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Nickel 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

Nickel Binding Sites:

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

Nickel binding site 1 out of 8 in 2hzv

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Nickel binding site 1 out of 8 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:84.0
occ:1.00
NE2 D:HIS76 1.7 80.4 1.0
ND1 B:HIS89 1.7 84.3 1.0
SG B:CYS95 2.0 76.7 1.0
NE2 B:HIS87 2.2 80.4 1.0
CE1 D:HIS76 2.4 75.9 1.0
CE1 B:HIS89 2.5 89.2 1.0
CD2 D:HIS76 2.8 87.0 1.0
CG B:HIS89 2.9 90.0 1.0
CD2 B:HIS87 3.1 81.9 1.0
CE1 B:HIS87 3.2 78.8 1.0
CB B:CYS95 3.3 74.9 1.0
CB B:HIS89 3.4 81.1 1.0
CA B:HIS89 3.5 85.1 1.0
ND1 D:HIS76 3.6 79.4 1.0
NE2 B:HIS89 3.7 91.2 1.0
CG D:HIS76 3.8 91.0 1.0
CD2 B:HIS89 3.9 92.2 1.0
CA B:CYS95 3.9 77.4 1.0
CG1 D:VAL72 4.0 63.3 1.0
N B:HIS89 4.0 82.8 1.0
O B:ASP94 4.2 83.6 1.0
CG B:HIS87 4.3 79.0 1.0
ND1 B:HIS87 4.3 79.5 1.0
C B:VAL88 4.4 77.8 1.0
O B:VAL88 4.4 80.1 1.0
N B:CYS95 4.6 81.3 1.0
CD2 B:HIS62 4.7 96.0 1.0
C B:ASP94 4.7 87.5 1.0
C B:HIS89 4.8 88.0 1.0

Nickel binding site 2 out of 8 in 2hzv

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Nickel binding site 2 out of 8 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:0.6
occ:1.00
SG A:CYS95 2.0 77.5 1.0
ND1 A:HIS89 2.0 92.7 1.0
NE2 C:HIS76 2.0 90.0 1.0
NE2 A:HIS87 2.1 86.9 1.0
CE1 A:HIS89 2.3 98.2 1.0
CE1 C:HIS76 2.8 92.4 1.0
CD2 C:HIS76 3.0 99.6 1.0
CE1 A:HIS87 3.0 88.9 1.0
CD2 A:HIS87 3.2 89.8 1.0
CG A:HIS89 3.3 91.4 1.0
CB A:CYS95 3.4 79.7 1.0
CG2 C:VAL72 3.5 0.7 1.0
NE2 A:HIS89 3.6 97.8 1.0
O A:VAL88 3.6 91.7 1.0
CA A:CYS95 3.9 86.7 1.0
ND1 C:HIS76 3.9 98.1 1.0
CG C:HIS76 4.0 0.5 1.0
CD2 A:HIS89 4.1 94.8 1.0
CA A:HIS89 4.2 84.3 1.0
CB A:HIS89 4.2 80.6 1.0
ND1 A:HIS87 4.2 91.0 1.0
O A:ASP94 4.2 91.0 1.0
CG A:HIS87 4.3 91.8 1.0
C A:VAL88 4.4 85.9 1.0
N A:CYS95 4.6 91.2 1.0
N A:HIS89 4.6 88.0 1.0
C A:ASP94 4.7 0.7 1.0
CB A:HIS62 4.9 0.1 1.0
CB C:VAL72 5.0 0.7 1.0

Nickel binding site 3 out of 8 in 2hzv

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Nickel binding site 3 out of 8 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni303

b:0.7
occ:1.00
ND1 C:HIS89 1.8 93.8 1.0
SG C:CYS95 2.2 85.0 1.0
NE2 C:HIS87 2.3 83.5 1.0
NE2 A:HIS76 2.4 0.0 1.0
CE1 C:HIS89 2.7 98.7 1.0
CE1 A:HIS76 2.7 0.4 1.0
CG C:HIS89 2.9 96.0 1.0
CD2 C:HIS87 3.3 81.0 1.0
CA C:HIS89 3.3 89.4 1.0
CE1 C:HIS87 3.3 84.8 1.0
CD2 A:HIS76 3.4 0.3 1.0
CB C:HIS89 3.4 91.4 1.0
CB C:CYS95 3.4 87.6 1.0
O C:VAL88 3.6 86.1 1.0
ND1 A:HIS76 3.7 0.4 1.0
NE2 C:HIS89 3.8 0.8 1.0
CG2 A:VAL72 3.8 0.7 1.0
CA C:CYS95 3.9 93.7 1.0
N C:HIS89 3.9 83.7 1.0
O C:ASP94 3.9 0.9 1.0
CD2 C:HIS89 3.9 98.1 1.0
C C:VAL88 4.0 85.4 1.0
CG A:HIS76 4.1 0.0 1.0
ND1 C:HIS87 4.4 83.5 1.0
CG C:HIS87 4.5 88.4 1.0
C C:ASP94 4.5 0.9 1.0
N C:CYS95 4.5 0.8 1.0
C C:HIS89 4.6 96.0 1.0

Nickel binding site 4 out of 8 in 2hzv

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Nickel binding site 4 out of 8 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni304

b:86.7
occ:1.00
ND1 D:HIS89 1.8 80.8 1.0
NE2 B:HIS76 1.9 72.5 1.0
SG D:CYS95 2.0 80.8 1.0
NE2 D:HIS87 2.0 87.5 1.0
CE1 D:HIS89 2.4 85.9 1.0
CE1 D:HIS87 2.7 77.6 1.0
CD2 B:HIS76 2.8 69.5 1.0
CE1 B:HIS76 2.9 76.9 1.0
CG D:HIS89 3.0 83.4 1.0
CD2 D:HIS87 3.1 85.0 1.0
CB D:CYS95 3.3 67.7 1.0
CG1 B:VAL72 3.4 74.9 1.0
NE2 D:HIS89 3.6 93.7 1.0
CB D:HIS89 3.7 77.1 1.0
ND1 D:HIS87 3.8 72.6 1.0
CD2 D:HIS89 3.9 89.6 1.0
CA D:HIS89 3.9 80.9 1.0
CG B:HIS76 4.0 78.3 1.0
ND1 B:HIS76 4.0 83.2 1.0
CG D:HIS87 4.0 79.2 1.0
CA D:CYS95 4.2 76.5 1.0
N D:HIS89 4.4 76.8 1.0
O D:ASP94 4.6 76.8 1.0
CD2 D:HIS62 4.8 96.0 1.0
CB B:VAL72 4.8 75.9 1.0
C D:VAL88 4.9 73.3 1.0

Nickel binding site 5 out of 8 in 2hzv

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Nickel binding site 5 out of 8 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni305

b:72.5
occ:1.00
ND1 F:HIS89 1.7 60.1 1.0
NE2 H:HIS76 1.9 73.7 1.0
NE2 F:HIS87 1.9 84.2 1.0
SG F:CYS95 2.1 66.8 1.0
CE1 F:HIS89 2.3 63.5 1.0
CE1 H:HIS76 2.8 68.2 1.0
CD2 F:HIS87 2.9 77.5 1.0
CE1 F:HIS87 2.9 70.8 1.0
CD2 H:HIS76 2.9 71.9 1.0
CG F:HIS89 3.0 69.7 1.0
CB F:CYS95 3.3 65.4 1.0
NE2 F:HIS89 3.5 67.4 1.0
CG1 H:VAL72 3.7 65.3 1.0
CB F:HIS89 3.7 66.1 1.0
CA F:HIS89 3.8 70.8 1.0
CD2 F:HIS89 3.8 71.8 1.0
ND1 H:HIS76 3.9 79.2 1.0
ND1 F:HIS87 3.9 74.8 1.0
CG F:HIS87 4.0 68.1 1.0
CG H:HIS76 4.0 82.2 1.0
CA F:CYS95 4.1 69.0 1.0
N F:HIS89 4.2 71.3 1.0
O F:ASP94 4.6 74.4 1.0
C F:VAL88 4.6 68.8 1.0
O F:VAL88 4.7 76.3 1.0
CD2 F:HIS62 4.7 90.7 1.0
N F:CYS95 4.9 77.1 1.0

Nickel binding site 6 out of 8 in 2hzv

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Nickel binding site 6 out of 8 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni306

b:0.8
occ:1.00
ND1 E:HIS89 1.7 89.7 1.0
NE2 G:HIS76 1.9 83.7 1.0
SG E:CYS95 2.1 84.1 1.0
CE1 E:HIS89 2.1 91.7 1.0
NE2 E:HIS87 2.2 78.0 1.0
CE1 G:HIS76 2.7 85.7 1.0
CD2 G:HIS76 2.9 91.5 1.0
CG E:HIS89 3.1 92.5 1.0
CD2 E:HIS87 3.2 85.9 1.0
CE1 E:HIS87 3.2 84.0 1.0
NE2 E:HIS89 3.4 95.5 1.0
CB E:CYS95 3.5 75.5 1.0
O E:VAL88 3.6 88.5 1.0
CG2 G:VAL72 3.6 0.0 1.0
ND1 G:HIS76 3.7 93.5 1.0
CD2 E:HIS89 3.8 96.4 1.0
CG G:HIS76 3.8 94.2 1.0
CB E:HIS89 3.9 79.7 1.0
CA E:HIS89 3.9 80.1 1.0
CA E:CYS95 4.0 81.9 1.0
O E:ASP94 4.1 95.3 1.0
ND1 E:HIS87 4.3 89.5 1.0
C E:VAL88 4.3 82.2 1.0
CG E:HIS87 4.3 91.8 1.0
N E:HIS89 4.5 82.0 1.0
N E:CYS95 4.7 89.6 1.0
C E:ASP94 4.7 100.0 1.0
O G:VAL72 4.9 0.1 1.0

Nickel binding site 7 out of 8 in 2hzv

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Nickel binding site 7 out of 8 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni307

b:78.5
occ:1.00
ND1 G:HIS89 1.7 86.4 1.0
SG G:CYS95 2.3 52.8 1.0
NE2 G:HIS87 2.3 65.2 1.0
NE2 E:HIS76 2.3 0.4 1.0
CE1 G:HIS89 2.4 84.6 1.0
CE1 E:HIS76 2.7 0.5 1.0
CG G:HIS89 2.9 90.1 1.0
CE1 G:HIS87 3.2 74.5 1.0
CD2 E:HIS76 3.2 0.3 1.0
CD2 G:HIS87 3.3 70.4 1.0
CG2 E:VAL72 3.5 0.3 1.0
CB G:HIS89 3.5 87.6 1.0
CA G:HIS89 3.6 88.9 1.0
NE2 G:HIS89 3.6 88.5 1.0
ND1 E:HIS76 3.6 0.1 1.0
CB G:CYS95 3.7 75.3 1.0
O G:VAL88 3.9 65.0 1.0
CD2 G:HIS89 3.9 91.2 1.0
CG E:HIS76 3.9 0.5 1.0
N G:HIS89 4.1 78.4 1.0
CA G:CYS95 4.2 85.2 1.0
C G:VAL88 4.2 69.4 1.0
O G:ASP94 4.3 77.0 1.0
ND1 G:HIS87 4.3 77.3 1.0
CG G:HIS87 4.4 77.9 1.0
C G:ASP94 4.8 92.9 1.0
N G:CYS95 4.9 83.9 1.0
C G:HIS89 4.9 98.4 1.0
CB E:VAL72 5.0 0.2 1.0

Nickel binding site 8 out of 8 in 2hzv

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Nickel binding site 8 out of 8 in the Nikr-Operator Dna Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Nikr-Operator Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni308

b:73.2
occ:1.00
ND1 H:HIS89 1.8 79.3 1.0
NE2 F:HIS76 1.9 52.7 1.0
SG H:CYS95 2.0 60.4 1.0
NE2 H:HIS87 2.0 64.7 1.0
CE1 H:HIS89 2.5 90.2 1.0
CE1 H:HIS87 2.6 57.0 1.0
CD2 F:HIS76 2.8 56.1 1.0
CE1 F:HIS76 2.9 50.5 1.0
CG H:HIS89 3.0 70.4 1.0
CD2 H:HIS87 3.1 64.3 1.0
CB H:CYS95 3.3 57.1 1.0
CG1 F:VAL72 3.5 65.2 1.0
CB H:HIS89 3.6 60.3 1.0
NE2 H:HIS89 3.6 89.5 1.0
CA H:HIS89 3.7 63.7 1.0
ND1 H:HIS87 3.8 53.5 1.0
CD2 H:HIS89 3.9 80.5 1.0
CG F:HIS76 4.0 70.8 1.0
ND1 F:HIS76 4.0 62.3 1.0
CG H:HIS87 4.0 55.3 1.0
N H:HIS89 4.2 61.0 1.0
CA H:CYS95 4.3 62.6 1.0
O H:ASP94 4.7 56.4 1.0
C H:VAL88 4.8 61.0 1.0
CB F:VAL72 5.0 63.7 1.0
O H:VAL88 5.0 70.1 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
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