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Zinc in PDB 5g5y: S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure

Protein crystallography data

The structure of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure, PDB code: 5g5y was solved by S.Culurgioni, G.Harris, A.K.Singh, S.J.King, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.76 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.070, 72.170, 77.660, 108.02, 104.99, 92.49
R / Rfree (%) 16.1 / 19.3

Other elements in 5g5y:

The structure of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure (pdb code 5g5y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure, PDB code: 5g5y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5g5y

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Zinc binding site 1 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1539

b:22.9
occ:1.00
 OE2 A:GLU73 2.0 17.4 1.0
ND1 A:HIS79 2.1 17.2 1.0
CD A:GLU73 2.7 16.8 1.0
OE1 A:GLU73 2.7 14.4 1.0
CE1 A:HIS79 3.0 19.2 1.0
CG A:HIS79 3.1 17.6 1.0
CB A:HIS79 3.4 17.2 1.0
NE2 A:HIS79 4.1 19.1 1.0
CG A:GLU73 4.1 17.0 1.0
CD2 A:HIS79 4.1 18.1 1.0
CA A:HIS79 4.2 17.1 1.0
CG A:PRO46 4.4 36.0 1.0
O A:HOH2034 4.9 35.9 1.0
O A:HOH2020 4.9 13.3 1.0

Zinc binding site 2 out of 10 in 5g5y

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Zinc binding site 2 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1540

b:56.3
occ:1.00
 OD1 A:ASP305 2.0 41.2 1.0
OD2 B:ASP88 2.2 50.7 1.0
O A:HOH2439 2.4 38.4 1.0
ND1 A:HIS304 2.6 48.8 1.0
CG A:ASP305 2.7 38.8 1.0
OD2 A:ASP305 2.9 40.3 1.0
CG B:ASP88 3.0 48.7 1.0
OD1 B:ASP88 3.2 50.8 1.0
CG A:HIS304 3.3 45.4 1.0
CE1 A:HIS304 3.4 50.8 1.0
CB A:HIS304 3.7 36.1 1.0
O A:ALA301 3.8 26.9 1.0
N A:ASP305 3.9 30.7 1.0
CB A:ASP305 4.0 36.3 1.0
C A:HIS304 4.1 31.5 1.0
NE2 A:HIS304 4.3 49.0 1.0
CD2 A:HIS304 4.3 48.4 1.0
CA A:ASP305 4.3 33.4 1.0
CB B:ASP88 4.4 42.1 1.0
CA A:HIS304 4.5 31.6 1.0
CD B:GLU91 4.5 60.3 1.0
O A:HIS304 4.5 28.8 1.0
OE2 B:GLU91 4.5 65.9 1.0
CG B:GLU91 4.6 52.5 1.0
O A:HOH2441 4.7 49.4 1.0
C A:ALA301 4.8 28.9 1.0
CB B:GLU91 4.9 43.3 1.0
OE1 B:GLU91 5.0 57.9 1.0

Zinc binding site 3 out of 10 in 5g5y

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Zinc binding site 3 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1541

b:24.3
occ:1.00
 NE2 A:HIS481 2.0 22.3 1.0
OD2 A:ASP485 2.0 21.0 1.0
CG A:ASP485 2.9 21.6 1.0
CD2 A:HIS481 3.0 26.1 1.0
CE1 A:HIS481 3.0 28.1 1.0
OD1 A:ASP485 3.1 20.8 1.0
O A:HOH2615 3.7 21.2 1.0
ND1 A:HIS481 4.1 29.7 1.0
CG A:HIS481 4.1 24.6 1.0
CB A:ASP485 4.3 19.9 1.0
O A:HOH2311 4.9 36.1 1.0
O A:HIS481 5.0 16.8 1.0

Zinc binding site 4 out of 10 in 5g5y

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Zinc binding site 4 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1542

b:33.9
occ:1.00
 O4 A:SO4603 1.9 21.7 0.6
OE2 B:GLU221 2.0 30.9 1.0
O A:HOH2077 2.1 22.2 1.0
OD1 A:ASP96 2.1 26.5 1.0
O A:HOH2104 2.2 8.0 0.4
S A:SO4603 2.8 31.3 0.6
O3 A:SO4603 2.8 23.1 0.6
CD B:GLU221 2.9 32.1 1.0
CG A:ASP96 3.0 26.2 1.0
OE1 B:GLU221 3.1 30.9 1.0
OH A:TYR85 3.2 19.6 1.0
OD2 A:ASP96 3.3 26.8 1.0
O1 A:SO4603 3.4 27.5 0.6
O A:HOH2103 3.9 35.8 1.0
O B:HOH2264 4.1 31.8 1.0
O2 A:SO4603 4.1 26.8 0.6
CG B:GLU221 4.3 31.6 1.0
CZ A:TYR85 4.3 20.1 1.0
O A:LYS92 4.3 21.7 1.0
CB A:ASP96 4.4 24.2 1.0
OD2 A:ASP101 4.5 39.0 1.0
N A:ASP96 4.5 24.5 1.0
CA A:ASP96 4.6 23.7 1.0
O A:HOH2675 4.9 20.3 1.0
CB A:LEU95 4.9 25.4 1.0
CE1 A:TYR85 5.0 18.9 1.0

Zinc binding site 5 out of 10 in 5g5y

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Zinc binding site 5 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1543

b:45.9
occ:1.00
 OE1 A:GLU168 2.1 17.0 1.0
O A:HOH2199 2.3 15.2 1.0
OD2 A:ASP171 2.5 36.5 1.0
OD1 A:ASP171 2.5 38.9 1.0
NZ A:LYS146 2.7 41.5 1.0
CG A:ASP171 2.8 31.6 1.0
CD A:GLU168 3.0 17.7 1.0
CE A:LYS146 3.0 38.6 1.0
OE2 A:GLU168 3.2 18.1 1.0
CB A:ASP432 3.8 20.6 1.0
N A:ASP432 3.9 16.2 1.0
CD A:LYS146 3.9 35.1 1.0
C3 A:GOL1546 4.2 56.2 1.0
CB A:ASP171 4.3 26.4 1.0
CG A:GLU168 4.3 15.7 1.0
O3 A:GOL1546 4.4 54.6 1.0
CA A:ASP432 4.4 18.2 1.0
CB A:GLU168 4.6 14.9 1.0
CB A:LEU431 4.7 17.3 1.0
CG A:LYS146 4.8 29.3 1.0
N A:SER433 4.9 18.9 1.0
C A:LEU431 4.9 15.9 1.0
CA A:LEU431 4.9 16.0 1.0

Zinc binding site 6 out of 10 in 5g5y

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Zinc binding site 6 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1544

b:52.0
occ:1.00
 O A:HOH2220 1.6 33.1 1.0
O A:HOH2221 2.0 45.4 1.0
NE2 A:HIS159 2.3 28.7 1.0
O A:HOH2218 2.5 43.1 1.0
CD2 A:HIS159 3.1 26.7 1.0
CE1 A:HIS159 3.4 30.5 1.0
CG A:HIS159 4.3 24.7 1.0
ND1 A:HIS159 4.5 27.8 1.0
O A:ASP157 4.8 21.8 1.0
O A:HOH2224 4.9 44.6 1.0
OD2 A:ASP157 5.0 27.3 1.0

Zinc binding site 7 out of 10 in 5g5y

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Zinc binding site 7 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1545

b:36.4
occ:1.00
 OD1 A:ASP81 2.1 19.9 1.0
O A:HOH2068 2.1 39.0 1.0
O A:HOH2066 2.2 38.9 1.0
O A:HOH2067 2.3 35.6 1.0
O A:HOH2065 2.4 35.0 1.0
O A:HOH2676 2.4 37.7 1.0
CG A:ASP81 3.0 20.1 1.0
OD2 A:ASP81 3.2 24.6 1.0
O A:TRP82 3.9 17.3 1.0
O A:HOH2021 4.2 58.9 1.0
O A:HOH2016 4.2 22.9 1.0
O A:HOH2070 4.3 38.0 1.0
CB A:ASP81 4.4 17.2 1.0
N A:TRP82 4.6 15.8 1.0
O A:HOH2004 4.6 32.2 1.0
CA A:ASP81 4.7 15.9 1.0
C A:ASP81 4.7 16.0 1.0
O A:HOH2029 4.8 41.5 1.0
C A:TRP82 4.9 18.9 1.0
O A:HOH2006 4.9 24.0 1.0

Zinc binding site 8 out of 10 in 5g5y

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Zinc binding site 8 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1539

b:51.0
occ:1.00
 OE1 B:GLU168 2.2 21.5 1.0
O B:HOH2173 2.3 16.2 1.0
OD2 B:ASP171 2.6 46.3 1.0
NZ B:LYS146 2.6 41.1 1.0
OD1 B:ASP171 2.6 41.5 1.0
CG B:ASP171 2.9 38.0 1.0
CD B:GLU168 3.0 21.6 1.0
OE2 B:GLU168 3.2 21.2 1.0
CE B:LYS146 3.6 41.2 1.0
CB B:ASP432 3.8 26.1 1.0
CD B:LYS146 3.9 37.3 1.0
N B:ASP432 3.9 22.0 1.0
O B:HOH2146 4.3 50.7 1.0
CG B:GLU168 4.3 20.2 1.0
CB B:ASP171 4.4 30.7 1.0
CA B:ASP432 4.5 23.6 1.0
CB B:GLU168 4.7 17.8 1.0
CB B:LEU431 4.8 20.2 1.0
CG B:LYS146 4.8 34.2 1.0
O B:HOH2176 4.8 58.8 1.0
O B:HOH2061 4.8 55.1 1.0
C B:LEU431 4.9 20.8 1.0
N B:SER433 4.9 23.0 1.0
CA B:LEU431 5.0 20.9 1.0

Zinc binding site 9 out of 10 in 5g5y

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Zinc binding site 9 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1540

b:51.2
occ:1.00
 O B:HOH2040 2.1 48.6 1.0
OD1 B:ASP81 2.2 23.1 1.0
O B:HOH2597 2.3 38.8 1.0
O B:HOH2041 2.4 38.6 1.0
O B:HOH2598 2.6 52.9 1.0
CG B:ASP81 3.1 22.3 1.0
OD2 B:ASP81 3.3 25.0 1.0
O B:TRP82 4.0 20.9 1.0
O B:HOH2039 4.1 27.3 1.0
O B:HOH2013 4.3 21.9 1.0
CB B:ASP81 4.4 20.4 1.0
O B:HOH2003 4.6 26.0 1.0
N B:TRP82 4.7 19.1 1.0
CA B:ASP81 4.8 19.2 1.0
C B:ASP81 4.9 18.1 1.0
C B:TRP82 4.9 22.3 1.0

Zinc binding site 10 out of 10 in 5g5y

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Zinc binding site 10 out of 10 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1541

b:63.6
occ:1.00
 O B:HOH2601 1.7 38.5 1.0
O B:HOH2600 2.0 42.5 1.0
NE2 B:HIS159 2.4 35.4 1.0
O B:HOH2599 2.7 51.9 1.0
CE1 B:HIS159 3.2 35.1 1.0
CD2 B:HIS159 3.5 35.0 1.0
O B:HOH2163 3.8 62.6 1.0
ND1 B:HIS159 4.3 32.7 1.0
CG B:HIS159 4.5 32.3 1.0
O B:ASP157 4.7 32.2 1.0

Reference:

S.Culurgioni, G.Harris, A.K.Singh, S.J.King, M.A.Walsh. Structural Basis For Regulation and Specificity of Fructooligosaccharide Import in Streptococcus Pneumoniae. Structure V. 25 79 2017.
ISSN: ISSN 1878-4186
PubMed: 27939783
DOI: 10.1016/J.STR.2016.11.008
Page generated: Sun Oct 27 16:58:00 2024

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