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Potassium in PDB 2hzv: Nikr-Operator Dna Complex

Protein crystallography data

The structure of Nikr-Operator Dna Complex, PDB code: 2hzv was solved by E.R.Schreiter, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.28 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 197.203, 76.132, 132.092, 90.00, 110.27, 90.00
R / Rfree (%) 26.1 / 30.3

Other elements in 2hzv:

The structure of Nikr-Operator Dna Complex also contains other interesting chemical elements:

Nickel (Ni) 8 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Potassium atom in the Nikr-Operator Dna Complex (pdb code 2hzv). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 11 binding sites of Potassium where determined in the Nikr-Operator Dna Complex, PDB code: 2hzv:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 1 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:97.6
occ:1.00
 O B:ILE116 2.4 96.2 1.0
O B:VAL121 2.5 81.3 1.0
OE2 A:GLU30 2.7 73.4 1.0
OD1 A:ASP34 2.8 85.9 1.0
OD2 A:ASP34 2.9 76.4 1.0
CG A:ASP34 3.2 82.2 1.0
O B:GLN118 3.2 87.7 1.0
C B:VAL121 3.6 75.0 1.0
C B:ILE116 3.6 90.9 1.0
CD A:GLU30 3.6 73.1 1.0
O B:ALA117 3.9 0.1 1.0
OE1 A:GLU30 3.9 78.9 1.0
C B:ALA117 4.0 100.0 1.0
C B:GLN118 4.2 92.2 1.0
CB B:VAL121 4.3 63.5 1.0
CA B:ALA117 4.3 94.7 1.0
CA B:VAL121 4.3 69.6 1.0
N B:VAL121 4.3 75.9 1.0
CG2 B:ILE116 4.4 94.5 1.0
N B:ALA117 4.4 88.2 1.0
N B:GLN118 4.5 97.6 1.0
N B:ARG122 4.5 80.7 1.0
CA B:ILE116 4.6 88.3 1.0
CB A:ASP34 4.6 80.1 1.0
CA B:ARG122 4.7 84.5 1.0
NH1 A:ARG37 4.8 74.1 1.0
CE2 A:TYR25 4.9 94.5 1.0
CG A:GLU30 4.9 67.4 1.0
CG1 B:VAL121 4.9 60.6 1.0
CA B:GLN118 5.0 95.4 1.0

Potassium binding site 2 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 2 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:0.2
occ:1.00
 O D:ILE116 2.6 89.1 1.0
O D:VAL121 2.8 91.2 1.0
OE2 C:GLU30 2.8 77.4 1.0
OD2 C:ASP34 2.8 94.1 1.0
O D:GLN118 2.9 90.2 1.0
OD1 C:ASP34 3.0 89.0 1.0
CG C:ASP34 3.2 92.0 1.0
O D:ALA117 3.4 97.4 1.0
CD C:GLU30 3.6 75.6 1.0
C D:VAL121 3.7 75.5 1.0
C D:ALA117 3.8 99.9 1.0
OE1 C:GLU30 3.8 77.7 1.0
C D:ILE116 3.8 86.4 1.0
C D:GLN118 4.0 90.5 1.0
N D:VAL121 4.3 72.6 1.0
CA D:ALA117 4.3 98.8 1.0
CB D:VAL121 4.4 65.0 1.0
CA D:VAL121 4.4 69.5 1.0
N D:GLN118 4.5 98.4 1.0
N D:ARG122 4.5 73.7 1.0
N D:ALA117 4.5 93.1 1.0
CE2 C:TYR25 4.6 92.4 1.0
CA D:ARG122 4.6 78.8 1.0
CB C:ASP34 4.7 85.4 1.0
CG C:GLU30 4.8 71.0 1.0
CA D:GLN118 4.8 95.4 1.0
N D:ARG119 4.9 90.1 1.0
N D:GLY120 4.9 95.2 1.0
CD2 C:TYR25 4.9 81.4 1.0
CA D:ARG119 4.9 92.9 1.0
CG2 D:ILE116 5.0 90.2 1.0
CA D:ILE116 5.0 85.4 1.0

Potassium binding site 3 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 3 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K403

b:0.1
occ:1.00
 OE2 E:GLU30 2.4 70.9 1.0
O F:VAL121 2.6 83.5 1.0
O F:GLN118 2.9 90.1 1.0
O F:ILE116 2.9 71.8 1.0
OD1 E:ASP34 3.0 95.5 1.0
OD2 E:ASP34 3.1 78.3 1.0
CG E:ASP34 3.4 88.2 1.0
CD E:GLU30 3.4 75.9 1.0
C F:VAL121 3.5 76.7 1.0
O F:ALA117 3.7 0.4 1.0
OE1 E:GLU30 3.8 78.8 1.0
C F:GLN118 3.9 89.6 1.0
N F:VAL121 3.9 78.8 1.0
C F:ALA117 4.0 99.6 1.0
CA F:VAL121 4.1 69.9 1.0
C F:ILE116 4.1 75.6 1.0
CB F:VAL121 4.2 63.0 1.0
N F:ARG122 4.4 76.8 1.0
N F:GLN118 4.5 99.2 1.0
N F:GLY120 4.6 82.3 1.0
CA F:ALA117 4.6 91.9 1.0
CG E:GLU30 4.6 65.4 1.0
CA F:ARG119 4.7 88.8 1.0
CE2 E:TYR25 4.7 88.4 1.0
N F:ARG119 4.7 86.8 1.0
CA F:ARG122 4.7 77.9 1.0
CA F:GLN118 4.8 89.8 1.0
CB E:ASP34 4.8 80.0 1.0
N F:ALA117 4.9 86.1 1.0
NH1 E:ARG37 4.9 64.6 1.0
NH2 E:ARG37 5.0 57.2 1.0
CD2 E:TYR25 5.0 86.5 1.0
C F:ARG119 5.0 87.3 1.0

Potassium binding site 4 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 4 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K404

b:94.3
occ:1.00
 O H:GLN118 2.5 79.0 1.0
OE2 G:GLU30 2.6 63.2 1.0
O H:ILE116 2.6 69.9 1.0
O H:VAL121 3.1 73.3 1.0
OD2 G:ASP34 3.1 67.4 1.0
O H:ALA117 3.2 84.3 1.0
OD1 G:ASP34 3.2 74.5 1.0
CD G:GLU30 3.5 61.6 1.0
CG G:ASP34 3.5 74.9 1.0
C H:ALA117 3.6 76.5 1.0
C H:GLN118 3.6 84.3 1.0
C H:VAL121 3.7 56.2 1.0
C H:ILE116 3.8 70.5 1.0
OE1 G:GLU30 3.8 63.0 1.0
N H:VAL121 4.1 59.0 1.0
CA H:ALA117 4.2 75.3 1.0
N H:GLN118 4.2 76.7 1.0
CB H:VAL121 4.2 38.6 1.0
CA H:VAL121 4.3 49.6 1.0
N H:ALA117 4.5 75.4 1.0
CA H:GLN118 4.5 81.5 1.0
N H:ARG122 4.5 52.1 1.0
N H:ARG119 4.5 89.6 1.0
N H:GLY120 4.6 93.1 1.0
CA H:ARG119 4.6 90.0 1.0
CG G:GLU30 4.7 62.8 1.0
CA H:ARG122 4.7 58.8 1.0
CE2 G:TYR25 4.8 90.5 1.0
CB G:ASP34 4.9 68.4 1.0
CA H:ILE116 5.0 67.0 1.0
C H:ARG119 5.0 91.4 1.0
CD2 G:TYR25 5.0 87.7 1.0

Potassium binding site 5 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 5 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K405

b:90.6
occ:1.00
 O H:SER82 2.5 86.2 1.0
O H:HIS79 2.8 0.7 1.0
O F:HIS89 2.8 71.7 1.0
C H:SER82 3.7 79.8 1.0
C H:HIS79 3.9 0.0 1.0
C F:HIS89 4.0 74.9 1.0
CA H:SER82 4.5 81.8 1.0
O H:VAL83 4.5 71.6 1.0
N H:SER82 4.6 84.5 1.0
CB F:HIS89 4.6 66.1 1.0
N F:HIS89 4.6 71.3 1.0
CB H:SER82 4.6 79.8 1.0
CA F:HIS89 4.6 70.8 1.0
N H:VAL83 4.7 73.2 1.0
CA H:HIS79 4.7 0.6 1.0
CA H:VAL83 4.8 72.1 1.0
CB H:HIS79 4.8 0.2 1.0
C H:VAL83 4.8 73.4 1.0
N H:ASP80 4.9 0.1 1.0
CD2 H:HIS79 5.0 0.4 1.0

Potassium binding site 6 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 6 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K406

b:0.4
occ:1.00
 O E:SER82 2.6 0.7 1.0
O G:HIS89 3.3 0.3 1.0
O E:HIS79 3.4 0.5 1.0
C E:SER82 3.7 95.6 1.0
O E:VAL83 3.8 84.2 1.0
C G:HIS89 4.0 98.4 1.0
CG1 G:VAL88 4.2 49.5 1.0
N G:HIS89 4.2 78.4 1.0
C E:VAL83 4.4 76.6 1.0
CB G:HIS89 4.5 87.6 1.0
CA G:HIS89 4.5 88.9 1.0
CA E:VAL83 4.5 79.0 1.0
N E:VAL83 4.5 85.6 1.0
C E:HIS79 4.6 0.3 1.0
CB E:SER82 4.6 1.0 1.0
CA E:SER82 4.7 0.3 1.0
OG E:SER82 4.8 98.7 1.0
N G:ILE90 4.8 0.8 1.0

Potassium binding site 7 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 7 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K407

b:0.3
occ:1.00
 O G:SER82 2.3 78.5 1.0
O G:HIS79 2.7 0.6 1.0
C G:SER82 3.5 76.0 1.0
O E:HIS89 3.6 78.9 1.0
C G:HIS79 3.9 0.1 1.0
CA G:SER82 4.4 81.2 1.0
N G:VAL83 4.4 66.2 1.0
O G:VAL83 4.5 68.5 1.0
N G:SER82 4.5 84.1 1.0
C E:HIS89 4.5 82.7 1.0
CA G:VAL83 4.5 57.1 1.0
CB G:SER82 4.6 86.7 1.0
C G:VAL83 4.7 62.3 1.0
CA G:HIS79 4.8 0.3 1.0
CB E:HIS89 4.8 79.7 1.0
CA G:ASP80 4.9 0.1 1.0
N E:HIS89 4.9 82.0 1.0
N G:ASP80 4.9 0.1 1.0
CB G:HIS79 5.0 0.7 1.0

Potassium binding site 8 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 8 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K408

b:0.1
occ:1.00
 O F:SER82 2.4 77.7 1.0
O F:HIS79 3.2 0.2 1.0
C F:SER82 3.6 76.8 1.0
O H:HIS89 3.7 80.9 1.0
O F:VAL83 4.1 69.8 1.0
C F:HIS79 4.4 1.0 1.0
CA F:VAL83 4.4 69.7 1.0
N F:VAL83 4.5 68.2 1.0
C F:VAL83 4.5 73.5 1.0
CA F:SER82 4.6 80.9 1.0
CB F:SER82 4.8 86.2 1.0
C H:HIS89 4.8 71.7 1.0
N F:SER82 4.8 87.0 1.0
OG F:SER82 4.9 94.9 1.0

Potassium binding site 9 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 9 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K409

b:0.9
occ:1.00
 O A:SER82 2.7 91.5 1.0
O C:HIS89 3.1 0.8 1.0
O A:HIS79 3.3 0.9 1.0
C A:SER82 3.5 96.8 1.0
C C:HIS89 3.7 96.0 1.0
N C:HIS89 3.7 83.7 1.0
CB C:HIS89 3.7 91.4 1.0
CB A:SER82 3.9 0.9 1.0
CA C:HIS89 3.9 89.4 1.0
O A:VAL83 3.9 81.6 1.0
OG A:SER82 4.2 0.2 1.0
CA A:SER82 4.2 0.6 1.0
C A:HIS79 4.3 0.7 1.0
N A:VAL83 4.3 92.6 1.0
C A:VAL83 4.4 80.9 1.0
CG1 C:VAL88 4.4 74.4 1.0
CG C:HIS89 4.5 96.0 1.0
CA A:VAL83 4.6 84.0 1.0
CA A:HIS79 4.6 0.2 1.0
N C:ILE90 4.7 0.5 1.0
CD2 C:HIS89 4.7 98.1 1.0
N A:SER82 4.7 0.5 1.0
CB A:HIS79 4.8 0.8 1.0
C C:VAL88 4.8 85.4 1.0

Potassium binding site 10 out of 11 in 2hzv

Go back to Potassium Binding Sites List in 2hzv
Potassium binding site 10 out of 11 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K410

b:0.9
occ:1.00
 O B:SER82 2.6 84.2 1.0
O D:HIS89 3.1 91.3 1.0
O B:HIS79 3.1 0.3 1.0
C B:SER82 3.7 80.2 1.0
O B:VAL83 4.1 77.5 1.0
C D:HIS89 4.1 87.6 1.0
C B:HIS79 4.3 0.7 1.0
N D:HIS89 4.6 76.8 1.0
CB B:SER82 4.6 94.5 1.0
CA B:SER82 4.6 87.0 1.0
N B:VAL83 4.6 74.0 1.0
C B:VAL83 4.6 75.5 1.0
CA B:VAL83 4.7 74.9 1.0
CG1 D:VAL88 4.7 65.4 1.0
CA D:HIS89 4.7 80.9 1.0
OG B:SER82 4.7 92.9 1.0
CB D:HIS89 4.8 77.1 1.0
CD2 B:HIS79 4.9 1.0 1.0
N B:SER82 5.0 85.0 1.0

Reference:

E.R.Schreiter, S.C.Wang, D.B.Zamble, C.L.Drennan. Nikr-Operator Complex Structure and the Mechanism of Repressor Activation By Metal Ions. Proc.Natl.Acad.Sci.Usa V. 103 13676 2006.
ISSN: ISSN 0027-8424
PubMed: 16945905
DOI: 10.1073/PNAS.0606247103
Page generated: Sun Dec 13 23:10:22 2020

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