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Sodium in PDB 4adn: Fusidic Acid Resistance Protein Fusb

Protein crystallography data

The structure of Fusidic Acid Resistance Protein Fusb, PDB code: 4adn was solved by X.Guo, K.Peisker, K.Backbro, Y.Chen, R.K.Kiran, S.Sanyal, M.Selmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.774 / 1.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 75.020, 122.410, 52.920, 90.00, 90.00, 90.00
R / Rfree (%) 16.31 / 20.21

Other elements in 4adn:

The structure of Fusidic Acid Resistance Protein Fusb also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Fusidic Acid Resistance Protein Fusb (pdb code 4adn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Fusidic Acid Resistance Protein Fusb, PDB code: 4adn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4adn

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Sodium binding site 1 out of 8 in the Fusidic Acid Resistance Protein Fusb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fusidic Acid Resistance Protein Fusb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1224

b:21.4
occ:1.00
O A:HOH2192 2.8 20.2 1.0
O A:HOH2193 2.9 14.2 1.0
ND2 A:ASN31 3.0 12.5 1.0
NH1 B:ARG28 3.6 14.7 1.0
CG2 A:THR35 3.8 17.5 1.0
OG1 A:THR35 3.9 14.8 1.0
CE1 B:TYR21 3.9 14.7 1.0
CG A:ASN31 4.0 13.3 1.0
OD1 A:ASN31 4.2 14.2 1.0
CZ B:ARG28 4.2 14.8 1.0
CB A:THR35 4.2 13.9 1.0
CG1 B:VAL25 4.2 14.6 1.0
O A:HOH2184 4.4 30.5 1.0
NH2 B:ARG28 4.6 16.8 1.0
OH B:TYR21 4.6 17.6 1.0
OG B:SER24 4.6 16.6 1.0
CZ B:TYR21 4.6 15.1 1.0
O B:HOH2022 4.6 32.3 1.0
CD1 B:TYR21 4.7 13.1 1.0
O A:HOH2038 4.7 20.5 1.0
O A:HOH2195 4.7 14.8 1.0
NE B:ARG28 4.9 13.5 1.0

Sodium binding site 2 out of 8 in 4adn

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Sodium binding site 2 out of 8 in the Fusidic Acid Resistance Protein Fusb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Fusidic Acid Resistance Protein Fusb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1225

b:18.9
occ:1.00
O A:HOH2195 2.7 14.8 1.0
O A:HOH2194 2.8 15.4 1.0
O A:HOH2024 2.8 18.5 1.0
O A:HOH2025 2.8 14.3 1.0
CA A:ARG28 3.8 11.8 1.0
OD1 A:ASN31 4.0 14.2 1.0
CG B:ARG28 4.0 12.2 1.0
CB A:ASN31 4.0 11.8 1.0
CG A:ARG28 4.1 11.1 1.0
CG A:ASN31 4.1 13.3 1.0
CD B:ARG28 4.1 14.0 1.0
CB A:ARG28 4.1 11.7 1.0
O B:HOH2024 4.2 18.5 1.0
O B:HOH2021 4.2 15.7 1.0
CB B:ARG28 4.4 10.6 1.0
O A:HOH2020 4.5 14.9 1.0
O A:ARG28 4.5 11.4 1.0
O B:HOH2026 4.5 13.8 1.0
O A:HOH2021 4.6 14.3 1.0
O A:HOH2197 4.6 24.4 1.0
NA A:NA1231 4.6 24.7 1.0
N A:ARG28 4.7 11.0 1.0
C A:ARG28 4.7 12.2 1.0
O A:LEU27 4.8 14.3 1.0
O A:HOH2011 4.9 23.9 1.0
ND2 A:ASN31 4.9 12.5 1.0
CA B:ARG28 4.9 11.5 1.0
O A:HOH2193 4.9 14.2 1.0

Sodium binding site 3 out of 8 in 4adn

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Sodium binding site 3 out of 8 in the Fusidic Acid Resistance Protein Fusb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Fusidic Acid Resistance Protein Fusb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1226

b:24.4
occ:1.00
O A:HOH2196 2.7 25.6 1.0
O A:HOH2021 2.8 14.3 1.0
ND2 B:ASN31 3.8 14.1 1.0
OG A:SER24 4.0 13.7 1.0
CE A:LYS171 4.0 29.8 1.0
O A:HOH2022 4.3 17.1 1.0
O B:HOH2024 4.3 18.5 1.0
CG B:ASN31 4.3 13.4 1.0
CB B:ASN31 4.4 14.3 1.0
O B:HOH2025 4.5 23.2 1.0
O A:HOH2194 4.6 15.4 1.0
O A:HOH2069 4.6 34.0 1.0
O A:HOH2020 4.7 14.9 1.0
CD A:LYS171 4.7 26.1 1.0
O A:HOH2009 4.9 31.9 1.0
NZ A:LYS171 4.9 31.8 1.0
NA B:NA1224 5.0 21.9 1.0

Sodium binding site 4 out of 8 in 4adn

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Sodium binding site 4 out of 8 in the Fusidic Acid Resistance Protein Fusb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Fusidic Acid Resistance Protein Fusb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1227

b:31.3
occ:1.00
O A:HOH2198 2.6 37.0 1.0
O A:LEU27 2.7 14.3 1.0
O A:HOH2197 3.1 24.4 1.0
C A:LEU27 3.6 12.2 1.0
N A:ASN31 3.6 13.8 1.0
CB A:ASN31 3.7 11.8 1.0
CA A:LEU27 3.9 11.4 1.0
CB A:LEU27 4.0 12.1 1.0
CB A:LYS30 4.0 15.3 1.0
CA A:ASN31 4.0 13.0 1.0
CG A:LYS30 4.1 15.2 1.0
C A:LYS30 4.3 14.8 1.0
O A:HOH2024 4.3 18.5 1.0
NA A:NA1231 4.3 24.7 1.0
CD2 A:LEU27 4.5 15.5 1.0
O B:HOH2136 4.5 23.1 1.0
CA A:LYS30 4.6 15.0 1.0
N A:ARG28 4.7 11.0 1.0
CG A:LEU27 4.8 12.2 1.0
O A:HOH2185 4.9 31.4 1.0
CG A:ASN31 5.0 13.3 1.0

Sodium binding site 5 out of 8 in 4adn

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Sodium binding site 5 out of 8 in the Fusidic Acid Resistance Protein Fusb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Fusidic Acid Resistance Protein Fusb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1231

b:24.7
occ:1.00
O B:HOH2022 2.7 32.3 1.0
O A:HOH2197 2.7 24.4 1.0
O A:HOH2195 2.9 14.8 1.0
CE B:LYS171 3.7 26.4 1.0
ND2 A:ASN31 3.7 12.5 1.0
OG B:SER24 4.1 16.6 1.0
CG A:ASN31 4.3 13.3 1.0
CB A:ASN31 4.3 11.8 1.0
NA A:NA1227 4.3 31.3 1.0
O A:HOH2024 4.3 18.5 1.0
O A:HOH2193 4.4 14.2 1.0
NZ B:LYS171 4.6 27.1 1.0
NA A:NA1225 4.6 18.9 1.0
CD B:LYS171 4.6 23.1 1.0
O A:HOH2185 4.7 31.4 1.0
O B:HOH2021 4.7 15.7 1.0
O B:HOH2011 4.9 34.4 1.0
O2 B:PEG1230 4.9 48.5 1.0

Sodium binding site 6 out of 8 in 4adn

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Sodium binding site 6 out of 8 in the Fusidic Acid Resistance Protein Fusb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Fusidic Acid Resistance Protein Fusb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1224

b:21.9
occ:1.00
O A:HOH2022 2.7 17.1 1.0
O A:HOH2017 2.8 19.0 1.0
ND2 B:ASN31 3.0 14.1 1.0
NH1 A:ARG28 3.5 15.8 1.0
OG1 B:THR35 3.9 16.5 1.0
CG2 B:THR35 3.9 18.2 1.0
CE1 A:TYR21 4.0 14.3 1.0
CG B:ASN31 4.0 13.4 1.0
CZ A:ARG28 4.1 13.3 1.0
OD1 B:ASN31 4.2 15.2 1.0
CB B:THR35 4.2 16.4 1.0
CG1 A:VAL25 4.3 15.6 1.0
NA B:NA1231 4.5 39.9 1.0
NH2 A:ARG28 4.5 14.2 1.0
OG A:SER24 4.6 13.7 1.0
O A:HOH2026 4.6 19.9 1.0
O A:HOH2021 4.7 14.3 1.0
OH A:TYR21 4.7 15.7 1.0
CD1 A:TYR21 4.7 14.2 1.0
CZ A:TYR21 4.8 16.7 1.0
NE A:ARG28 4.8 13.2 1.0
NA A:NA1226 5.0 24.4 1.0

Sodium binding site 7 out of 8 in 4adn

Go back to Sodium Binding Sites List in 4adn
Sodium binding site 7 out of 8 in the Fusidic Acid Resistance Protein Fusb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Fusidic Acid Resistance Protein Fusb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1225

b:37.9
occ:1.00
OD1 B:ASP210 2.7 34.0 1.0
C1 B:GOL1227 2.7 42.7 1.0
O1 B:GOL1227 2.9 48.2 1.0
N B:ILE211 3.0 20.4 1.0
CA B:ASP210 3.3 21.9 1.0
C B:ASP210 3.5 20.4 1.0
CG2 B:ILE211 3.5 22.1 0.5
CG B:ASP210 3.5 32.5 1.0
N1 B:IMD1226 3.6 65.9 1.0
CD2 B:HIS17 3.7 14.7 1.0
NE2 B:HIS17 3.7 16.9 1.0
C3 B:GOL1227 3.7 41.8 1.0
C2 B:GOL1227 3.8 43.2 1.0
N B:ASN212 3.9 21.1 1.0
CB B:ASP210 3.9 26.4 1.0
CA B:ILE211 4.0 19.7 0.5
C5 B:IMD1226 4.0 65.3 1.0
CA B:ILE211 4.1 19.7 0.5
ND2 B:ASN212 4.1 37.5 1.0
CB B:ILE211 4.2 21.8 0.5
CG2 B:ILE211 4.2 23.4 0.5
O B:THR209 4.3 18.8 1.0
CG B:ASN212 4.4 34.9 1.0
CB B:ILE211 4.4 21.3 0.5
N B:ASP210 4.5 19.9 1.0
C B:ILE211 4.5 19.7 1.0
C2 B:IMD1226 4.5 66.2 1.0
OD2 B:ASP210 4.5 35.3 1.0
O B:ASP210 4.5 20.7 1.0
O2 B:GOL1227 4.6 47.7 1.0
CB B:ASN212 4.7 29.9 1.0
CE1 B:HIS17 4.7 15.7 1.0
CG B:HIS17 4.8 13.1 1.0
C B:THR209 4.8 17.0 1.0
OD1 B:ASN212 4.9 37.5 1.0
CA B:ASN212 4.9 24.9 1.0

Sodium binding site 8 out of 8 in 4adn

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Sodium binding site 8 out of 8 in the Fusidic Acid Resistance Protein Fusb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Fusidic Acid Resistance Protein Fusb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1231

b:39.9
occ:1.00
O A:HOH2017 2.9 19.0 1.0
CG2 B:THR35 3.7 18.2 1.0
OH A:TYR21 4.0 15.7 1.0
CB B:THR35 4.0 16.4 1.0
CE1 A:TYR21 4.2 14.3 1.0
O A:HOH2016 4.4 32.0 1.0
NA B:NA1224 4.5 21.9 1.0
CZ A:TYR21 4.5 16.7 1.0
O A:HOH2026 4.8 19.9 1.0
CA B:THR35 4.9 17.4 1.0

Reference:

X.Guo, K.Peisker, K.Backbro, Y.Chen, R.K.Kiran, C.S.Mandava, S.Sanyal, M.Selmer. Structure and Function of Fusb: An Elongation Factor G-Binding Fusidic Acid Resistance Protein Active in Ribosomal Translocation and Recycling Open Biol. V. 2 20016 2012.
ISSN: ISSN 2046-2441
PubMed: 22645663
DOI: 10.1098/RSOB.120016
Page generated: Tue Dec 15 06:32:48 2020

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