Atomistry » Nickel » PDB 2gw4-2pos » 2hzv
Atomistry »
  Nickel »
    PDB 2gw4-2pos »
      2hzv »

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

Other elements in 2hzv:

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

Potassium (K) 11 atoms

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

Go back to Nickel Binding Sites List in 2hzv
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

Go back to Nickel Binding Sites List in 2hzv
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

Go back to Nickel Binding Sites List in 2hzv
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

Go back to Nickel Binding Sites List in 2hzv
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

Go back to Nickel Binding Sites List in 2hzv
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

Go back to Nickel Binding Sites List in 2hzv
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

Go back to Nickel Binding Sites List in 2hzv
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

Go back to Nickel Binding Sites List in 2hzv
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
Page generated: Wed Dec 16 01:18:50 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy