 10.1016/S0092-8674(00)81824-3
Page generated: Fri Aug 28 11:57:26 2020
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