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Chlorine in PDB 5acg: X-Ray Structure of Lpmo

Protein crystallography data

The structure of X-Ray Structure of Lpmo, PDB code: 5acg was solved by K.E.H.Frandsen, J.N.Poulsen, M.Tovborg, K.S.Johansen, L.Lo Leggio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.91
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 125.240, 125.240, 125.240, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.8

Other elements in 5acg:

The structure of X-Ray Structure of Lpmo also contains other interesting chemical elements:

Copper (Cu) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of Lpmo (pdb code 5acg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the X-Ray Structure of Lpmo, PDB code: 5acg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5acg

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Chlorine binding site 1 out of 8 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1236

b:16.1
occ:1.00
O A:HOH2031 3.0 13.6 1.0
OD1 A:ASN27 3.2 10.0 1.0
ND2 A:ASN29 3.7 11.8 1.0
O A:HOH2088 3.7 37.5 1.0
O A:HOH2087 3.8 23.6 1.0
CG A:ASN27 4.2 9.5 1.0
ND2 A:ASN27 4.5 8.9 1.0
O A:HOH2076 4.7 11.7 1.0
CG A:ASN29 4.9 11.3 1.0
O A:HOH2078 5.0 11.1 1.0

Chlorine binding site 2 out of 8 in 5acg

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Chlorine binding site 2 out of 8 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1237

b:25.5
occ:1.00
O A:HOH2291 3.1 21.7 1.0
N A:ASP176 3.1 17.3 1.0
ND1 A:HIS131 3.2 23.2 1.0
CG A:ASP176 3.5 23.3 1.0
CA A:SER175 3.6 14.8 1.0
CE1 A:HIS131 3.7 21.5 1.0
OD2 A:ASP176 3.7 23.0 1.0
O A:HOH2246 3.7 30.6 1.0
CB A:ASP176 3.8 21.1 1.0
OD1 A:ASP176 3.9 26.1 1.0
C A:SER175 3.9 16.6 1.0
CB A:ALA56 4.0 11.2 1.0
CA A:ASP176 4.1 20.2 1.0
OG A:SER175 4.3 13.1 1.0
O A:HOH2151 4.4 21.9 1.0
CG A:HIS131 4.4 20.5 1.0
N A:SER175 4.5 14.2 1.0
CB A:SER175 4.6 14.4 1.0
O A:SER174 4.7 14.4 1.0
O A:HOH2153 4.7 35.8 1.0
O A:HOH2295 4.8 18.5 1.0
C A:SER174 4.9 15.4 1.0
NE2 A:HIS131 5.0 22.2 1.0
CB A:HIS131 5.0 18.8 1.0

Chlorine binding site 3 out of 8 in 5acg

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Chlorine binding site 3 out of 8 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1238

b:21.6
occ:1.00
O A:HOH2238 3.1 27.6 1.0
N A:GLN228 3.3 14.1 1.0
O A:HOH2236 3.4 17.2 1.0
CA A:ALA121 3.6 13.7 1.0
O A:HOH2351 3.6 33.7 1.0
CA A:ALA227 3.8 14.4 1.0
CB A:ALA121 3.8 14.4 1.0
N A:ALA121 4.0 14.4 1.0
CB A:GLN228 4.1 14.6 1.0
C A:ALA227 4.1 13.9 1.0
O A:THR120 4.1 14.4 1.0
O A:HOH2350 4.1 31.8 1.0
C A:THR120 4.3 15.6 1.0
CA A:GLN228 4.3 13.9 1.0
CB A:ALA227 4.5 15.1 1.0
CG2 A:THR120 4.7 19.1 1.0
O A:HOH2116 4.8 29.3 1.0
C A:ALA121 4.8 13.2 1.0
N A:ALA227 4.9 14.2 1.0

Chlorine binding site 4 out of 8 in 5acg

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Chlorine binding site 4 out of 8 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1239

b:19.4
occ:1.00
O A:HOH2107 2.9 29.1 1.0
N A:LYS32 3.1 9.4 1.0
O A:HOH2035 3.2 24.9 1.0
N A:ASN33 3.4 10.3 1.0
CB A:ASN33 3.7 11.9 1.0
CA A:LYS32 3.9 9.8 1.0
CA A:VAL31 4.0 9.1 1.0
C A:VAL31 4.0 9.8 1.0
C A:LYS32 4.1 10.1 1.0
CG1 A:VAL31 4.1 9.2 1.0
CB A:LYS32 4.2 10.3 1.0
CA A:ASN33 4.2 11.0 1.0
O A:HOH2100 4.6 20.4 1.0
OH A:TYR153 4.6 10.6 1.0
O A:HOH2089 4.6 29.6 1.0
CB A:VAL31 4.7 9.3 1.0
CZ A:TYR153 4.7 10.5 1.0
O A:PRO30 4.7 8.6 1.0
CG A:LYS32 4.9 10.8 1.0
O A:HOH2090 4.9 15.4 1.0
CE1 A:TYR153 4.9 10.6 1.0

Chlorine binding site 5 out of 8 in 5acg

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Chlorine binding site 5 out of 8 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Structure of Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1240

b:21.5
occ:1.00
OG A:SER225 3.2 20.5 1.0
CA A:GLY224 3.5 17.6 1.0
N A:SER225 3.7 16.0 1.0
C A:GLY224 3.7 16.6 1.0
CB A:SER126 3.8 11.3 1.0
CB A:SER225 4.0 17.7 1.0
N A:GLY224 4.1 17.6 1.0
O A:SER126 4.3 13.1 1.0
C A:SER126 4.3 11.7 1.0
CG2 A:THR59 4.4 9.6 1.0
O A:GLY224 4.4 17.9 1.0
CA A:SER225 4.4 16.4 1.0
CG2 A:VAL128 4.4 11.8 1.0
CA A:SER126 4.7 11.0 1.0
OG A:SER126 4.7 11.6 1.0
N A:VAL127 4.8 11.4 1.0
C A:GLY223 4.8 21.0 1.0
O A:HOH2348 4.9 35.4 1.0
O A:HOH2243 4.9 15.7 1.0
C A:VAL127 4.9 11.5 1.0
CA A:VAL127 4.9 11.8 1.0
O A:SER225 5.0 15.8 1.0

Chlorine binding site 6 out of 8 in 5acg

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Chlorine binding site 6 out of 8 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Structure of Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1241

b:24.9
occ:1.00
O A:HOH2131 3.1 15.9 0.5
O A:HOH2132 3.1 29.2 1.0
O A:HOH2131 3.1 15.0 0.5
N A:SER51 3.2 12.4 1.0
CA A:LYS50 3.6 12.1 1.0
CE A:LYS50 3.7 18.8 1.0
O A:SER51 3.7 16.0 1.0
C A:LYS50 3.9 11.9 1.0
O A:HOH2138 4.0 38.1 1.0
CD A:LYS50 4.1 17.2 1.0
O A:PRO49 4.2 12.1 1.0
CA A:SER51 4.2 13.3 1.0
CB A:LYS50 4.3 13.7 1.0
CB A:SER51 4.4 14.7 1.0
C A:SER51 4.4 14.0 1.0
N A:LYS50 4.7 11.2 1.0
CG A:LYS50 4.8 15.4 1.0
C A:PRO49 4.9 11.1 1.0
NZ A:LYS50 5.0 19.7 1.0

Chlorine binding site 7 out of 8 in 5acg

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Chlorine binding site 7 out of 8 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Structure of Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1242

b:27.0
occ:0.50
CL A:CL1242 0.0 27.0 0.5
CL A:CL1242 1.9 27.9 0.5
N A:ARG69 3.2 13.9 1.0
O A:HOH2057 3.6 18.2 0.5
CB A:THR68 3.7 17.1 1.0
O A:HOH2012 3.8 35.6 1.0
CB A:ARG69 3.8 12.9 1.0
CA A:THR68 3.8 15.9 1.0
C A:THR68 4.0 14.1 1.0
CA A:ARG69 4.1 13.6 1.0
O A:HOH2058 4.2 25.3 1.0
CG2 A:THR68 4.3 18.6 1.0
OG1 A:THR68 4.9 19.0 1.0
O A:ARG69 5.0 14.7 1.0

Chlorine binding site 8 out of 8 in 5acg

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Chlorine binding site 8 out of 8 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Structure of Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1242

b:27.9
occ:0.50
CL A:CL1242 0.0 27.9 0.5
CL A:CL1242 1.9 27.0 0.5
O A:HOH2057 2.1 18.2 0.5
N A:ARG69 3.4 13.9 1.0
NH1 A:ARG18 3.5 12.2 1.0
O A:HOH2058 3.5 25.3 1.0
NH2 A:ARG18 3.7 13.5 1.0
O A:HOH2012 3.7 35.6 1.0
CA A:THR68 3.8 15.9 1.0
CZ A:ARG18 4.0 12.5 1.0
C A:THR68 4.1 14.1 1.0
CB A:ARG69 4.2 12.9 1.0
CA A:ARG69 4.3 13.6 1.0
CB A:THR68 4.3 17.1 1.0
CD1 A:TRP5 4.5 14.5 1.0
O A:ASN67 4.6 15.2 1.0
NE1 A:TRP5 4.6 16.2 1.0
CE2 A:TYR65 4.7 10.5 1.0
CG2 A:THR68 4.7 18.6 1.0
O A:HOH2056 4.8 37.2 1.0
CD2 A:TYR65 5.0 10.3 1.0
N A:THR68 5.0 14.8 1.0

Reference:

K.E.Frandsen, T.J.Simmons, P.Dupree, J.C.Poulsen, G.R.Hemsworth, L.Ciano, E.M.Johnston, M.Tovborg, K.S.Johansen, P.Von Freiesleben, L.Marmuse, S.Fort, S.Cottaz, H.Driguez, B.Henrissat, N.Lenfant, F.Tuna, A.Baldansuren, G.J.Davies, L.Lo Leggio, P.H.Walton. The Molecular Basis of Polysaccharide Cleavage By Lytic Polysaccharide Monooxygenases. Nat. Chem. Biol. V. 12 298 2016.
ISSN: ESSN 1552-4469
PubMed: 26928935
DOI: 10.1038/NCHEMBIO.2029
Page generated: Sat Dec 12 11:30:10 2020

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