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Chlorine in PDB 6fq3: Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna

Enzymatic activity of Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna

All present enzymatic activity of Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna, PDB code: 6fq3 was solved by P.Kumari, F.Aeschimann, D.Gaidatzis, J.J.Keusch, P.Ghosh, A.Neagu, K.Pachulska-Wieczorek, J.M.Bujnicki, H.Gut, H.Grosshans, R.Ciosk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.64 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.850, 101.850, 109.890, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 18

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna (pdb code 6fq3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna, PDB code: 6fq3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6fq3

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Chlorine binding site 1 out of 8 in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna


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 Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:73.5
occ:0.70
 O A:HOH1147 3.2 61.5 1.0
NZ A:LYS649 4.4 62.3 1.0
CA A:GLY650 4.4 48.5 1.0
CG2 A:THR651 4.9 48.4 1.0

Chlorine binding site 2 out of 8 in 6fq3

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Chlorine binding site 2 out of 8 in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna


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 Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl902

b:94.7
occ:1.00
 NE2 A:HIS678 3.0 43.2 1.0
O A:HOH1169 3.7 79.9 1.0
CD2 A:HIS678 3.9 44.2 1.0
CE1 A:HIS678 3.9 45.2 1.0
CE2 A:TRP700 4.1 52.0 1.0
O A:HOH1117 4.2 66.8 1.0
NE1 A:TRP700 4.3 56.1 1.0
CZ2 A:TRP700 4.3 54.5 1.0
CD2 A:TRP700 4.4 45.5 1.0
CD1 A:TRP700 4.6 53.2 1.0
CG A:TRP700 4.7 44.2 1.0
CH2 A:TRP700 4.7 51.9 1.0
CE3 A:TRP700 4.8 44.7 1.0
CZ3 A:TRP700 5.0 44.5 1.0

Chlorine binding site 3 out of 8 in 6fq3

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Chlorine binding site 3 out of 8 in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna


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 Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl903

b:0.8
occ:1.00
 O A:HOH1179 3.4 68.4 1.0
O A:HOH1062 3.6 63.6 1.0
CE1 A:HIS702 4.1 55.2 1.0
O A:LYS701 4.2 42.2 1.0
NE2 A:HIS702 4.2 52.2 1.0
ND1 A:HIS702 4.2 52.1 1.0
C A:LYS701 4.3 43.3 1.0
CB A:LYS701 4.3 50.1 1.0
CD2 A:HIS702 4.4 52.7 1.0
N A:HIS702 4.4 40.3 1.0
CG A:HIS702 4.4 49.4 1.0
CA A:HIS702 4.6 39.7 1.0
CL A:CL907 4.6 87.3 1.0
CA A:LYS701 5.0 42.8 1.0

Chlorine binding site 4 out of 8 in 6fq3

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Chlorine binding site 4 out of 8 in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna


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 Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl904

b:0.9
occ:1.00
 OE2 A:GLU555 3.5 0.4 1.0
O A:HOH1180 3.6 72.3 1.0
CD A:GLU555 4.0 0.6 1.0
ND2 A:ASN819 4.0 59.6 1.0
O A:HOH1056 4.1 53.0 1.0
CG A:ARG564 4.2 52.6 1.0
N4 B:C6 4.3 95.6 1.0
OD1 A:ASN819 4.4 60.7 1.0
OE1 A:GLU555 4.5 0.7 1.0
CG A:GLU555 4.6 89.7 1.0
SG A:CYS563 4.6 67.8 1.0
CG A:ASN819 4.6 61.0 1.0
CD A:ARG564 4.7 54.4 1.0
O A:HOH1027 4.8 67.0 1.0
C4 B:C6 4.9 90.0 1.0

Chlorine binding site 5 out of 8 in 6fq3

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Chlorine binding site 5 out of 8 in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna


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 Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl905

b:99.3
occ:1.00
 N A:ASN653 3.5 51.4 1.0
O A:HOH1099 3.8 63.0 1.0
CG A:ASN653 3.8 56.1 1.0
CB A:LYS652 3.8 48.6 1.0
ND2 A:ASN653 3.8 58.0 1.0
CA A:LYS652 3.9 49.9 1.0
OD1 A:ASN653 4.0 55.2 1.0
CG A:LYS652 4.1 53.8 1.0
C A:LYS652 4.2 50.2 1.0
CB A:ASN653 4.2 56.8 1.0
CA A:ASN653 4.5 52.8 1.0
O A:HOH1101 5.0 73.7 1.0

Chlorine binding site 6 out of 8 in 6fq3

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Chlorine binding site 6 out of 8 in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna


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 Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl906

b:93.0
occ:1.00
 O A:GLY694 3.6 52.3 1.0
CE1 A:PHE695 3.7 48.2 1.0
O A:HOH1153 3.8 72.5 1.0
CE1 A:TYR693 3.9 51.5 1.0
CD1 A:PHE695 4.0 47.2 1.0
CZ A:PHE695 4.2 44.1 1.0
CZ A:TYR693 4.3 50.6 1.0
CD1 A:TYR693 4.4 51.1 1.0
C A:GLY694 4.4 51.6 1.0
OH A:TYR693 4.5 50.9 1.0
O A:HOH1007 4.6 62.8 1.0
CG A:PHE695 4.6 45.4 1.0
CE2 A:PHE695 4.8 44.5 1.0
N A:GLY694 4.8 47.8 1.0
O A:GLN735 4.9 63.7 1.0
CD2 A:PHE695 5.0 45.4 1.0
O A:HOH1026 5.0 60.7 1.0

Chlorine binding site 7 out of 8 in 6fq3

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Chlorine binding site 7 out of 8 in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna


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 Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl907

b:87.3
occ:1.00
 O A:HOH1156 2.6 63.5 1.0
NE A:ARG726 3.6 42.1 1.0
NH2 A:ARG726 4.0 42.4 1.0
CZ A:ARG726 4.2 42.1 1.0
CD A:ARG726 4.4 43.1 1.0
CL A:CL903 4.6 0.8 1.0
ND2 A:ASN724 4.6 44.8 1.0
CD2 A:HIS702 4.7 52.7 1.0
O A:HIS702 4.7 45.2 1.0
CA A:HIS702 4.8 39.7 1.0
O A:HOH1049 4.8 44.4 1.0
CG A:ASN724 4.9 44.2 1.0

Chlorine binding site 8 out of 8 in 6fq3

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Chlorine binding site 8 out of 8 in the Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Danio Rerio LIN41 Filamin-Nhl Domains in Complex with Lin-29A 5'Utr 13MER Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl101

b:0.4
occ:1.00
 N7 B:A9 3.2 46.9 1.0
O A:HOH1097 3.4 70.7 1.0
O A:HOH1113 3.6 72.1 1.0
N6 B:A9 3.7 48.4 1.0
NH2 A:ARG676 3.8 59.3 0.5
C5 B:A9 4.1 45.3 1.0
C8 B:A9 4.2 45.9 1.0
C6 B:A9 4.3 48.5 1.0
O B:HOH251 4.5 69.1 1.0
O B:HOH233 4.6 63.0 1.0
O B:HOH252 4.7 72.2 1.0
O B:HOH216 4.8 53.9 1.0
CZ A:ARG676 4.9 58.4 0.5
N7 B:A8 5.0 51.9 1.0

Reference:

P.Kumari, F.Aeschimann, D.Gaidatzis, J.J.Keusch, P.Ghosh, A.Neagu, K.Pachulska-Wieczorek, J.M.Bujnicki, H.Gut, H.Grosshans, R.Ciosk. Evolutionary Plasticity of the Nhl Domain Underlies Distinct Solutions to Rna Recognition. Nat Commun V. 9 1549 2018.
ISSN: ESSN 2041-1723
PubMed: 29674686
DOI: 10.1038/S41467-018-03920-7
Page generated: Sat Jul 27 23:28:09 2024

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