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Chlorine in PDB 5n04: X-Ray Crystal Structure of An Lpmo

Protein crystallography data

The structure of X-Ray Crystal Structure of An Lpmo, PDB code: 5n04 was solved by K.E.H.Frandsen, J.-C.N.Poulsen, L.Lo Leggio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.62 / 1.76
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 125.330, 125.330, 125.330, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.7

Other elements in 5n04:

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

Copper (Cu) 1 atom
Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the X-Ray Crystal Structure of An Lpmo (pdb code 5n04). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the X-Ray Crystal Structure of An Lpmo, PDB code: 5n04:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 5n04

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Chlorine binding site 1 out of 12 in the X-Ray Crystal Structure of An 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 Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:19.7
occ:1.00
O A:HOH433 2.9 34.2 1.0
N A:LYS32 3.1 11.2 1.0
O A:HOH762 3.3 29.8 1.0
N A:ASN33 3.3 11.2 1.0
CB A:ASN33 3.7 11.8 1.0
CA A:LYS32 4.0 11.9 1.0
CA A:VAL31 4.0 10.5 1.0
C A:VAL31 4.0 11.2 1.0
C A:LYS32 4.1 11.4 1.0
CG1 A:VAL31 4.1 10.7 1.0
CA A:ASN33 4.2 11.8 1.0
CB A:LYS32 4.3 12.8 1.0
O A:HOH764 4.3 36.5 1.0
O A:HOH628 4.4 32.3 1.0
OH A:TYR153 4.6 15.6 1.0
O A:HOH453 4.6 31.8 1.0
CB A:VAL31 4.6 11.0 1.0
O A:PRO30 4.7 11.9 1.0
CZ A:TYR153 4.7 13.9 1.0
O A:HOH509 4.9 17.8 1.0
CG A:LYS32 5.0 13.4 1.0

Chlorine binding site 2 out of 12 in 5n04

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Chlorine binding site 2 out of 12 in the X-Ray Crystal Structure of An 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 Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:20.4
occ:1.00
O A:HOH761 3.2 45.5 1.0
NH2 A:ARG117 3.2 16.9 0.5
O A:HOH463 3.2 29.0 1.0
N A:GLN228 3.2 15.8 1.0
O A:HOH481 3.5 22.7 0.5
NH1 A:ARG117 3.5 16.9 0.5
CA A:ALA121 3.6 15.2 1.0
O A:HOH455 3.7 27.0 1.0
CZ A:ARG117 3.8 16.7 0.5
CA A:ALA227 3.8 15.3 1.0
CB A:ALA121 3.8 15.4 1.0
CB A:GLN228 3.9 16.8 1.0
O A:THR120 4.0 15.9 1.0
C A:ALA227 4.0 14.8 1.0
N A:ALA121 4.1 15.5 1.0
CA A:GLN228 4.2 15.7 1.0
C A:THR120 4.3 16.5 1.0
CB A:ALA227 4.4 16.1 1.0
CG2 A:THR120 4.5 18.8 1.0
C A:ALA121 4.8 14.6 1.0
N A:ALA227 5.0 14.2 1.0
O A:GLN228 5.0 15.9 1.0
O A:HOH782 5.0 40.9 1.0

Chlorine binding site 3 out of 12 in 5n04

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Chlorine binding site 3 out of 12 in the X-Ray Crystal Structure of An 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 Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:18.9
occ:1.00
O A:HOH565 3.1 36.9 1.0
O A:HOH750 3.1 15.4 1.0
N A:ASP16 3.2 12.0 1.0
CA A:GLY15 3.5 13.0 1.0
CH2 A:TRP5 3.8 15.3 0.8
C A:GLY15 3.9 12.7 1.0
CZ2 A:TRP5 4.0 15.4 0.8
CB A:ASP16 4.0 11.7 1.0
CA A:ASP16 4.2 11.9 1.0
O A:HOH694 4.4 43.7 1.0
O A:HOH727 4.7 32.9 1.0
N A:GLY15 4.8 12.2 1.0
O A:HOH533 4.9 17.7 1.0
O A:HOH450 4.9 12.5 1.0
CZ3 A:TRP5 5.0 16.1 0.8

Chlorine binding site 4 out of 12 in 5n04

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Chlorine binding site 4 out of 12 in the X-Ray Crystal Structure of An 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 Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:30.7
occ:1.00
ND1 A:HIS131 2.9 37.6 1.0
O A:HOH548 3.1 24.7 1.0
CE1 A:HIS131 3.3 33.5 1.0
O A:HOH627 3.3 51.5 1.0
N A:ASP176 3.3 18.9 1.0
CG A:ASP176 3.5 28.2 1.0
OD2 A:ASP176 3.6 27.0 1.0
OD1 A:ASP176 3.7 27.8 1.0
CA A:SER175 3.8 16.7 1.0
CB A:ASP176 3.9 24.9 1.0
CB A:ALA56 4.0 14.3 1.0
C A:SER175 4.1 18.6 1.0
CA A:ASP176 4.2 24.4 1.0
CG A:HIS131 4.2 27.9 1.0
O A:HOH563 4.5 18.5 1.0
OG A:SER175 4.5 16.2 1.0
NE2 A:HIS131 4.5 34.7 1.0
O A:HOH408 4.6 43.2 1.0
N A:SER175 4.7 15.8 1.0
CB A:SER175 4.7 16.3 1.0
O A:HOH748 4.8 21.0 1.0
O A:SER174 4.9 16.5 1.0
CB A:HIS131 4.9 23.0 1.0

Chlorine binding site 5 out of 12 in 5n04

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Chlorine binding site 5 out of 12 in the X-Ray Crystal Structure of An 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 Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:16.5
occ:0.50
CD2 A:HIS78 0.9 18.2 0.5
NE2 A:HIS78 0.9 18.3 0.5
CG A:HIS78 2.1 18.3 0.5
CE1 A:HIS78 2.1 19.5 0.5
CU A:CU301 2.3 17.8 1.0
ND1 A:HIS78 2.5 19.1 0.5
ND1 A:HIS78 2.8 19.5 0.5
N A:HIC1 3.2 14.3 1.0
OH A:TYR164 3.2 12.1 1.0
CB A:HIS78 3.4 18.5 0.5
O A:HOH626 3.4 22.3 0.5
OE1 A:GLN162 3.6 16.0 1.0
CG A:HIS78 3.6 19.0 0.5
CE1 A:HIS147 3.6 21.5 1.0
CB A:HIS78 3.7 19.0 0.5
CZ A:TYR164 3.7 11.9 1.0
CE2 A:TYR164 3.7 11.5 1.0
CE1 A:HIS78 3.8 19.4 0.5
CB A:ALA145 3.8 13.1 1.0
ND1 A:HIC1 4.2 14.6 1.0
CG1 A:ILE74 4.2 19.5 1.0
CD1 A:ILE74 4.3 19.5 1.0
O A:HOH683 4.3 37.5 1.0
NE2 A:HIS147 4.3 21.9 1.0
CA A:HIS78 4.4 18.5 0.5
ND1 A:HIS147 4.5 20.0 1.0
CA A:HIC1 4.6 13.4 1.0
O A:HOH623 4.6 15.2 1.0
CD A:GLN162 4.8 15.9 1.0
CD2 A:HIS78 4.8 19.0 0.5
CD2 A:TYR164 4.8 11.8 1.0
CE1 A:TYR164 4.8 11.4 1.0
NE2 A:HIS78 4.9 19.5 0.5
O A:HOH626 4.9 18.8 0.5
N A:HIS78 5.0 19.2 0.5

Chlorine binding site 6 out of 12 in 5n04

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Chlorine binding site 6 out of 12 in the X-Ray Crystal Structure of An 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 Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:27.7
occ:0.50
CL A:CL308 0.0 27.7 0.5
CL A:CL308 1.7 38.9 0.5
CZ3 A:TRP5 2.1 12.1 0.2
O A:HOH553 2.3 21.7 0.5
CH2 A:TRP5 2.3 12.1 0.2
N A:ARG69 3.3 16.0 1.0
CE3 A:TRP5 3.4 11.9 0.2
O A:HOH618 3.5 20.1 0.8
O A:HOH670 3.6 30.9 1.0
CZ2 A:TRP5 3.7 12.3 0.2
NH2 A:ARG18 3.7 14.5 1.0
CA A:THR68 3.8 16.9 1.0
NH1 A:ARG18 3.8 16.3 1.0
C A:THR68 4.0 15.5 1.0
CB A:ARG69 4.1 15.2 1.0
CZ A:ARG18 4.1 14.5 1.0
CB A:THR68 4.2 19.5 1.0
O A:HOH778 4.3 23.1 0.5
CA A:ARG69 4.3 15.2 1.0
CD1 A:TRP5 4.4 14.1 0.8
CD2 A:TRP5 4.5 11.8 0.2
NE1 A:TRP5 4.5 14.7 0.8
CE2 A:TRP5 4.6 12.0 0.2
O A:ASN67 4.7 16.0 1.0
CG2 A:THR68 4.7 22.6 1.0
CE2 A:TYR65 4.8 10.9 1.0
N A:THR68 5.0 15.0 1.0

Chlorine binding site 7 out of 12 in 5n04

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Chlorine binding site 7 out of 12 in the X-Ray Crystal Structure of An 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 Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:38.9
occ:0.50
CL A:CL308 0.0 38.9 0.5
CL A:CL308 1.7 27.7 0.5
O A:HOH778 3.2 23.1 0.5
N A:ARG69 3.2 16.0 1.0
CH2 A:TRP5 3.3 12.1 0.2
CZ3 A:TRP5 3.5 12.1 0.2
CB A:THR68 3.6 19.5 1.0
O A:HOH553 3.6 21.7 0.5
O A:HOH618 3.6 20.1 0.8
CA A:THR68 3.7 16.9 1.0
O A:HOH448 3.8 36.1 1.0
CB A:ARG69 3.9 15.2 1.0
C A:THR68 3.9 15.5 1.0
CG2 A:THR68 4.1 22.6 1.0
CA A:ARG69 4.2 15.2 1.0
O A:HOH778 4.2 25.3 0.5
O A:HOH670 4.2 30.9 1.0
CZ2 A:TRP5 4.4 12.3 0.2
CE3 A:TRP5 4.7 11.9 0.2
OG1 A:THR68 4.8 21.8 1.0

Chlorine binding site 8 out of 12 in 5n04

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Chlorine binding site 8 out of 12 in the X-Ray Crystal Structure of An 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 Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:21.0
occ:0.50
O A:HOH803 1.7 17.2 0.5
O A:HOH803 3.5 22.6 0.5
O A:LEU181 3.5 25.5 1.0
O A:HOH518 3.9 11.2 1.0
O A:HOH529 4.1 16.8 1.0
N A:LEU181 4.3 23.8 1.0
C A:LEU181 4.5 22.0 1.0
CB A:LEU181 4.5 24.0 1.0
CA A:LEU181 4.7 25.3 1.0
CB A:PRO180 4.9 27.1 1.0

Chlorine binding site 9 out of 12 in 5n04

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Chlorine binding site 9 out of 12 in the X-Ray Crystal Structure of An Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of X-Ray Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:25.6
occ:1.00
NH1 A:ARG159 3.2 13.9 1.0
O A:HOH673 3.3 27.1 1.0
CD1 A:ILE158 3.3 16.3 0.5
CD A:ARG159 3.5 13.0 1.0
CG A:ARG159 3.6 12.8 1.0
CZ A:ARG159 4.2 13.9 1.0
NE A:ARG159 4.3 13.7 1.0
CG1 A:ILE158 4.6 15.4 0.5
CD1 A:ILE158 4.6 12.7 0.5
CG1 A:ILE158 4.7 12.5 0.5
O A:ILE158 4.9 13.5 1.0

Chlorine binding site 10 out of 12 in 5n04

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Chlorine binding site 10 out of 12 in the X-Ray Crystal Structure of An Lpmo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of X-Ray Crystal Structure of An Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:20.3
occ:0.50
O A:HOH734 1.1 22.3 0.5
O A:HOH714 1.5 24.8 0.5
O A:HOH461 3.3 21.5 0.5
O A:HOH442 3.5 28.5 1.0
CA A:GLY189 3.6 17.4 1.0
N A:GLY189 3.7 15.7 1.0
CA A:THR35 3.8 15.7 1.0
CG2 A:THR35 3.8 19.6 1.0
CB A:THR35 3.9 17.8 1.0
CB A:PRO188 4.0 14.4 1.0
C A:PRO188 4.0 15.7 1.0
O A:HOH476 4.1 35.3 1.0
O A:LEU34 4.3 13.3 1.0
O A:HOH547 4.3 36.0 1.0
O A:PRO188 4.3 16.5 1.0
O A:THR35 4.5 16.1 1.0
CG A:PRO188 4.6 15.1 1.0
C A:THR35 4.6 15.3 1.0
CA A:PRO188 4.6 14.4 1.0
N A:THR35 4.8 14.7 1.0
C A:GLY189 4.8 18.5 1.0
O A:HOH492 4.8 15.7 1.0
C A:LEU34 4.9 14.4 1.0

Reference:

K.E.H.Frandsen, J.N.Poulsen, T.Tandrup, L.Lo Leggio. Unliganded and Substrate Bound Structures of the Cellooligosaccharide Active Lytic Polysaccharide Monooxygenase LSAA9A at Low pH. Carbohydr. Res. V. 448 187 2017.
ISSN: ISSN 1873-426X
PubMed: 28364950
DOI: 10.1016/J.CARRES.2017.03.010
Page generated: Sat Dec 12 12:08:11 2020

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