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Nickel in PDB 2ga0: Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)

Protein crystallography data

The structure of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1), PDB code: 2ga0 was solved by C.L.Lawson, B.H.Yung, A.G.Barbour, W.R.Zuckert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 241.835, 69.105, 87.578, 90.00, 104.95, 90.00
R / Rfree (%) 21.6 / 27.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) (pdb code 2ga0). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 14 binding sites of Nickel where determined in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1), PDB code: 2ga0:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14;

Nickel binding site 1 out of 14 in 2ga0

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Nickel binding site 1 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni7

b:41.1
occ:1.00
OD1 A:ASP184 2.0 29.6 1.0
NE2 A:HIS62 2.1 28.1 1.0
O A:HOH234 2.2 31.7 1.0
CG A:ASP184 2.8 21.6 1.0
OD2 A:ASP184 2.9 24.1 1.0
CE A:LYS66 2.9 26.0 1.0
CE1 A:HIS62 2.9 24.1 1.0
CD2 A:HIS62 3.1 23.4 1.0
CD A:LYS66 3.5 25.5 1.0
NZ A:LYS66 3.9 24.7 1.0
OD1 A:ASN180 4.0 17.8 1.0
ND1 A:HIS62 4.1 22.1 1.0
O A:HOH217 4.1 26.1 1.0
CG A:HIS62 4.2 21.6 1.0
CB A:ASP184 4.3 19.3 1.0
O A:ASN180 4.3 18.8 1.0
CA A:ASP184 4.8 19.1 1.0
CG A:ASN180 5.0 18.6 1.0
CG A:LYS66 5.0 22.8 1.0

Nickel binding site 2 out of 14 in 2ga0

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Nickel binding site 2 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni14

b:62.0
occ:1.00
OD2 A:ASP87 2.0 31.0 1.0
NZ A:LYS90 2.1 32.6 1.0
CG A:ASP87 3.0 20.4 1.0
OD1 A:ASP87 3.3 20.8 1.0
CE A:LYS90 3.3 26.1 1.0
OD1 B:ASP150 3.4 24.6 1.0
CG B:ASP150 4.2 23.9 1.0
O A:ALA88 4.3 18.4 1.0
CB A:ASP87 4.4 19.5 1.0
OD2 B:ASP150 4.4 26.6 1.0
CD A:LYS90 4.5 25.2 1.0
C A:ASP87 4.7 18.8 1.0
CA A:ASP87 4.7 18.8 1.0
O B:HOH226 4.8 37.6 1.0
O A:ASP87 4.8 19.1 1.0
NZ B:LYS93 4.9 19.2 1.0
N A:ALA88 5.0 18.5 1.0

Nickel binding site 3 out of 14 in 2ga0

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Nickel binding site 3 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni2

b:42.9
occ:1.00
OD1 B:ASP184 2.0 28.3 1.0
NE2 B:HIS62 2.1 27.6 1.0
O B:HOH229 2.1 32.4 1.0
CG B:ASP184 2.8 21.5 1.0
OD2 B:ASP184 2.9 21.8 1.0
CE1 B:HIS62 2.9 23.2 1.0
CD2 B:HIS62 3.2 22.3 1.0
ND1 B:HIS62 4.0 21.1 1.0
CG B:HIS62 4.2 19.7 1.0
CB B:ASP184 4.3 19.7 1.0
OD1 B:ASN180 4.3 16.4 1.0
O B:ASN180 4.5 18.9 1.0
CA B:ASP184 4.8 19.1 1.0
CG B:LYS66 4.9 22.3 1.0

Nickel binding site 4 out of 14 in 2ga0

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Nickel binding site 4 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni4

b:65.0
occ:1.00
OD1 B:ASP87 2.0 32.1 1.0
CG B:ASP87 2.8 21.9 1.0
OD2 B:ASP87 2.9 26.8 1.0
OD1 A:ASP150 3.0 26.8 1.0
OD2 A:ASP150 3.2 26.4 1.0
CG A:ASP150 3.5 24.8 1.0
NZ B:LYS90 3.8 25.4 1.0
CB B:ASP87 4.2 19.6 1.0
CA B:ASP87 4.7 18.9 1.0
O B:ALA88 4.7 18.6 1.0
CD B:LYS90 4.8 24.1 1.0
CE B:LYS90 4.9 25.2 1.0
C B:ASP87 4.9 18.9 1.0

Nickel binding site 5 out of 14 in 2ga0

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Nickel binding site 5 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni3

b:43.6
occ:1.00
OD1 C:ASP184 2.0 29.5 1.0
NE2 C:HIS62 2.1 30.5 1.0
OD2 C:ASP184 2.7 21.8 1.0
CG C:ASP184 2.7 21.6 1.0
CE1 C:HIS62 3.0 24.2 1.0
CD2 C:HIS62 3.1 23.5 1.0
OD1 C:ASN180 4.0 17.3 1.0
ND1 C:HIS62 4.1 22.0 1.0
CG C:HIS62 4.2 19.7 1.0
CB C:ASP184 4.2 19.0 1.0
O C:ASN180 4.4 18.9 1.0
CA C:ASP184 4.7 19.1 1.0
N C:ASP184 5.0 18.8 1.0
CG C:LYS66 5.0 20.8 1.0
CG C:ASN180 5.0 18.2 1.0

Nickel binding site 6 out of 14 in 2ga0

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Nickel binding site 6 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1

b:42.4
occ:1.00
OD1 D:ASP184 2.0 30.0 1.0
NE2 D:HIS62 2.1 28.8 1.0
CG D:ASP184 2.8 22.4 1.0
OD2 D:ASP184 2.8 25.0 1.0
CE1 D:HIS62 2.9 23.8 1.0
CD2 D:HIS62 3.2 22.3 1.0
ND1 D:HIS62 4.1 21.0 1.0
OD1 D:ASN180 4.2 15.6 1.0
CB D:ASP184 4.2 18.7 1.0
O D:HOH216 4.2 27.3 1.0
CG D:HIS62 4.3 20.4 1.0
O D:ASN180 4.4 18.9 1.0
CA D:ASP184 4.7 18.9 1.0
CG2 D:ILE183 4.9 18.1 1.0
N D:ASP184 4.9 18.8 1.0

Nickel binding site 7 out of 14 in 2ga0

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Nickel binding site 7 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni8

b:67.8
occ:1.00
OD1 D:ASP87 2.0 31.0 1.0
O D:HOH223 3.0 45.5 1.0
CG D:ASP87 3.1 21.6 1.0
OD2 C:ASP150 3.5 21.0 1.0
OD2 D:ASP87 3.5 23.5 1.0
OD1 C:ASP150 4.3 20.7 1.0
CG C:ASP150 4.3 21.5 1.0
CB D:ASP87 4.4 20.1 1.0
CA D:ASP87 4.9 19.0 1.0

Nickel binding site 8 out of 14 in 2ga0

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Nickel binding site 8 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni5

b:49.0
occ:1.00
OD1 E:ASP184 2.0 31.1 1.0
NE2 E:HIS62 2.0 27.9 1.0
CE1 E:HIS62 2.9 23.6 1.0
CG E:ASP184 3.0 21.8 1.0
CD2 E:HIS62 3.1 22.6 1.0
OD2 E:ASP184 3.3 21.4 1.0
OD1 E:ASN180 3.9 17.5 1.0
ND1 E:HIS62 4.1 21.3 1.0
CG E:HIS62 4.2 20.9 1.0
O E:HOH220 4.3 36.4 1.0
CB E:ASP184 4.4 19.6 1.0
O E:ASN180 4.6 19.0 1.0
CA E:ASP184 4.7 19.1 1.0
CG E:LYS66 4.9 20.9 1.0
CG E:ASN180 5.0 17.8 1.0
N E:ASP184 5.0 18.7 1.0

Nickel binding site 9 out of 14 in 2ga0

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Nickel binding site 9 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni12

b:74.3
occ:1.00
OD1 E:ASP150 2.0 33.9 1.0
NZ F:LYS90 2.8 22.5 1.0
CG E:ASP150 2.9 23.2 1.0
OD2 F:ASP87 3.2 24.3 1.0
OD2 E:ASP150 3.4 24.0 1.0
OD1 F:ASP87 3.5 22.7 1.0
CG F:ASP87 3.8 20.7 1.0
CB E:ASP150 4.0 21.0 1.0
CE F:LYS90 4.1 23.1 1.0
CA E:ASP150 4.2 19.8 1.0
N E:ASP150 4.6 19.5 1.0

Nickel binding site 10 out of 14 in 2ga0

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Nickel binding site 10 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni6

b:44.0
occ:1.00
OD1 F:ASP184 2.0 31.5 1.0
NE2 F:HIS62 2.0 28.6 1.0
CE1 F:HIS62 2.8 24.0 1.0
CG F:ASP184 3.0 22.5 1.0
CD2 F:HIS62 3.2 21.2 1.0
OD2 F:ASP184 3.2 25.5 1.0
ND1 F:HIS62 4.0 21.2 1.0
CG F:HIS62 4.2 19.9 1.0
OD1 F:ASN180 4.3 18.8 1.0
CB F:ASP184 4.4 19.9 1.0
O F:HOH219 4.4 17.6 1.0
O F:ASN180 4.5 19.0 1.0
CA F:ASP184 4.8 19.2 1.0
NZ F:LYS66 4.8 28.0 1.0
CG2 F:ILE183 4.9 18.6 1.0
CD F:LYS66 4.9 27.5 1.0

Nickel binding site 11 out of 14 in 2ga0

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Nickel binding site 11 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 11 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni9

b:47.0
occ:1.00
OD1 G:ASP184 2.0 30.2 1.0
NE2 G:HIS62 2.0 29.8 1.0
CE G:LYS66 2.5 23.9 1.0
OD2 G:ASP184 2.7 20.6 1.0
CG G:ASP184 2.7 22.2 1.0
CE1 G:HIS62 2.9 25.0 1.0
CD2 G:HIS62 3.1 24.1 1.0
CD G:LYS66 3.2 24.0 1.0
NZ G:LYS66 3.7 24.9 1.0
OD1 G:ASN180 4.0 18.5 1.0
ND1 G:HIS62 4.1 23.0 1.0
CG G:HIS62 4.2 20.9 1.0
CB G:ASP184 4.3 19.4 1.0
CG G:LYS66 4.4 23.4 1.0
O G:ASN180 4.5 19.0 1.0
O G:HOH222 4.5 32.7 1.0
O G:HOH229 4.6 41.9 1.0
CG2 G:ILE183 4.8 17.9 1.0
CA G:ASP184 4.8 19.1 1.0
CG G:ASN180 5.0 19.2 1.0

Nickel binding site 12 out of 14 in 2ga0

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Nickel binding site 12 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 12 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni11

b:67.6
occ:1.00
OD2 G:ASP87 1.9 33.7 1.0
CG G:ASP87 2.8 21.7 1.0
OD1 G:ASP87 3.0 22.0 1.0
OD2 H:ASP150 3.2 24.9 1.0
CB G:ASP87 4.1 19.9 1.0
CG H:ASP150 4.3 22.2 1.0
O G:ALA88 4.4 18.3 1.0
C G:ASP87 4.4 18.6 1.0
CA G:ASP87 4.5 18.9 1.0
O G:ASP87 4.6 19.0 1.0
O G:HOH228 4.6 36.4 1.0
NZ H:LYS93 4.7 18.7 1.0
N G:ALA88 4.9 18.3 1.0
OD1 H:ASP150 5.0 22.4 1.0

Nickel binding site 13 out of 14 in 2ga0

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Nickel binding site 13 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 13 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni10

b:49.7
occ:1.00
OD1 H:ASP184 2.0 29.6 1.0
NE2 H:HIS62 2.1 28.8 1.0
O H:HOH231 2.3 35.5 1.0
CG H:ASP184 2.9 21.1 1.0
CE1 H:HIS62 3.0 23.2 1.0
OD2 H:ASP184 3.0 22.5 1.0
CD2 H:HIS62 3.1 21.6 1.0
ND1 H:HIS62 4.1 20.9 1.0
CG H:HIS62 4.2 19.5 1.0
OD1 H:ASN180 4.3 18.3 1.0
CB H:ASP184 4.4 19.6 1.0
O H:HOH226 4.4 35.5 1.0
O H:ASN180 4.5 18.8 1.0
CA H:ASP184 4.9 19.2 1.0

Nickel binding site 14 out of 14 in 2ga0

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Nickel binding site 14 out of 14 in the Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 14 of Variable Small Protein 1 of Borrelia Turicatae (Vspa or VSP1) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni13

b:80.4
occ:1.00
O H:HOH232 2.4 41.3 1.0
OD1 H:ASP87 2.4 21.6 1.0
O G:HOH215 2.8 46.4 1.0
OD1 G:ASP150 3.0 24.0 1.0
CG H:ASP87 3.3 20.0 1.0
OD2 G:ASP150 3.3 23.9 1.0
OD2 H:ASP87 3.3 22.9 1.0
CG G:ASP150 3.6 22.9 1.0
CB H:ASP87 4.7 19.1 1.0

Reference:

C.L.Lawson, B.H.Yung, A.G.Barbour, W.R.Zuckert. Crystal Structure of Neurotropism-Associated Variable Surface Protein 1 (VSP1) of Borrelia Turicatae. J.Bacteriol. V. 188 4522 2006.
ISSN: ISSN 0021-9193
PubMed: 16740958
DOI: 10.1128/JB.00028-06
Page generated: Fri Sep 25 08:08:53 2020
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