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Zinc in PDB 5lsv: X-Ray Crystal Structure of AA13 Lpmo

Protein crystallography data

The structure of X-Ray Crystal Structure of AA13 Lpmo, PDB code: 5lsv was solved by K.E.H.Frandsen, J.-C.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 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.400, 58.840, 71.900, 90.00, 90.00, 90.00
R / Rfree (%) 10.1 / 12.5

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of AA13 Lpmo (pdb code 5lsv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the X-Ray Crystal Structure of AA13 Lpmo, PDB code: 5lsv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 5lsv

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Zinc binding site 1 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:5.3
occ:0.80
ZN A:ZN404 0.0 5.3 0.8
ZN A:ZN404 0.6 5.5 0.2
OH A:TYR224 1.7 4.3 0.2
ND1 A:HIC1 2.0 7.0 0.8
OH A:TYR224 2.0 10.1 0.8
NE2 A:HIS91 2.0 4.1 0.2
NE2 A:HIS91 2.1 7.5 0.8
O A:HOH619 2.1 8.1 1.0
N A:HIC1 2.2 4.2 0.8
N A:HIC1 2.3 4.4 0.2
ND1 A:HIC1 2.3 6.1 0.2
CE1 A:HIC1 2.9 10.9 0.8
CZ A:TYR224 2.9 3.2 0.2
CE1 A:HIS91 2.9 3.7 0.2
CG A:HIC1 3.0 7.2 0.8
CZ A:TYR224 3.0 5.2 0.8
CD2 A:HIS91 3.0 3.8 0.2
CE1 A:HIS91 3.1 8.2 0.8
CD2 A:HIS91 3.1 7.0 0.8
CE1 A:HIC1 3.1 9.2 0.2
CA A:HIC1 3.2 4.6 0.8
CG A:HIC1 3.2 6.7 0.2
CA A:HIC1 3.2 4.3 0.2
CB A:HIC1 3.4 5.5 0.8
CE2 A:TYR224 3.5 3.3 0.2
CE1 A:TYR224 3.5 5.5 0.8
NE2 A:GLN222 3.7 9.4 0.2
CB A:HIC1 3.7 5.3 0.2
O A:HOH657 3.8 10.1 0.2
O A:HOH657 3.9 19.3 0.8
CE2 A:TYR224 4.0 6.0 0.8
O A:GLY89 4.0 6.9 1.0
CE1 A:TYR224 4.0 3.1 0.2
NE2 A:HIC1 4.0 10.0 0.8
CD2 A:HIC1 4.1 9.7 0.8
ND1 A:HIS91 4.1 3.4 0.2
CG A:HIS91 4.2 4.3 0.2
ND1 A:HIS91 4.2 8.5 0.8
CG A:HIS91 4.3 8.9 0.8
NE2 A:HIC1 4.3 7.1 0.2
CD2 A:HIC1 4.3 7.9 0.2
CA A:GLY89 4.5 7.4 1.0
C A:HIC1 4.5 3.8 0.8
OE1 A:GLN222 4.5 19.9 0.8
C A:HIC1 4.6 3.7 0.2
CD A:GLN222 4.7 11.3 0.2
C A:GLY89 4.7 5.6 1.0
NE2 A:GLN222 4.7 18.4 0.8
CD2 A:TYR224 4.8 3.0 0.2
OE1 A:GLN222 4.8 15.8 0.2
CD1 A:TYR224 4.8 5.1 0.8
CD A:GLN222 4.9 14.2 0.8
CD1 A:ILE27 4.9 3.5 0.3

Zinc binding site 2 out of 12 in 5lsv

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Zinc binding site 2 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:5.5
occ:0.20
ZN A:ZN404 0.0 5.5 0.2
ZN A:ZN404 0.6 5.3 0.8
ND1 A:HIC1 1.8 7.0 0.8
NE2 A:HIS91 2.0 7.5 0.8
ND1 A:HIC1 2.0 6.1 0.2
N A:HIC1 2.0 4.2 0.8
NE2 A:HIS91 2.0 4.1 0.2
N A:HIC1 2.1 4.4 0.2
OH A:TYR224 2.2 4.3 0.2
O A:HOH619 2.4 8.1 1.0
OH A:TYR224 2.6 10.1 0.8
CG A:HIC1 2.8 7.2 0.8
CE1 A:HIS91 2.8 8.2 0.8
CE1 A:HIC1 2.9 10.9 0.8
CG A:HIC1 2.9 6.7 0.2
CE1 A:HIC1 2.9 9.2 0.2
CD2 A:HIS91 3.0 3.8 0.2
CE1 A:HIS91 3.0 3.7 0.2
CA A:HIC1 3.1 4.6 0.8
CA A:HIC1 3.1 4.3 0.2
CD2 A:HIS91 3.1 7.0 0.8
CB A:HIC1 3.1 5.5 0.8
CB A:HIC1 3.3 5.3 0.2
CZ A:TYR224 3.4 3.2 0.2
O A:GLY89 3.5 6.9 1.0
CZ A:TYR224 3.6 5.2 0.8
CA A:GLY89 3.8 7.4 1.0
CE2 A:TYR224 3.9 3.3 0.2
CD2 A:HIC1 3.9 9.7 0.8
ND1 A:HIS91 4.0 8.5 0.8
NE2 A:HIC1 4.0 10.0 0.8
CD2 A:HIC1 4.0 7.9 0.2
CE1 A:TYR224 4.0 5.5 0.8
NE2 A:HIC1 4.0 7.1 0.2
ND1 A:HIS91 4.1 3.4 0.2
C A:GLY89 4.1 5.6 1.0
CG A:HIS91 4.1 4.3 0.2
CG A:HIS91 4.1 8.9 0.8
NE2 A:GLN222 4.2 9.4 0.2
O A:HOH657 4.3 19.3 0.8
O A:HOH657 4.3 10.1 0.2
C A:HIC1 4.4 3.8 0.8
C A:HIC1 4.4 3.7 0.2
CE2 A:TYR224 4.5 6.0 0.8
CE1 A:TYR224 4.5 3.1 0.2
O A:HOH629 4.6 20.4 0.8
O A:HIC1 4.8 4.8 0.8
O A:HOH758 4.9 25.7 0.8
O A:HIC1 4.9 4.6 0.2

Zinc binding site 3 out of 12 in 5lsv

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Zinc binding site 3 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:7.5
occ:0.70
ZN A:ZN405 0.0 7.5 0.7
ZN A:ZN405 1.2 12.0 0.1
O A:HOH731 1.9 15.4 0.9
OD1 A:ASP38 2.0 11.8 1.0
OD1 A:ASP36 2.0 7.2 1.0
ZN A:ZN405 2.2 15.2 0.2
OD2 A:ASP36 2.6 11.3 1.0
CG A:ASP36 2.6 6.5 1.0
CG A:ASP38 3.1 11.5 1.0
OD2 A:ASP38 3.7 11.8 1.0
N A:ALA39 3.8 5.9 1.0
O A:HOH703 3.9 24.2 1.0
N A:ASP38 4.0 4.6 1.0
C A:ASP38 4.1 5.8 1.0
CB A:ASP36 4.1 6.1 1.0
O A:HOH773 4.1 41.8 1.0
CB A:ASP38 4.2 8.8 1.0
O A:HOH784 4.2 31.8 1.0
CA A:ASP38 4.2 6.0 1.0
O A:HOH811 4.2 33.8 0.7
CA A:ALA39 4.4 7.2 1.0
CB A:ALA39 4.4 9.5 1.0
O A:HOH555 4.4 5.8 1.0
O A:HOH722 4.5 25.9 0.8
CA A:ASP36 4.7 4.6 1.0
C A:ASP36 4.7 4.2 1.0
O A:HOH685 4.7 19.3 0.3
N A:LEU37 4.7 4.1 1.0
O A:ASP38 4.8 8.0 1.0

Zinc binding site 4 out of 12 in 5lsv

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Zinc binding site 4 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:15.2
occ:0.20
ZN A:ZN405 0.0 15.2 0.2
ZN A:ZN405 1.3 12.0 0.1
OD2 A:ASP36 1.8 11.3 1.0
ZN A:ZN405 2.2 7.5 0.7
O A:HOH722 2.5 25.9 0.8
O A:HOH731 2.5 15.4 0.9
CG A:ASP36 2.8 6.5 1.0
OD1 A:ASP36 3.1 7.2 1.0
O A:HOH784 3.6 31.8 1.0
O A:HOH722 3.6 10.7 0.2
CB A:ASP36 4.1 6.1 1.0
OD1 A:ASP38 4.1 11.8 1.0
CB A:ALA154 4.8 6.6 1.0

Zinc binding site 5 out of 12 in 5lsv

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Zinc binding site 5 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:12.0
occ:0.10
ZN A:ZN405 0.0 12.0 0.1
ZN A:ZN405 1.2 7.5 0.7
O A:HOH731 1.3 15.4 0.9
ZN A:ZN405 1.3 15.2 0.2
OD2 A:ASP36 2.3 11.3 1.0
OD1 A:ASP36 2.7 7.2 1.0
CG A:ASP36 2.9 6.5 1.0
OD1 A:ASP38 3.0 11.8 1.0
O A:HOH784 3.2 31.8 1.0
O A:HOH722 3.8 25.9 0.8
O A:HOH811 3.9 33.8 0.7
O A:HOH773 4.2 41.8 1.0
CG A:ASP38 4.2 11.5 1.0
CB A:ASP36 4.3 6.1 1.0
O A:HOH703 4.4 24.2 1.0
CB A:ALA39 4.4 9.5 1.0
N A:ALA39 4.4 5.9 1.0
CA A:ALA39 4.6 7.2 1.0
OD2 A:ASP38 4.8 11.8 1.0
C A:ASP38 4.8 5.8 1.0
O A:HOH722 4.9 10.7 0.2
O A:HOH685 5.0 19.3 0.3

Zinc binding site 6 out of 12 in 5lsv

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Zinc binding site 6 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:11.6
occ:0.80
O A:HOH701 2.0 22.4 1.0
O A:HOH562 2.0 24.8 1.0
OD1 A:ASP102 2.1 10.4 1.0
O A:HOH615 2.1 9.5 1.0
OG A:SER104 2.2 10.2 1.0
O A:HOH749 2.2 24.3 1.0
CG A:ASP102 3.0 9.5 1.0
CB A:SER104 3.2 7.9 1.0
OD2 A:ASP102 3.3 12.2 1.0
N A:SER104 3.8 5.6 1.0
CA A:SER104 4.0 5.9 1.0
O A:HOH786 4.2 42.0 1.0
O A:HOH534 4.3 19.1 1.0
CB A:ASP102 4.3 6.7 1.0
O A:HOH799 4.4 19.0 1.0
C A:ASP102 4.6 5.0 1.0
CA A:ASP102 4.6 5.2 1.0
N A:GLN103 4.6 4.8 1.0
N A:ILE105 4.7 5.8 1.0
C A:SER104 4.8 5.8 1.0
C A:GLN103 5.0 5.3 1.0

Zinc binding site 7 out of 12 in 5lsv

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Zinc binding site 7 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:9.7
occ:0.70
ZN A:ZN407 0.0 9.7 0.7
ZN A:ZN407 2.0 14.3 0.2
O A:HOH541 2.0 19.9 0.7
NE2 A:HIS15 2.0 8.9 0.7
CE1 A:HIS15 3.0 8.9 0.7
CD2 A:HIS15 3.0 8.2 0.7
NE2 A:HIS15 3.4 4.9 0.3
O A:HOH541 3.4 11.2 0.3
OE1 A:GLU16 3.6 8.5 0.2
CD2 A:HIS15 3.7 5.1 0.3
CG A:TYR186 4.0 6.8 1.0
CB A:TYR186 4.1 7.7 1.0
ND1 A:HIS15 4.1 7.7 0.7
CD A:GLU16 4.1 7.5 0.2
CG A:HIS15 4.1 6.8 0.7
CD1 A:TYR186 4.1 7.2 1.0
OE2 A:GLU16 4.1 6.7 0.2
O A:HOH526 4.4 6.3 0.2
CG A:GLU16 4.5 10.2 0.8
CD2 A:TYR186 4.6 6.5 1.0
O A:HOH702 4.6 11.8 0.3
CE1 A:HIS15 4.7 6.0 0.3
CE1 A:TYR186 4.8 7.8 1.0

Zinc binding site 8 out of 12 in 5lsv

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Zinc binding site 8 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:14.3
occ:0.20
ZN A:ZN407 0.0 14.3 0.2
CE1 A:HIS15 1.6 8.9 0.7
NE2 A:HIS15 1.7 8.9 0.7
ZN A:ZN407 2.0 9.7 0.7
NE2 A:HIS15 2.0 4.9 0.3
ND1 A:HIS15 2.9 7.7 0.7
CD2 A:HIS15 2.9 5.1 0.3
CD2 A:HIS15 3.0 8.2 0.7
CE1 A:HIS15 3.0 6.0 0.3
CG A:HIS15 3.5 6.8 0.7
O A:HOH541 3.8 19.9 0.7
CD1 A:TYR186 3.9 7.2 1.0
CE1 A:TYR186 3.9 7.8 1.0
CG A:TYR186 4.0 6.8 1.0
CG A:HIS15 4.1 4.2 0.3
ND1 A:HIS15 4.1 4.8 0.3
CZ A:TYR186 4.1 7.2 1.0
CD2 A:TYR186 4.2 6.5 1.0
CE2 A:TYR186 4.3 7.5 1.0
OE1 A:GLU16 4.7 8.5 0.2
CB A:TYR186 4.7 7.7 1.0
OH A:TYR186 4.8 9.2 1.0
O A:HIS15 4.8 7.6 0.3
O A:HIS15 4.8 7.9 0.7
O A:HOH530 4.9 11.8 0.7
O A:HOH541 5.0 11.2 0.3

Zinc binding site 9 out of 12 in 5lsv

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Zinc binding site 9 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:7.2
occ:0.35
O A:HOH801 1.7 30.0 1.0
O A:HOH755 1.9 16.1 1.0
O A:HOH538 2.1 13.3 1.0
O A:HOH760 2.1 18.4 1.0
O A:HOH757 2.2 20.9 1.0
OE2 A:GLU153 2.2 15.4 1.0
CD A:GLU153 3.1 8.6 1.0
OE1 A:GLU153 3.3 9.2 1.0
O A:HOH849 3.8 56.1 1.0
O A:HOH800 3.8 59.4 0.5
O A:HOH800 3.9 86.0 0.5
O A:HOH835 4.1 24.1 1.0
O A:HOH533 4.1 36.7 1.0
O A:HOH682 4.3 16.9 1.0
CG A:GLU153 4.5 7.8 1.0
O A:ASP148 4.7 5.5 1.0
NE1 A:TRP34 4.9 6.7 1.0
O A:HOH837 4.9 35.9 1.0

Zinc binding site 10 out of 12 in 5lsv

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Zinc binding site 10 out of 12 in the X-Ray Crystal Structure of AA13 Lpmo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of X-Ray Crystal Structure of AA13 Lpmo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:8.3
occ:0.20
O A:HOH746 1.7 25.5 0.5
OXT A:GLN233 2.1 13.7 1.0
O A:HOH756 2.2 20.8 1.0
O A:HOH742 2.3 26.4 0.5
O A:HOH764 2.4 26.1 1.0
OG A:SER74 2.8 11.1 0.5
O A:HOH746 3.0 12.0 0.5
C A:GLN233 3.2 8.7 1.0
CB A:SER74 3.2 9.3 0.5
O A:HOH828 3.6 83.2 1.0
CB A:SER74 3.7 8.0 0.5
O A:HOH742 3.7 29.3 0.5
O A:GLN233 3.7 11.3 1.0
CA A:SER74 3.9 6.1 0.5
CA A:SER74 3.9 5.7 0.5
O A:TYR73 4.1 7.5 1.0
CA A:GLN233 4.3 6.7 1.0
N A:SER74 4.4 6.2 1.0
OG A:SER74 4.4 12.7 0.5
O A:HOH503 4.4 26.2 1.0
CB A:GLN233 4.4 7.7 1.0
C A:TYR73 4.5 5.2 1.0
N A:GLN233 4.7 5.2 1.0
CD A:PRO75 4.8 5.9 1.0
O A:HOH710 4.9 28.2 0.5
O A:HOH517 5.0 13.8 0.5

Reference:

K.E.Frandsen, J.C.Poulsen, M.Tovborg, K.S.Johansen, L.Lo Leggio. Learning From Oligosaccharide Soaks of Crystals of An AA13 Lytic Polysaccharide Monooxygenase: Crystal Packing, Ligand Binding and Active-Site Disorder. Acta Crystallogr D Struct V. 73 64 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28045386
DOI: 10.1107/S2059798316019641
Page generated: Wed Dec 16 06:30:43 2020

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