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Chlorine in PDB 5nkw: X-Ray Crystal Structure of An AA9 Lpmo

Protein crystallography data

The structure of X-Ray Crystal Structure of An AA9 Lpmo, PDB code: 5nkw was solved by T.Tandrup, 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) 50.00 / 1.48
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 125.290, 125.290, 125.290, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 17

Other elements in 5nkw:

The structure of X-Ray Crystal Structure of An AA9 Lpmo also contains other interesting chemical elements:

Copper (Cu) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Chlorine atom in the X-Ray Crystal Structure of An AA9 Lpmo (pdb code 5nkw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 17 binding sites of Chlorine where determined in the X-Ray Crystal Structure of An AA9 Lpmo, PDB code: 5nkw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 17 in 5nkw

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Chlorine binding site 1 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:17.4
occ:0.40
 O A:HOH585 0.9 23.5 0.6
O A:HOH846 0.9 32.9 0.6
O A:HOH683 3.1 38.9 1.0
N A:GLN228 3.3 19.5 1.0
O A:HOH630 3.4 28.6 1.0
CA A:ALA121 3.6 18.8 1.0
O A:HOH654 3.7 37.7 0.6
O A:HOH464 3.9 35.2 0.8
O A:THR120 3.9 22.5 1.0
CB A:ALA121 3.9 20.9 1.0
CA A:ALA227 3.9 21.2 1.0
CB A:GLN228 3.9 21.6 1.0
N A:ALA121 4.0 19.0 1.0
C A:ALA227 4.2 19.8 1.0
C A:THR120 4.2 19.4 1.0
CA A:GLN228 4.3 19.3 1.0
CB A:ALA227 4.6 22.2 1.0
CG2 A:THR120 4.6 31.3 1.0
C A:ALA121 4.8 18.1 1.0
O A:HOH937 4.9 43.4 1.0

Chlorine binding site 2 out of 17 in 5nkw

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Chlorine binding site 2 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:21.7
occ:0.90
 OD1 A:ASN27 3.2 21.1 1.0
O A:HOH757 3.2 48.1 1.0
ND2 A:ASN29 3.5 26.7 1.0
O A:HOH745 3.8 37.0 1.0
CG A:ASN27 4.2 16.9 1.0
ND2 A:ASN27 4.4 13.3 1.0
O A:HOH808 4.5 56.8 1.0
O A:HOH599 4.7 18.4 1.0
CG A:ASN29 4.8 21.1 1.0

Chlorine binding site 3 out of 17 in 5nkw

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Chlorine binding site 3 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:34.3
occ:0.80
 O A:HOH863 1.2 22.0 0.2
O A:HOH892 1.4 19.0 0.2
O A:HOH971 3.1 37.2 0.5
O A:HOH497 3.2 39.2 1.0
O A:HOH475 3.3 39.4 1.0
CA A:GLY189 3.6 25.4 1.0
N A:GLY189 3.7 24.1 1.0
CA A:THR35 3.8 24.1 1.0
CB A:THR35 3.9 27.0 1.0
O A:HOH589 4.0 48.4 1.0
CB A:PRO188 4.0 23.5 1.0
CG2 A:THR35 4.0 36.7 1.0
C A:PRO188 4.1 22.4 1.0
O A:LEU34 4.2 22.6 1.0
O A:HOH498 4.3 45.2 1.0
O A:PRO188 4.4 23.8 1.0
O A:THR35 4.5 26.9 1.0
O A:HOH429 4.5 20.6 0.8
C A:THR35 4.6 23.1 1.0
N A:THR35 4.7 23.3 1.0
CA A:PRO188 4.7 20.8 1.0
CG A:PRO188 4.7 22.7 1.0
C A:GLY189 4.7 30.1 1.0
C A:LEU34 4.8 21.8 1.0
O A:GLY189 4.9 28.5 1.0

Chlorine binding site 4 out of 17 in 5nkw

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Chlorine binding site 4 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:23.1
occ:0.70
 O A:HOH622 1.7 17.4 0.4
O A:HOH684 3.0 39.8 1.0
O A:HOH628 3.2 44.4 1.0
NE2 A:GLN162 3.2 22.3 1.0
NE2 A:HIS147 3.3 20.9 1.0
C1 A:BGC323 3.7 27.4 1.0
C5 A:BGC323 3.7 28.7 1.0
OE1 A:GLN162 3.9 20.4 1.0
CE1 A:HIC1 3.9 16.3 1.0
O5 A:BGC323 3.9 26.7 1.0
CU A:CU301 3.9 17.8 1.0
CD A:GLN162 4.0 16.7 1.0
O A:HOH867 4.0 33.3 0.8
C4 A:BMA322 4.0 23.5 1.0
CE1 A:HIS78 4.1 17.9 1.0
CD2 A:HIS147 4.2 22.3 1.0
CE1 A:HIS147 4.2 22.8 1.0
NE2 A:HIS78 4.3 17.4 1.0
ND1 A:HIC1 4.3 16.3 1.0
O3 A:BMA322 4.3 27.3 1.0
O4 A:BMA322 4.3 23.2 1.0
C3 A:BGC323 4.6 27.1 1.0
O2 A:BMA322 4.6 29.3 1.0
C2 A:BGC323 4.7 25.2 1.0
C6 A:BGC323 4.7 31.8 1.0
O6 A:BGC323 4.7 43.2 1.0
C4 A:BGC323 4.7 25.0 1.0
C3 A:BMA322 4.8 25.6 1.0
O A:HOH608 4.9 42.6 1.0
OE1 A:GLU148 4.9 27.5 1.0
C6 A:BMA322 4.9 21.6 1.0
OH A:TYR164 5.0 17.8 1.0
O4 A:BGC323 5.0 25.6 1.0
O2 A:BGC323 5.0 25.7 1.0

Chlorine binding site 5 out of 17 in 5nkw

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Chlorine binding site 5 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:43.6
occ:0.80
 O A:HOH813 0.9 13.4 0.2
N A:ALA212 3.1 29.1 1.0
O A:HOH821 3.3 56.0 1.0
O A:HOH703 3.7 39.2 1.0
CB A:ALA212 3.8 30.9 1.0
CA A:VAL211 3.9 31.1 1.0
C A:VAL211 4.0 26.4 1.0
CA A:ALA212 4.0 27.6 1.0
CB A:ALA105 4.1 26.8 1.0
O A:TYR210 4.2 30.8 1.0
O A:HOH460 4.3 51.1 1.0
CG1 A:VAL211 4.8 38.5 1.0
N A:VAL211 4.8 29.6 1.0
O A:HOH698 4.8 29.6 1.0
C A:TYR210 4.8 30.0 1.0
O A:HOH467 4.9 32.6 0.5
CB A:VAL211 4.9 34.5 1.0
O A:ALA212 4.9 29.6 1.0
O A:HOH949 5.0 25.6 0.3
C A:ALA212 5.0 29.6 1.0

Chlorine binding site 6 out of 17 in 5nkw

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Chlorine binding site 6 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:36.9
occ:0.80
 O A:HOH731 0.6 9.8 0.2
O6 A:BMA322 2.9 22.0 1.0
O A:HOH851 3.0 36.4 0.5
O A:HOH567 3.2 28.6 1.0
O A:HOH426 3.3 35.2 1.0
CE1 A:HIS66 3.5 23.3 1.0
C6 A:BMA322 3.6 21.6 1.0
C5 A:BMA322 3.9 23.2 1.0
CB A:ALA75 4.0 20.2 1.0
NE2 A:HIS66 4.3 19.0 1.0
ND1 A:HIS66 4.5 23.4 1.0
O A:HOH722 4.5 51.9 1.0
O A:HOH766 4.5 26.2 1.0
O3 A:BGC321 4.7 23.3 1.0
O5 A:BMA322 4.7 23.6 1.0
O A:HOH560 4.7 20.2 1.0
CA A:ALA75 4.8 19.4 1.0
OD2 A:ASP72 4.9 43.6 1.0
O4 A:BMA322 4.9 23.2 1.0

Chlorine binding site 7 out of 17 in 5nkw

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Chlorine binding site 7 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:29.4
occ:0.90
 O A:HOH675 2.8 18.4 0.5
OG1 A:THR59 3.0 16.8 1.0
CL A:CL312 3.0 26.7 0.5
CG2 A:THR59 3.6 19.5 1.0
O A:HOH609 3.6 31.3 0.5
CB A:THR59 3.8 14.2 1.0
O A:HOH969 4.1 32.0 0.5
CG2 A:VAL128 4.2 19.9 1.0
O A:HOH752 4.7 39.3 1.0
CA A:THR59 4.9 14.7 1.0

Chlorine binding site 8 out of 17 in 5nkw

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Chlorine binding site 8 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:26.9
occ:0.50
 O A:HOH778 0.8 16.5 0.5
O A:HOH715 3.0 57.6 1.0
N A:SER51 3.2 16.7 1.0
O A:HOH804 3.3 42.3 1.0
O A:HOH793 3.5 49.4 0.8
CE A:LYS50 3.5 30.0 0.8
O A:SER51 3.5 31.1 1.0
CA A:LYS50 3.6 16.6 0.8
CA A:LYS50 3.6 15.7 0.2
CD A:LYS50 3.7 32.9 0.8
O A:HOH437 3.8 31.9 0.5
C A:LYS50 3.9 14.0 0.8
C A:LYS50 3.9 16.4 0.2
OG A:SER51 3.9 44.6 0.5
CB A:LYS50 4.0 17.6 0.8
CD A:LYS50 4.0 17.9 0.2
O A:HOH636 4.1 26.7 0.5
O A:HOH616 4.1 66.8 1.0
CB A:LYS50 4.1 17.0 0.2
CA A:SER51 4.2 14.7 0.5
CA A:SER51 4.3 19.2 0.5
C A:SER51 4.3 21.6 1.0
O A:PRO49 4.3 22.2 1.0
CG A:LYS50 4.4 24.9 0.8
CE A:LYS50 4.4 22.9 0.2
O A:HOH909 4.5 58.3 1.0
CB A:SER51 4.6 19.9 0.5
CB A:SER51 4.6 31.5 0.5
CG A:LYS50 4.7 14.7 0.2
N A:LYS50 4.8 15.4 0.8
N A:LYS50 4.8 15.2 0.2
NZ A:LYS50 4.8 38.1 0.8
O A:HOH747 4.9 42.4 1.0

Chlorine binding site 9 out of 17 in 5nkw

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Chlorine binding site 9 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:24.4
occ:0.50
 O A:HOH743 0.8 14.7 0.5
O A:HOH469 2.8 48.2 1.0
N A:LYS32 2.9 18.4 1.0
O A:HOH581 3.1 42.0 1.0
N A:ASN33 3.3 15.8 1.0
O A:HOH550 3.4 39.1 1.0
CA A:LYS32 3.7 15.6 1.0
CB A:ASN33 3.8 18.6 1.0
CB A:LYS32 3.9 17.6 1.0
C A:VAL31 3.9 16.2 1.0
CA A:VAL31 3.9 15.2 1.0
C A:LYS32 4.0 13.9 1.0
CA A:ASN33 4.2 19.0 1.0
CG1 A:VAL31 4.3 18.6 1.0
OH A:TYR153 4.4 26.5 1.0
O A:HOH725 4.4 27.5 0.8
O A:PRO30 4.5 15.6 1.0
CZ A:TYR153 4.5 22.5 1.0
O A:HOH557 4.5 43.2 1.0
CG A:LYS32 4.6 18.0 1.0
CB A:VAL31 4.7 15.2 1.0
O A:HOH624 4.8 22.9 1.0
CE1 A:TYR153 4.8 21.4 1.0

Chlorine binding site 10 out of 17 in 5nkw

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Chlorine binding site 10 out of 17 in the X-Ray Crystal Structure of An AA9 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 AA9 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl312

b:26.7
occ:0.50
 O A:HOH675 0.8 18.4 0.5
CL A:CL309 3.0 29.4 0.9
O A:HOH609 3.4 31.3 0.5
OG A:SER225 3.4 30.3 1.0
CA A:GLY224 3.5 22.7 1.0
CB A:SER126 3.7 18.1 1.0
C A:GLY224 3.7 19.8 1.0
N A:SER225 3.8 17.5 1.0
CG2 A:VAL128 4.1 19.9 1.0
O A:SER126 4.1 17.2 1.0
CB A:SER225 4.1 26.2 1.0
CG2 A:THR59 4.1 19.5 1.0
C A:SER126 4.2 17.5 1.0
N A:GLY224 4.2 27.6 1.0
O A:GLY224 4.4 24.2 1.0
CA A:SER225 4.5 19.9 1.0
N A:VAL127 4.5 16.0 1.0
CA A:SER126 4.5 16.8 1.0
OG A:SER126 4.6 17.9 1.0
O A:HOH752 4.6 39.3 1.0
C A:VAL127 4.6 16.1 1.0
CA A:VAL127 4.7 17.5 1.0
O A:HOH440 4.7 46.4 1.0
N A:VAL128 4.7 15.4 1.0
OG1 A:THR59 4.9 16.8 1.0
O A:GLY223 4.9 23.6 1.0
C A:GLY223 5.0 27.4 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: Fri Jul 26 13:40:50 2024

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