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Nickel in PDB 2y1v: Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae

Protein crystallography data

The structure of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae, PDB code: 2y1v was solved by L.El-Mortaji, C.Contreras-Martel, C.Manzano, T.Vernet, A.Dessen, A.M.Diguilmi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 113.53 / 2.39
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 74.619, 74.619, 340.527, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 23.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae (pdb code 2y1v). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 9 binding sites of Nickel where determined in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae, PDB code: 2y1v:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Nickel binding site 1 out of 9 in 2y1v

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Nickel binding site 1 out of 9 in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni800

b:62.5
occ:1.00
 OD1 A:ASP319 2.2 37.0 1.0
OD1 A:ASP438 2.4 40.7 1.0
O A:PRO439 2.5 44.1 1.0
OE2 A:GLU441 2.6 35.7 1.0
O A:VAL320 2.7 30.4 1.0
OE1 A:GLU441 2.8 35.6 1.0
CD A:GLU441 3.0 35.5 1.0
CG A:ASP319 3.4 42.1 1.0
N A:VAL320 3.5 32.7 1.0
CG A:ASP438 3.5 45.9 1.0
O A:HOH2071 3.7 42.7 1.0
C A:VAL320 3.7 30.2 1.0
C A:PRO439 3.7 44.1 1.0
C A:ASP319 4.0 35.9 1.0
OD2 A:ASP438 4.1 57.4 1.0
N A:PRO439 4.1 40.6 1.0
CA A:VAL320 4.1 32.2 1.0
CA A:ASP319 4.2 38.0 1.0
OD2 A:ASP319 4.2 44.5 1.0
CD A:PRO439 4.2 41.1 1.0
C A:ASP438 4.3 41.7 1.0
CB A:ASP319 4.4 39.7 1.0
CA A:PRO439 4.5 42.8 1.0
CG A:PRO439 4.5 37.9 1.0
CA A:ASP438 4.5 40.0 1.0
CG A:GLU441 4.5 35.9 1.0
CB A:ASP438 4.6 40.1 1.0
N A:THR440 4.7 44.5 1.0
O A:ASP438 4.8 42.4 1.0
N A:THR321 4.8 29.6 1.0
OG1 A:THR321 4.9 27.1 1.0
O A:ASP319 4.9 37.6 1.0
CB A:VAL320 4.9 30.5 1.0
CA A:THR440 4.9 43.4 1.0

Nickel binding site 2 out of 9 in 2y1v

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Nickel binding site 2 out of 9 in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni801

b:78.3
occ:1.00
 OE2 A:GLU489 2.2 70.1 1.0
OD2 A:ASP308 2.3 48.4 1.0
O A:ALA536 2.5 37.4 1.0
O A:HOH2136 2.6 50.6 1.0
OD1 A:ASN539 2.6 53.1 1.0
CD A:GLU489 3.3 65.5 1.0
CG A:ASN539 3.4 48.0 1.0
ND2 A:ASN539 3.5 48.7 1.0
CG A:ASP308 3.5 48.3 1.0
C A:ALA536 3.6 40.6 1.0
OE1 A:GLU489 3.6 57.7 1.0
O A:HOH2134 4.1 49.6 1.0
CA A:ALA536 4.1 40.1 1.0
OD1 A:ASP308 4.4 57.9 1.0
CB A:ASP308 4.4 42.8 1.0
CB A:ALA536 4.4 38.1 1.0
CG A:GLU489 4.6 62.0 1.0
N A:ALA537 4.6 43.3 1.0
CB A:ASN539 4.9 46.1 1.0
CA A:ALA537 4.9 45.8 1.0

Nickel binding site 3 out of 9 in 2y1v

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Nickel binding site 3 out of 9 in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni802

b:77.8
occ:1.00
 OE2 A:GLU245 1.9 45.5 1.0
O A:HOH2069 2.5 28.9 1.0
O A:HOH2093 2.6 49.2 1.0
CD A:GLU245 3.0 48.8 1.0
CG A:GLU245 3.7 45.5 1.0
O A:HOH2091 3.7 33.5 1.0
O A:ASN398 4.0 45.3 1.0
OE1 A:GLU245 4.1 48.7 1.0
O A:LYS309 4.1 42.5 1.0
OE1 A:GLN373 4.1 39.2 1.0
CG1 A:ILE311 4.1 38.9 1.0
OE2 A:GLU316 4.2 40.0 1.0
NZ A:LYS338 4.5 39.2 1.0
O A:HOH2068 4.5 34.1 1.0
NE2 A:GLN373 4.6 38.5 1.0
OE2 A:GLU400 4.7 40.5 1.0
CD A:GLN373 4.7 38.1 1.0
CE A:LYS338 4.7 37.8 1.0
CB A:ILE311 4.9 42.2 1.0
OE1 A:GLU316 5.0 42.0 1.0

Nickel binding site 4 out of 9 in 2y1v

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Nickel binding site 4 out of 9 in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni800

b:59.8
occ:1.00
 OE1 B:GLU441 2.3 42.1 1.0
O B:PRO439 2.4 40.2 1.0
O B:HOH2104 2.5 28.7 1.0
OD1 B:ASP438 2.5 48.0 1.0
OD1 B:ASP319 2.5 51.4 1.0
O B:VAL320 2.6 39.0 1.0
OE2 B:GLU441 2.8 51.6 1.0
CD B:GLU441 2.9 49.3 1.0
N B:VAL320 3.4 42.8 1.0
C B:VAL320 3.6 39.7 1.0
C B:PRO439 3.6 43.1 1.0
CG B:ASP319 3.6 44.4 1.0
CG B:ASP438 3.7 46.0 1.0
O B:HOH2071 4.0 51.4 1.0
C B:ASP319 4.0 42.0 1.0
N B:PRO439 4.0 44.9 1.0
CA B:VAL320 4.0 40.0 1.0
CA B:ASP319 4.1 42.4 1.0
CD B:PRO439 4.1 43.0 1.0
CG B:PRO439 4.3 45.2 1.0
OD2 B:ASP438 4.3 52.0 1.0
C B:ASP438 4.3 44.7 1.0
CG B:GLU441 4.3 44.6 1.0
CA B:PRO439 4.4 43.7 1.0
CB B:ASP319 4.4 41.4 1.0
OD2 B:ASP319 4.5 41.8 1.0
N B:THR440 4.6 44.1 1.0
CA B:ASP438 4.6 44.9 1.0
CA B:THR440 4.7 43.8 1.0
N B:THR321 4.7 38.9 1.0
CB B:ASP438 4.8 43.9 1.0
CB B:VAL320 4.8 40.6 1.0
O B:ASP438 4.8 47.3 1.0
C B:THR440 4.9 43.1 1.0
OG1 B:THR321 4.9 41.3 1.0
CB B:PRO439 4.9 43.5 1.0
O B:ASP319 4.9 44.2 1.0

Nickel binding site 5 out of 9 in 2y1v

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Nickel binding site 5 out of 9 in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni801

b:78.2
occ:1.00
 O B:ALA536 2.3 47.2 1.0
OD2 B:ASP308 2.3 59.3 1.0
OD1 B:ASN539 2.6 48.6 1.0
O B:HOH2067 3.2 48.0 1.0
CG B:ASN539 3.3 51.4 1.0
ND2 B:ASN539 3.3 52.2 1.0
C B:ALA536 3.4 46.4 1.0
OE2 B:GLU489 3.5 63.5 1.0
CG B:ASP308 3.5 53.8 1.0
CD B:GLU489 3.5 62.5 1.0
OE1 B:GLU489 3.6 65.1 1.0
CA B:ALA536 4.1 46.1 1.0
CB B:ASP308 4.2 49.7 1.0
CG B:GLU489 4.3 62.3 1.0
O B:HOH2121 4.4 47.9 1.0
N B:ALA537 4.4 46.7 1.0
CB B:ALA536 4.4 44.0 1.0
OD1 B:ASP308 4.4 55.7 1.0
CA B:ALA537 4.7 47.5 1.0
CB B:ASN539 4.8 50.5 1.0

Nickel binding site 6 out of 9 in 2y1v

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Nickel binding site 6 out of 9 in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni802

b:82.2
occ:1.00
 OE2 B:GLU245 2.5 51.0 1.0
O B:HOH2070 3.0 50.9 1.0
CD B:GLU245 3.5 51.5 1.0
CG B:GLU245 3.9 50.6 1.0
O B:ASN398 4.0 47.8 1.0
OE2 B:GLU316 4.1 48.3 1.0
CG1 B:ILE311 4.2 45.2 1.0
OE1 B:GLN373 4.2 44.4 1.0
O B:LYS309 4.3 49.8 1.0
CE B:LYS338 4.6 59.9 1.0
O B:HOH2069 4.6 39.1 1.0
NZ B:LYS338 4.6 56.7 1.0
NE2 B:GLN373 4.6 50.8 1.0
OE1 B:GLU245 4.7 51.0 1.0
OE1 B:GLU400 4.7 48.4 1.0
CD B:GLN373 4.8 46.9 1.0

Nickel binding site 7 out of 9 in 2y1v

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Nickel binding site 7 out of 9 in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni800

b:74.3
occ:1.00
 OD1 C:ASP319 2.1 51.8 1.0
OD1 C:ASP438 2.3 56.3 1.0
OE2 C:GLU441 2.4 48.8 1.0
O C:VAL320 2.6 53.6 1.0
O C:PRO439 3.0 48.8 1.0
CD C:GLU441 3.1 52.2 1.0
OE1 C:GLU441 3.2 51.7 1.0
CG C:ASP438 3.3 57.3 1.0
CG C:ASP319 3.4 54.5 1.0
C C:VAL320 3.7 51.6 1.0
N C:VAL320 3.8 52.6 1.0
OD2 C:ASP438 3.8 54.7 1.0
OD2 C:ASP319 4.1 55.7 1.0
C C:ASP319 4.2 52.0 1.0
C C:PRO439 4.2 49.9 1.0
CG2 C:THR321 4.2 55.1 1.0
CA C:ASP319 4.2 51.2 1.0
C C:ASP438 4.4 52.2 1.0
CA C:VAL320 4.4 51.5 1.0
CB C:ASP319 4.4 51.9 1.0
N C:PRO439 4.5 50.3 1.0
CD C:PRO439 4.5 49.1 1.0
CG C:GLU441 4.5 51.4 1.0
CB C:ASP438 4.5 54.7 1.0
O C:ASP438 4.6 52.9 1.0
CA C:ASP438 4.6 54.0 1.0
N C:THR321 4.7 51.7 1.0
O C:HOH2088 4.7 48.7 1.0
CG C:PRO439 4.8 48.4 1.0
O C:ASP319 4.9 53.3 1.0
CA C:PRO439 5.0 49.7 1.0

Nickel binding site 8 out of 9 in 2y1v

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Nickel binding site 8 out of 9 in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni801

b:74.3
occ:1.00
 OD2 C:ASP308 2.4 48.4 1.0
OD1 C:ASN539 2.4 46.6 1.0
OE2 C:GLU489 2.6 57.7 1.0
O C:ALA536 2.6 46.1 1.0
CG C:ASN539 3.2 45.5 1.0
ND2 C:ASN539 3.3 49.2 1.0
CG C:ASP308 3.4 51.6 1.0
CD C:GLU489 3.7 63.4 1.0
C C:ALA536 3.8 48.1 1.0
CB C:ASP308 4.1 50.4 1.0
O C:HOH2054 4.2 48.2 1.0
OD1 C:ASP308 4.3 53.1 1.0
CA C:ALA536 4.4 48.0 1.0
OE1 C:GLU489 4.4 64.3 1.0
CB C:ASN539 4.6 48.1 1.0
CG C:GLU489 4.7 60.2 1.0
CB C:ALA536 4.8 46.3 1.0
O C:HOH2056 4.8 48.6 1.0
N C:ALA537 4.9 48.4 1.0

Nickel binding site 9 out of 9 in 2y1v

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Nickel binding site 9 out of 9 in the Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Full Length Structure of Rrgb Pilus Protein From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni802

b:78.1
occ:1.00
 OE2 C:GLU245 2.4 57.9 1.0
O C:HOH2070 2.7 46.8 1.0
CD C:GLU245 3.4 58.0 1.0
O C:HOH2059 3.6 48.1 1.0
CG C:GLU245 3.7 52.2 1.0
OE2 C:GLU316 3.9 54.4 1.0
OE1 C:GLN373 3.9 59.5 1.0
O C:LYS309 4.1 49.9 1.0
O C:ASN398 4.3 61.0 1.0
OE2 C:GLU400 4.4 57.0 1.0
CG1 C:ILE311 4.4 48.6 1.0
OE1 C:GLU245 4.5 58.4 1.0
O C:HOH2075 4.7 37.4 1.0
NZ C:LYS338 4.8 51.0 1.0
CD C:GLU316 4.8 51.8 1.0
CE C:LYS338 4.8 54.8 1.0
CD C:GLN373 4.8 57.7 1.0
OE1 C:GLU316 4.9 50.8 1.0
C C:LYS309 5.0 50.2 1.0

Reference:

L.El Mortaji, C.Contreras-Martel, M.Moschioni, I.Ferlenghi, C.Manzano, T.Vernet, A.Dessen, A.M.Di Guilmi. The Full-Length Streptococcus Pneumoniae Major Pilin Rrgb Crystallizes in A Fibre-Like Structure, Which Presents the D1 Isopeptide Bond and Provides Details on the Mechanism of Pilus Polymerization. Biochem.J. V. 441 833 2012.
ISSN: ISSN 0264-6021
PubMed: 22013894
DOI: 10.1042/BJ20111397
Page generated: Wed Oct 9 17:05:40 2024

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