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Nickel in PDB 3qsi: Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy

Protein crystallography data

The structure of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy, PDB code: 3qsi was solved by J.M.Gonzalez, E.Pozharski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.50 / 3.08
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.379, 79.400, 122.423, 90.00, 122.28, 90.00
R / Rfree (%) 25.7 / 30.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy (pdb code 3qsi). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 9 binding sites of Nickel where determined in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy, PDB code: 3qsi:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Nickel binding site 1 out of 9 in 3qsi

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Nickel binding site 1 out of 9 in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni5

b:63.1
occ:1.00
NE2 B:HIS74 2.0 76.3 1.0
NE2 A:HIS88 2.1 70.8 1.0
NE2 B:HIS101 2.1 81.6 1.0
CE1 B:HIS101 2.9 81.1 1.0
CE1 B:HIS74 3.0 75.6 1.0
CD2 A:HIS88 3.0 67.2 1.0
CD2 B:HIS74 3.1 74.7 1.0
CE1 A:HIS88 3.1 68.2 1.0
CD2 B:HIS101 3.3 81.2 1.0
ND1 B:HIS101 4.1 80.5 1.0
ND1 B:HIS74 4.1 75.0 1.0
CG B:HIS74 4.2 74.0 1.0
CG A:HIS88 4.2 64.0 1.0
ND1 A:HIS88 4.2 65.9 1.0
CG B:HIS101 4.3 79.6 1.0
CG2 A:ILE84 4.9 49.7 1.0

Nickel binding site 2 out of 9 in 3qsi

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Nickel binding site 2 out of 9 in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni4

b:42.8
occ:1.00
NE2 C:HIS99 2.0 47.6 1.0
NE2 D:HIS88 2.0 52.5 1.0
ND1 C:HIS101 2.1 53.4 1.0
SG C:CYS107 2.3 51.1 1.0
CD2 C:HIS99 3.0 45.2 1.0
CE1 D:HIS88 3.0 52.1 1.0
CE1 C:HIS99 3.0 45.5 1.0
CG C:HIS101 3.0 52.4 1.0
CD2 D:HIS88 3.0 50.7 1.0
CE1 C:HIS101 3.1 52.0 1.0
CB C:HIS101 3.3 52.9 1.0
CA C:HIS101 3.3 52.0 1.0
CB C:CYS107 3.4 50.9 1.0
CG2 D:ILE84 3.4 48.5 1.0
N C:HIS101 3.9 51.1 1.0
ND1 C:HIS99 4.1 45.6 1.0
ND1 D:HIS88 4.1 51.7 1.0
CA C:CYS107 4.1 51.2 1.0
CG C:HIS99 4.1 44.9 1.0
O C:ILE100 4.1 49.0 1.0
CG D:HIS88 4.2 51.4 1.0
CD2 C:HIS101 4.2 52.2 1.0
NE2 C:HIS101 4.2 52.0 1.0
C C:ILE100 4.3 48.6 1.0
C C:HIS101 4.6 54.2 1.0
O C:ASN106 4.7 57.2 1.0
CB D:ILE84 4.8 48.5 1.0
N C:CYS107 4.9 53.1 1.0
CG1 D:ILE84 5.0 47.8 1.0
N C:MET102 5.0 56.2 1.0

Nickel binding site 3 out of 9 in 3qsi

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Nickel binding site 3 out of 9 in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni7

b:68.8
occ:1.00
NE2 D:HIS101 2.0 83.9 1.0
NE2 C:HIS88 2.1 74.1 1.0
NE2 D:HIS74 2.1 78.6 1.0
CE1 D:HIS101 2.9 83.2 1.0
CD2 C:HIS88 2.9 69.7 1.0
CE1 D:HIS74 3.0 77.3 1.0
CE1 C:HIS88 3.1 71.1 1.0
CD2 D:HIS101 3.2 83.0 1.0
CD2 D:HIS74 3.2 76.3 1.0
ND1 D:HIS101 4.1 82.7 1.0
CG C:HIS88 4.1 66.1 1.0
ND1 D:HIS74 4.1 76.0 1.0
ND1 C:HIS88 4.1 68.3 1.0
CG D:HIS101 4.2 81.4 1.0
CG D:HIS74 4.3 75.1 1.0

Nickel binding site 4 out of 9 in 3qsi

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Nickel binding site 4 out of 9 in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni3

b:43.6
occ:1.00
NE2 A:HIS99 2.0 45.8 1.0
NE2 B:HIS88 2.0 55.2 1.0
ND1 A:HIS101 2.1 50.6 1.0
SG A:CYS107 2.3 48.9 1.0
CE1 A:HIS99 2.9 43.8 1.0
CD2 B:HIS88 2.9 53.5 1.0
CE1 A:HIS101 3.0 49.4 1.0
CD2 A:HIS99 3.0 44.0 1.0
CE1 B:HIS88 3.1 55.1 1.0
CG A:HIS101 3.1 49.7 1.0
CG2 B:ILE84 3.2 49.3 1.0
CB A:CYS107 3.5 49.2 1.0
CB A:HIS101 3.5 50.2 1.0
CA A:HIS101 3.6 49.9 1.0
ND1 A:HIS99 4.0 44.5 1.0
CG B:HIS88 4.1 54.7 1.0
NE2 A:HIS101 4.1 49.5 1.0
CG A:HIS99 4.1 43.8 1.0
ND1 B:HIS88 4.1 55.3 1.0
CD2 A:HIS101 4.2 49.6 1.0
N A:HIS101 4.2 49.2 1.0
CA A:CYS107 4.3 49.4 1.0
O A:ILE100 4.4 47.1 1.0
CB B:ILE84 4.5 49.0 1.0
C A:ILE100 4.6 47.0 1.0
CG1 B:ILE84 4.8 48.0 1.0
O A:ASN106 4.9 54.0 1.0
C A:HIS101 4.9 51.8 1.0

Nickel binding site 5 out of 9 in 3qsi

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Nickel binding site 5 out of 9 in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni6

b:64.7
occ:1.00
NE2 F:HIS101 2.0 80.6 1.0
NE2 E:HIS88 2.0 69.7 1.0
NE2 F:HIS74 2.1 76.2 1.0
CE1 F:HIS74 2.8 75.4 1.0
CD2 E:HIS88 2.8 65.9 1.0
CE1 F:HIS101 3.0 80.1 1.0
CD2 F:HIS101 3.0 80.3 1.0
CE1 E:HIS88 3.1 67.0 1.0
CD2 F:HIS74 3.3 74.2 1.0
ND1 F:HIS74 4.0 74.8 1.0
CG E:HIS88 4.0 62.5 1.0
ND1 F:HIS101 4.1 79.7 1.0
CG F:HIS101 4.1 78.7 1.0
ND1 E:HIS88 4.1 64.5 1.0
CG F:HIS74 4.3 73.8 1.0

Nickel binding site 6 out of 9 in 3qsi

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Nickel binding site 6 out of 9 in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni2

b:38.3
occ:1.00
NE2 G:HIS99 2.0 44.3 1.0
NE2 H:HIS88 2.0 57.4 1.0
ND1 G:HIS101 2.1 48.8 1.0
SG G:CYS107 2.3 52.4 1.0
CE1 G:HIS99 3.0 43.4 1.0
CE1 H:HIS88 3.0 57.5 1.0
CD2 G:HIS99 3.0 41.6 1.0
CD2 H:HIS88 3.1 55.1 1.0
CE1 G:HIS101 3.1 46.2 1.0
CG G:HIS101 3.1 47.8 1.0
CG2 H:ILE84 3.3 53.8 1.0
CB G:CYS107 3.4 52.3 1.0
CB G:HIS101 3.4 50.2 1.0
CA G:HIS101 3.4 50.9 1.0
O G:ILE100 4.0 47.7 1.0
N G:HIS101 4.0 48.5 1.0
ND1 G:HIS99 4.1 43.0 1.0
CA G:CYS107 4.1 54.1 1.0
ND1 H:HIS88 4.1 57.1 1.0
CG G:HIS99 4.2 41.0 1.0
CG H:HIS88 4.2 55.9 1.0
NE2 G:HIS101 4.2 45.6 1.0
CD2 G:HIS101 4.2 45.9 1.0
C G:ILE100 4.3 46.9 1.0
O G:ASN106 4.5 60.6 1.0
CB H:ILE84 4.6 54.0 1.0
C G:HIS101 4.7 54.9 1.0
CG1 H:ILE84 4.8 52.8 1.0
N G:CYS107 4.8 57.7 1.0
C G:ASN106 5.0 61.7 1.0

Nickel binding site 7 out of 9 in 3qsi

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Nickel binding site 7 out of 9 in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni9

b:73.2
occ:1.00
NE2 H:HIS101 2.0 90.2 1.0
NE2 G:HIS88 2.0 72.2 1.0
NE2 H:HIS74 2.1 88.4 1.0
O4 G:SO41 2.6 63.7 0.5
CE1 H:HIS74 2.7 88.0 1.0
CD2 G:HIS88 2.7 68.2 1.0
CD2 H:HIS101 2.9 88.8 1.0
CE1 H:HIS101 3.1 88.1 1.0
CE1 G:HIS88 3.2 70.7 1.0
CD2 H:HIS74 3.3 85.5 1.0
O2 G:SO41 3.4 61.1 0.5
S G:SO41 3.5 61.6 0.5
ND1 H:HIS74 3.9 87.3 1.0
CG G:HIS88 4.0 66.3 1.0
O1 G:SO41 4.1 61.2 0.5
CG H:HIS101 4.1 85.6 1.0
ND1 G:HIS88 4.1 69.7 1.0
ND1 H:HIS101 4.1 86.3 1.0
CG H:HIS74 4.2 85.3 1.0
O3 G:SO41 4.7 60.9 0.5

Nickel binding site 8 out of 9 in 3qsi

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Nickel binding site 8 out of 9 in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni8

b:45.7
occ:1.00
NE2 E:HIS99 2.0 43.0 1.0
NE2 F:HIS88 2.1 51.4 1.0
ND1 E:HIS101 2.1 47.3 1.0
SG E:CYS107 2.3 46.3 1.0
CD2 E:HIS99 3.0 41.0 1.0
CE1 E:HIS99 3.0 41.4 1.0
CE1 F:HIS88 3.0 51.1 1.0
CG E:HIS101 3.0 46.1 1.0
CE1 E:HIS101 3.1 45.8 1.0
CD2 F:HIS88 3.1 49.4 1.0
CB E:HIS101 3.3 46.5 1.0
CB E:CYS107 3.3 47.5 1.0
CA E:HIS101 3.3 46.5 1.0
CG2 F:ILE84 3.4 46.4 1.0
N E:HIS101 3.9 46.0 1.0
ND1 E:HIS99 4.1 41.9 1.0
CG E:HIS99 4.1 41.0 1.0
ND1 F:HIS88 4.1 51.2 1.0
CD2 E:HIS101 4.1 45.8 1.0
CA E:CYS107 4.1 47.5 1.0
NE2 E:HIS101 4.1 45.3 1.0
CG F:HIS88 4.2 50.7 1.0
O E:ILE100 4.2 44.9 1.0
C E:ILE100 4.3 44.0 1.0
C E:HIS101 4.7 48.4 1.0
CB F:ILE84 4.8 46.3 1.0
O E:ASN106 4.8 51.7 1.0
N E:CYS107 4.9 49.3 1.0
CG1 F:ILE84 5.0 45.4 1.0

Nickel binding site 9 out of 9 in 3qsi

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Nickel binding site 9 out of 9 in the Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ni1

b:42.7
occ:1.00
NE2 I:HIS99 2.0 44.0 1.0
ND1 I:HIS101 2.2 48.6 1.0
SG I:CYS107 2.2 47.3 1.0
CE1 I:HIS99 2.9 41.8 1.0
CE1 I:HIS101 3.1 47.1 1.0
CD2 I:HIS99 3.1 41.6 1.0
CG I:HIS101 3.2 47.6 1.0
CB I:CYS107 3.4 47.5 1.0
CB I:HIS101 3.6 48.6 1.0
CA I:HIS101 3.7 48.3 1.0
ND1 I:HIS99 4.1 42.3 1.0
CA I:CYS107 4.1 47.9 1.0
CG I:HIS99 4.2 41.1 1.0
NE2 I:HIS101 4.2 47.3 1.0
O I:ILE100 4.2 45.0 1.0
N I:HIS101 4.3 47.0 1.0
CD2 I:HIS101 4.3 47.2 1.0
C I:ILE100 4.5 44.7 1.0
O I:ASN106 4.7 53.5 1.0
N I:CYS107 4.8 50.3 1.0
CB I:HIS74 4.9 62.2 1.0
ND1 I:HIS74 5.0 63.5 1.0
C I:HIS101 5.0 50.9 1.0

Reference:

A.L.West, S.E.Evans, J.M.Gonzalez, L.G.Carter, H.Tsuruta, E.Pozharski, S.L.Michel. Ni(II) Coordination to Mixed Sites Modulates Dna Binding of Hpnikr Via A Long-Range Effect. Proc.Natl.Acad.Sci.Usa V. 109 5633 2012.
ISSN: ISSN 0027-8424
PubMed: 22451934
DOI: 10.1073/PNAS.1120283109
Page generated: Fri Sep 25 08:33:00 2020
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