Chlorine in PDB 5szd: Crystal Structure of Aquifex Aeolicus Hfq at 1.5A

Protein crystallography data

The structure of Crystal Structure of Aquifex Aeolicus Hfq at 1.5A, PDB code: 5szd was solved by K.Stanek, J.Patterson, P.S.Randolph, C.Mura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.35 / 1.49
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.460, 66.060, 66.100, 60.05, 83.94, 77.17
R / Rfree (%) 13.2 / 17

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Aquifex Aeolicus Hfq at 1.5A (pdb code 5szd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Aquifex Aeolicus Hfq at 1.5A, PDB code: 5szd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5szd

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Chlorine binding site 1 out of 7 in the Crystal Structure of Aquifex Aeolicus Hfq at 1.5A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Aquifex Aeolicus Hfq at 1.5A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl102

b:35.2
occ:1.00
O F:HOH201 2.8 35.0 1.0
N F:TYR6 3.0 13.4 1.0
C F:MET4 3.2 19.8 0.5
C F:MET4 3.2 20.9 0.5
CA F:MET4 3.3 22.1 0.5
CA F:MET4 3.3 24.0 0.5
N F:PRO5 3.4 18.7 1.0
CB F:MET4 3.5 24.3 0.5
CB F:MET4 3.6 27.5 0.5
CA F:TYR6 3.7 14.8 1.0
O F:MET4 3.7 19.2 0.5
CD F:PRO5 3.7 19.2 1.0
O F:MET4 3.7 20.4 0.5
N F:LYS7 3.7 16.0 1.0
CB F:TYR6 3.7 17.4 1.0
C F:TYR6 3.8 15.6 1.0
CD2 F:TYR6 3.8 21.8 1.0
C F:PRO5 4.1 15.3 1.0
CG F:TYR6 4.2 20.0 1.0
CA F:PRO5 4.3 17.4 1.0
CG F:PRO5 4.4 20.7 1.0
CG F:MET4 4.4 25.6 0.5
CA F:LYS7 4.4 18.6 1.0
CG F:MET4 4.5 30.3 0.5
O F:TYR6 4.7 18.1 1.0
OE1 F:GLU10 4.7 22.7 1.0
N F:MET4 4.7 23.9 0.5
N F:MET4 4.7 24.8 0.5
CB F:LYS7 4.8 23.0 1.0
CE2 F:TYR6 4.9 24.3 1.0

Chlorine binding site 2 out of 7 in 5szd

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Chlorine binding site 2 out of 7 in the Crystal Structure of Aquifex Aeolicus Hfq at 1.5A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Aquifex Aeolicus Hfq at 1.5A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl103

b:17.4
occ:1.00
O G:HOH215 2.9 25.6 1.0
O D:HOH217 3.0 17.7 1.0
O D:HOH207 3.1 15.9 1.0
N G:TYR6 3.1 11.7 1.0
CB G:MET4 3.6 24.5 1.0
CB G:TYR6 3.6 12.9 1.0
CA G:TYR6 3.6 13.9 1.0
N G:LYS7 3.7 14.0 0.6
N G:LYS7 3.7 13.6 0.4
CE2 D:TYR26 3.8 13.6 1.0
C G:TYR6 3.8 14.0 1.0
N G:PRO5 3.8 15.4 1.0
CD G:PRO5 3.9 14.4 1.0
CD2 G:TYR6 4.0 14.6 1.0
C G:MET4 4.1 19.7 1.0
CG G:PRO5 4.2 16.5 1.0
C G:PRO5 4.2 11.0 1.0
CG G:TYR6 4.3 12.0 1.0
CA G:MET4 4.4 26.5 1.0
CA G:LYS7 4.4 14.6 0.4
CD2 D:TYR26 4.4 11.7 1.0
CA G:LYS7 4.5 16.2 0.6
O G:TYR6 4.5 15.8 1.0
O G:HOH212 4.5 23.1 1.0
CA G:PRO5 4.5 13.3 1.0
O G:MET4 4.5 19.4 1.0
CG G:MET4 4.6 24.7 1.0
CZ D:TYR26 4.7 12.5 1.0
OH D:TYR26 4.7 14.2 1.0
O D:HOH224 4.8 21.7 1.0
CD D:ARG32 4.8 15.8 1.0
CB G:LYS7 4.8 15.7 0.4
OE1 G:GLU10 4.9 25.1 1.0
CB D:ARG32 4.9 15.2 1.0
O D:GLY30 4.9 15.0 1.0
CB G:LYS7 5.0 19.0 0.6

Chlorine binding site 3 out of 7 in 5szd

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Chlorine binding site 3 out of 7 in the Crystal Structure of Aquifex Aeolicus Hfq at 1.5A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Aquifex Aeolicus Hfq at 1.5A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl104

b:16.6
occ:1.00
O H:HOH202 3.0 25.4 1.0
O E:HOH210 3.0 16.4 1.0
O E:HOH214 3.0 17.6 1.0
N H:TYR6 3.1 11.6 1.0
CB H:TYR6 3.6 11.3 1.0
CB H:MET4 3.6 15.7 0.6
CB H:MET4 3.6 24.5 0.4
CA H:TYR6 3.6 11.1 1.0
N H:LYS7 3.7 13.0 0.5
N H:LYS7 3.8 13.2 0.5
CE2 E:TYR26 3.8 11.7 1.0
C H:TYR6 3.8 13.2 1.0
N H:PRO5 3.8 14.3 1.0
CD H:PRO5 3.9 14.8 1.0
CD2 H:TYR6 3.9 13.2 1.0
C H:MET4 4.1 14.0 0.6
C H:MET4 4.1 20.1 0.4
CG H:PRO5 4.2 15.8 1.0
CG H:TYR6 4.2 10.7 1.0
C H:PRO5 4.2 12.3 1.0
CA H:MET4 4.4 13.7 0.6
CA H:MET4 4.4 26.1 0.4
CA H:LYS7 4.5 14.5 0.5
CA H:LYS7 4.5 13.6 0.5
CD2 E:TYR26 4.5 12.4 1.0
O H:HOH219 4.5 23.2 1.0
CA H:PRO5 4.5 12.2 1.0
CG H:MET4 4.5 18.5 0.6
O H:TYR6 4.5 14.8 1.0
O H:MET4 4.6 20.1 0.4
O H:MET4 4.6 13.8 0.6
CG H:MET4 4.6 24.2 0.4
O E:HOH227 4.7 21.7 1.0
OH E:TYR26 4.7 14.4 1.0
CZ E:TYR26 4.7 11.6 1.0
CB H:LYS7 4.8 18.3 0.5
OE1 H:GLU10 4.8 24.7 1.0
CD E:ARG32 4.9 14.6 1.0
O E:GLY30 4.9 13.2 1.0
CB H:PRO5 5.0 14.6 1.0
CB H:LYS7 5.0 16.9 0.5

Chlorine binding site 4 out of 7 in 5szd

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Chlorine binding site 4 out of 7 in the Crystal Structure of Aquifex Aeolicus Hfq at 1.5A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Aquifex Aeolicus Hfq at 1.5A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl103

b:15.6
occ:1.00
O F:HOH214 3.0 17.9 1.0
O I:HOH209 3.0 23.9 1.0
O F:HOH208 3.0 14.2 1.0
N I:TYR6 3.1 10.9 1.0
CB I:MET4 3.5 27.2 0.3
CB I:MET4 3.6 13.8 0.7
CB I:TYR6 3.6 10.4 1.0
CA I:TYR6 3.6 10.0 1.0
N I:LYS7 3.8 11.9 1.0
C I:TYR6 3.8 11.4 1.0
CE2 F:TYR26 3.8 12.1 1.0
N I:PRO5 3.8 12.7 1.0
CD I:PRO5 3.8 14.0 1.0
CD2 I:TYR6 3.9 13.1 1.0
C I:MET4 4.0 11.6 0.7
C I:MET4 4.1 19.5 0.3
CG I:PRO5 4.2 15.0 1.0
CG I:TYR6 4.2 10.1 1.0
C I:PRO5 4.2 11.4 1.0
CA I:MET4 4.4 10.6 0.7
CA I:MET4 4.4 25.6 0.3
O I:HOH219 4.5 26.8 1.0
CG I:MET4 4.5 28.8 0.3
CA I:PRO5 4.5 12.5 1.0
CD2 F:TYR26 4.5 11.0 1.0
CG I:MET4 4.5 16.2 0.7
CA I:LYS7 4.6 14.3 1.0
O I:MET4 4.6 13.6 0.7
O I:TYR6 4.6 15.4 1.0
O I:MET4 4.6 20.5 0.3
O F:HOH223 4.7 23.5 1.0
OH F:TYR26 4.8 14.4 1.0
CZ F:TYR26 4.8 12.7 1.0
CD F:ARG32 4.9 15.4 1.0
OE1 I:GLU10 4.9 22.7 1.0
O F:GLY30 4.9 14.3 1.0
CB I:PRO5 5.0 14.1 1.0
CB F:ARG32 5.0 12.4 1.0

Chlorine binding site 5 out of 7 in 5szd

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Chlorine binding site 5 out of 7 in the Crystal Structure of Aquifex Aeolicus Hfq at 1.5A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Aquifex Aeolicus Hfq at 1.5A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl103

b:17.1
occ:1.00
O A:HOH214 3.0 16.7 1.0
O A:HOH207 3.0 14.4 1.0
O J:HOH206 3.0 26.6 1.0
N J:TYR6 3.1 11.1 1.0
CB J:MET4 3.6 23.3 1.0
CB J:TYR6 3.6 11.8 1.0
CA J:TYR6 3.6 11.1 1.0
N J:LYS7 3.7 13.0 0.6
N J:LYS7 3.7 12.1 0.4
CE1 A:TYR26 3.7 10.9 1.0
C J:TYR6 3.7 11.8 1.0
N J:PRO5 3.8 13.7 1.0
CD J:PRO5 3.9 14.0 1.0
CD2 J:TYR6 3.9 12.8 1.0
C J:MET4 4.0 17.8 1.0
CG J:PRO5 4.2 15.4 1.0
C J:PRO5 4.2 10.5 1.0
CG J:TYR6 4.2 10.8 1.0
CA J:MET4 4.4 25.6 1.0
CA J:LYS7 4.4 13.5 0.4
CA J:LYS7 4.4 15.6 0.6
CD1 A:TYR26 4.5 10.8 1.0
O J:TYR6 4.5 14.3 1.0
O J:HOH210 4.5 22.5 1.0
CA J:PRO5 4.5 12.7 1.0
O J:MET4 4.5 16.5 1.0
CG J:MET4 4.6 23.5 1.0
O A:HOH223 4.7 21.9 1.0
CZ A:TYR26 4.7 11.1 1.0
OH A:TYR26 4.8 14.2 1.0
CB J:LYS7 4.8 16.0 0.4
OE1 J:GLU10 4.9 22.8 1.0
CD A:ARG32 4.9 15.4 1.0
CB A:ARG32 4.9 13.4 1.0
O A:GLY30 4.9 14.1 1.0
CB J:LYS7 4.9 20.4 0.6
CB J:PRO5 5.0 14.6 1.0

Chlorine binding site 6 out of 7 in 5szd

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Chlorine binding site 6 out of 7 in the Crystal Structure of Aquifex Aeolicus Hfq at 1.5A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Aquifex Aeolicus Hfq at 1.5A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl103

b:16.8
occ:1.00
O K:HOH207 3.0 23.4 1.0
O B:HOH213 3.1 15.6 1.0
O B:HOH216 3.1 18.0 1.0
N K:TYR6 3.1 11.6 1.0
CB K:MET4 3.6 19.9 1.0
CB K:TYR6 3.6 12.3 1.0
CA K:TYR6 3.6 12.3 1.0
N K:LYS7 3.7 13.0 0.5
C K:TYR6 3.7 12.3 1.0
CE2 B:TYR26 3.7 12.5 1.0
N K:LYS7 3.8 12.5 0.5
N K:PRO5 3.8 13.2 1.0
CD K:PRO5 3.9 13.9 1.0
CD2 K:TYR6 3.9 13.1 1.0
C K:MET4 4.1 16.4 1.0
CG K:TYR6 4.2 11.3 1.0
C K:PRO5 4.3 12.8 1.0
CG K:PRO5 4.3 15.2 1.0
CA K:MET4 4.4 18.9 1.0
CD2 B:TYR26 4.4 11.4 1.0
O K:TYR6 4.4 14.0 1.0
CA K:LYS7 4.4 13.8 0.5
CA K:LYS7 4.5 15.0 0.5
O K:HOH212 4.5 25.8 1.0
CA K:PRO5 4.5 13.0 1.0
O K:MET4 4.6 17.3 1.0
CG K:MET4 4.6 23.0 1.0
O B:HOH226 4.7 21.8 1.0
OH B:TYR26 4.7 15.1 1.0
CZ B:TYR26 4.7 11.9 1.0
CB K:LYS7 4.8 15.8 0.5
CD B:ARG32 4.9 16.5 1.0
OE1 K:GLU10 4.9 21.3 1.0
O B:GLY30 4.9 14.7 1.0
CB B:ARG32 4.9 13.3 1.0
CB K:LYS7 5.0 17.7 0.5

Chlorine binding site 7 out of 7 in 5szd

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Chlorine binding site 7 out of 7 in the Crystal Structure of Aquifex Aeolicus Hfq at 1.5A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Aquifex Aeolicus Hfq at 1.5A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl103

b:18.4
occ:1.00
O L:HOH213 2.9 26.3 1.0
O C:HOH207 3.0 16.0 1.0
O C:HOH215 3.0 18.3 1.0
N L:TYR6 3.1 12.2 1.0
CB L:MET4 3.6 18.4 1.0
CB L:TYR6 3.6 11.8 1.0
CA L:TYR6 3.6 12.3 1.0
N L:LYS7 3.7 14.0 0.5
N L:LYS7 3.7 13.4 0.5
C L:TYR6 3.7 12.8 1.0
CE2 C:TYR26 3.8 13.2 1.0
N L:PRO5 3.8 13.5 1.0
CD L:PRO5 3.9 13.7 1.0
CD2 L:TYR6 3.9 13.4 1.0
C L:MET4 4.0 16.3 1.0
C L:PRO5 4.2 12.0 1.0
CG L:PRO5 4.2 15.2 1.0
CG L:TYR6 4.2 11.5 1.0
CA L:MET4 4.4 18.1 1.0
CA L:LYS7 4.4 15.5 0.5
CD2 C:TYR26 4.4 11.1 1.0
CA L:LYS7 4.4 16.8 0.5
O L:TYR6 4.5 15.6 1.0
CA L:PRO5 4.5 13.7 1.0
O L:HOH214 4.5 24.6 1.0
O L:MET4 4.5 17.0 1.0
CG L:MET4 4.6 21.1 1.0
CZ C:TYR26 4.7 12.7 1.0
O C:HOH224 4.8 21.6 1.0
OH C:TYR26 4.8 15.9 1.0
CB L:LYS7 4.8 17.0 0.5
OE1 L:GLU10 4.9 24.3 1.0
O C:GLY30 4.9 14.9 1.0
CD C:ARG32 4.9 15.0 1.0
CB C:ARG32 4.9 13.4 1.0
CB L:PRO5 5.0 14.8 1.0
CB L:LYS7 5.0 19.9 0.5

Reference:

K.A.Stanek, J.Patterson-West, P.S.Randolph, C.Mura. Crystal Structure and Rna-Binding Properties of An Hfq Homolog From the Deep-Branching Aquificae: Conservation of the Lateral Rna-Binding Mode. Acta Crystallogr D Struct V. 73 294 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28375142
DOI: 10.1107/S2059798317000031
Page generated: Sat Dec 12 12:27:17 2020

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