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Chlorine in PDB 5nlo: Auxiliary Activity 9

Protein crystallography data

The structure of Auxiliary Activity 9, PDB code: 5nlo was solved by K.E.H.Frandsen, J.-C.N.Poulsen, T.Tandrup, L.Lo Leggio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.33
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 125.350, 125.350, 125.350, 90.00, 90.00, 90.00
R / Rfree (%) 11.5 / 14.3

Other elements in 5nlo:

The structure of Auxiliary Activity 9 also contains other interesting chemical elements:

Copper (Cu) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Auxiliary Activity 9 (pdb code 5nlo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Auxiliary Activity 9, PDB code: 5nlo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 5nlo

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Chlorine binding site 1 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:20.0
occ:0.70
O A:HOH615 2.0 17.3 0.3
O A:HOH552 3.2 26.9 0.7
NE2 A:HIS147 3.3 17.1 1.0
NE2 A:GLN162 3.3 15.8 1.0
O A:HOH402 3.4 18.0 0.3
C1B A:XYP316 3.8 21.8 1.0
C5B A:XYP315 3.8 23.6 1.0
O A:HOH735 3.8 29.2 0.5
C5B A:XYP316 4.0 23.7 1.0
CD2 A:HIS147 4.1 17.4 1.0
O5B A:XYP316 4.1 23.3 1.0
OE1 A:GLN162 4.1 16.6 1.0
CD A:GLN162 4.2 14.6 1.0
O A:HOH571 4.2 49.7 1.0
C4B A:XYP315 4.2 20.9 1.0
CE1 A:HIC1 4.3 16.0 1.0
CE1 A:HIS147 4.3 15.7 1.0
O5B A:XYP315 4.4 23.8 1.0
CE1 A:HIS78 4.5 16.0 1.0
CU A:CU301 4.5 15.5 1.0
O A:HOH751 4.5 59.1 1.0
O4B A:XYP315 4.5 22.6 1.0
NE2 A:HIS78 4.6 14.4 1.0
OE1 A:GLU148 4.7 18.4 1.0
ND1 A:HIC1 4.8 14.5 1.0
OE2 A:GLU148 4.8 16.3 1.0
O A:HOH585 4.8 30.7 0.7
CD A:GLU148 4.8 17.6 1.0
C2B A:XYP316 4.8 20.5 1.0
C3B A:XYP316 4.9 19.8 1.0
O A:HOH402 5.0 16.0 0.7
C4B A:XYP316 5.0 22.4 1.0

Chlorine binding site 2 out of 10 in 5nlo

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Chlorine binding site 2 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:27.7
occ:1.00
O A:HOH579 3.2 41.2 1.0
N A:GLN228 3.3 16.5 1.0
O A:HOH594 3.5 27.6 1.0
CA A:ALA121 3.7 15.9 1.0
O A:HOH472 3.8 42.7 1.0
CA A:ALA227 3.8 17.0 1.0
O A:HOH525 3.9 52.7 1.0
CB A:ALA121 3.9 17.4 1.0
CB A:GLN228 4.0 16.3 1.0
O A:THR120 4.0 20.1 1.0
C A:ALA227 4.1 17.1 1.0
N A:ALA121 4.2 15.6 1.0
CA A:GLN228 4.3 16.0 1.0
C A:THR120 4.3 17.9 1.0
CB A:ALA227 4.4 20.1 1.0
CG2 A:THR120 4.6 26.8 1.0
C A:ALA121 4.8 16.0 1.0
N A:ALA227 4.9 15.2 1.0
O A:HOH567 4.9 50.9 1.0

Chlorine binding site 3 out of 10 in 5nlo

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Chlorine binding site 3 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:21.5
occ:0.70
O A:HOH440 3.0 39.2 0.8
O A:HOH782 3.1 49.5 0.8
ND1 A:HIS131 3.1 27.7 1.0
N A:ASP176 3.2 19.7 1.0
CE1 A:HIS131 3.5 37.5 1.0
CG A:ASP176 3.6 23.3 1.0
CA A:SER175 3.6 18.1 1.0
OD1 A:ASP176 3.7 23.1 1.0
CB A:ASP176 3.8 20.7 1.0
OD2 A:ASP176 3.9 27.9 1.0
C A:SER175 3.9 18.2 1.0
CB A:ALA56 3.9 17.4 1.0
O A:HOH531 4.0 29.5 1.0
CA A:ASP176 4.1 19.5 1.0
CG A:HIS131 4.4 22.3 1.0
N A:SER175 4.5 17.9 1.0
OG A:SER175 4.5 18.0 1.0
CB A:SER175 4.6 16.6 1.0
O A:SER174 4.7 18.5 1.0
NE2 A:HIS131 4.8 35.6 1.0
C A:SER174 4.9 18.1 1.0
O A:HOH722 5.0 43.5 1.0

Chlorine binding site 4 out of 10 in 5nlo

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Chlorine binding site 4 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:20.8
occ:0.70
CL A:CL308 0.0 20.8 0.7
CL A:CL308 2.9 16.7 0.3
O A:HOH586 3.0 20.9 0.7
OG A:SER225 3.1 26.3 1.0
O A:HOH742 3.2 31.0 1.0
O A:HOH641 3.2 40.1 1.0
CA A:GLY224 3.6 20.3 1.0
C A:GLY224 3.6 17.8 1.0
N A:SER225 3.7 15.9 1.0
CB A:SER126 3.8 14.5 1.0
CB A:SER225 3.8 22.2 1.0
CG2 A:THR59 4.3 14.7 1.0
O A:GLY224 4.3 22.6 1.0
N A:GLY224 4.3 20.3 1.0
CA A:SER225 4.3 16.5 1.0
O A:SER126 4.4 13.6 1.0
CG2 A:VAL128 4.6 15.9 1.0
C A:SER126 4.6 11.2 1.0
OG A:SER126 4.6 15.2 1.0
O A:HOH433 4.8 22.2 1.0
CA A:SER126 4.8 12.6 1.0

Chlorine binding site 5 out of 10 in 5nlo

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Chlorine binding site 5 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:16.7
occ:0.30
CL A:CL308 0.0 16.7 0.3
O A:HOH586 0.1 20.9 0.7
CL A:CL308 2.9 20.8 0.7
OG1 A:THR59 3.0 13.7 1.0
CG2 A:THR59 3.5 14.7 1.0
CB A:THR59 3.8 12.6 1.0
O A:HOH641 3.9 40.1 1.0
CG2 A:VAL128 4.2 15.9 1.0
O A:HOH742 4.4 31.0 1.0
CA A:THR59 4.9 11.6 1.0

Chlorine binding site 6 out of 10 in 5nlo

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Chlorine binding site 6 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:21.0
occ:0.80
O A:HOH443 2.9 32.7 1.0
N A:LYS32 3.1 11.8 1.0
O A:HOH613 3.1 49.8 1.0
O A:HOH766 3.3 43.1 1.0
N A:ASN33 3.3 12.4 1.0
CB A:ASN33 3.8 13.0 1.0
CA A:LYS32 3.9 11.5 1.0
CA A:VAL31 4.0 12.0 1.0
C A:VAL31 4.0 11.4 1.0
C A:LYS32 4.1 12.5 1.0
CG1 A:VAL31 4.1 14.2 1.0
CA A:ASN33 4.2 12.9 1.0
CB A:LYS32 4.2 12.6 1.0
O A:HOH584 4.3 22.6 0.8
OH A:TYR153 4.6 19.4 1.0
CB A:VAL31 4.6 12.4 1.0
O A:PRO30 4.6 12.9 1.0
O A:HOH437 4.7 39.9 1.0
CZ A:TYR153 4.8 14.7 1.0
O A:HOH560 4.8 19.1 1.0
CG A:LYS32 5.0 14.4 1.0
OD2 A:ASP38 5.0 20.9 1.0

Chlorine binding site 7 out of 10 in 5nlo

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Chlorine binding site 7 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:27.4
occ:0.50
O A:HOH645 1.8 19.1 0.5
O A:HOH655 2.0 27.0 0.4
CZ3 A:TRP5 2.4 22.1 0.3
CH2 A:TRP5 3.0 22.3 0.3
N A:ARG69 3.4 16.2 1.0
NH2 A:ARG18 3.5 18.4 1.0
CE3 A:TRP5 3.5 17.2 0.3
O A:HOH666 3.6 37.5 1.0
NH1 A:ARG18 3.7 18.4 1.0
CA A:THR68 3.9 16.5 1.0
O A:HOH642 4.0 34.3 0.7
CZ A:ARG18 4.0 15.2 1.0
C A:THR68 4.1 16.6 1.0
CB A:ARG69 4.2 17.5 1.0
CA A:ARG69 4.4 15.4 1.0
CZ2 A:TRP5 4.4 17.1 0.3
O A:HOH688 4.4 46.0 1.0
CB A:THR68 4.4 20.6 1.0
CD1 A:TRP5 4.5 16.3 0.7
O A:HOH805 4.5 46.9 1.0
NE1 A:TRP5 4.6 22.1 0.7
CE2 A:TYR65 4.7 12.7 1.0
CD2 A:TRP5 4.7 16.3 0.3
CG2 A:THR68 4.8 28.2 1.0
O A:ASN67 4.8 18.0 1.0
O A:HOH714 5.0 56.7 1.0
CD2 A:TYR65 5.0 13.5 1.0

Chlorine binding site 8 out of 10 in 5nlo

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Chlorine binding site 8 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:18.3
occ:0.80
O A:HOH619 3.0 36.4 1.0
O A:HOH760 3.1 17.9 1.0
N A:ASP16 3.2 12.5 1.0
CA A:GLY15 3.5 14.6 1.0
O A:HOH616 3.7 35.5 1.0
CH2 A:TRP5 3.8 26.5 0.7
C A:GLY15 3.9 13.2 1.0
CZ2 A:TRP5 4.0 21.0 0.7
CB A:ASP16 4.1 12.0 1.0
CA A:ASP16 4.3 11.8 1.0
O A:HOH686 4.5 40.8 0.7
O A:HOH729 4.7 35.5 1.0
N A:GLY15 4.8 13.3 1.0
OE2 A:GLU235 4.9 23.8 1.0
O A:HOH493 4.9 19.5 1.0
O A:HOH717 5.0 41.9 1.0
CZ3 A:TRP5 5.0 20.8 0.7

Chlorine binding site 9 out of 10 in 5nlo

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Chlorine binding site 9 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl312

b:22.9
occ:0.30
O A:HOH785 1.4 26.1 0.7
O A:HOH709 1.8 18.1 0.7
O A:HOH546 3.3 17.7 1.0
CE1 A:HIS66 3.4 23.2 1.0
C5B A:XYP314 3.5 24.0 1.0
NE2 A:HIS66 3.5 18.1 1.0
O A:HOH556 3.6 47.9 1.0
CB A:ALA75 3.6 19.0 1.0
O5B A:XYP314 3.9 20.9 1.0
O A:HOH452 4.0 29.4 1.0
C1B A:XYP315 4.2 19.2 1.0
C5B A:XYP315 4.2 23.6 1.0
O5B A:XYP315 4.4 23.8 1.0
ND1 A:HIS66 4.4 22.2 1.0
CA A:ALA75 4.5 16.3 1.0
C4B A:XYP314 4.5 20.5 1.0
N A:ALA75 4.6 15.1 1.0
CD2 A:HIS66 4.6 15.1 1.0
O4B A:XYP314 4.9 21.4 1.0
O A:HOH678 4.9 19.9 1.0

Chlorine binding site 10 out of 10 in 5nlo

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Chlorine binding site 10 out of 10 in the Auxiliary Activity 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Auxiliary Activity 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl313

b:25.4
occ:0.80
O A:HOH706 3.1 38.1 1.0
O A:HOH679 3.2 49.9 1.0
N A:SER51 3.3 13.3 1.0
O A:HOH827 3.6 53.7 0.8
O A:HOH611 3.6 19.5 0.2
CA A:LYS50 3.6 13.3 0.3
CA A:LYS50 3.7 12.9 0.7
O A:SER51 3.7 23.9 1.0
CD A:LYS50 3.8 19.7 0.3
O A:HOH611 3.9 37.9 0.8
CE A:LYS50 3.9 21.5 0.7
C A:LYS50 3.9 12.5 1.0
CB A:LYS50 4.1 14.4 0.3
CD A:LYS50 4.1 23.1 0.7
CB A:LYS50 4.2 13.5 0.7
O A:PRO49 4.2 18.1 1.0
CA A:SER51 4.2 13.0 1.0
C A:SER51 4.4 15.0 1.0
CB A:SER51 4.5 18.3 1.0
CG A:LYS50 4.5 16.0 0.3
CG A:LYS50 4.7 20.0 0.7
N A:LYS50 4.8 13.4 1.0
C A:PRO49 5.0 14.1 1.0

Reference:

T.J.Simmons, K.E.H.Frandsen, L.Ciano, T.Tryfona, N.Lenfant, J.C.Poulsen, L.F.L.Wilson, T.Tandrup, M.Tovborg, K.Schnorr, K.S.Johansen, B.Henrissat, P.H.Walton, L.Lo Leggio, P.Dupree. Structural and Electronic Determinants of Lytic Polysaccharide Monooxygenase Reactivity on Polysaccharide Substrates. Nat Commun V. 8 1064 2017.
ISSN: ESSN 2041-1723
PubMed: 29057953
DOI: 10.1038/S41467-017-01247-3
Page generated: Sat Dec 12 12:10:03 2020

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