Zinc in PDB 5t7k: X-Ray Crystal Structure of AA13 Lpmo

Protein crystallography data

The structure of X-Ray Crystal Structure of AA13 Lpmo, PDB code: 5t7k 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 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.560, 59.080, 71.760, 90.00, 90.00, 90.00
R / Rfree (%) 9.1 / 13.5

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of AA13 Lpmo (pdb code 5t7k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Crystal Structure of AA13 Lpmo, PDB code: 5t7k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5t7k

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Zinc binding site 1 out of 4 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:Zn402

b:13.0
occ:0.50
 O A:HOH773 2.0 28.4 1.0
O A:HOH724 2.1 11.7 1.0
OD1 A:ASP102 2.2 11.0 1.0
OG A:SER104 2.2 15.3 1.0
O A:HOH808 2.3 0.7 0.2
O A:HOH566 2.3 56.5 1.0
CB A:SER104 3.1 11.2 1.0
CG A:ASP102 3.2 8.3 1.0
OD2 A:ASP102 3.5 12.7 1.0
N A:SER104 3.6 5.8 1.0
O A:HOH808 3.9 20.2 0.8
CA A:SER104 3.9 7.3 1.0
CB A:ASP102 4.4 6.6 1.0
O A:HOH568 4.4 21.5 1.0
N A:GLN103 4.5 5.3 1.0
O A:HOH839 4.5 22.6 1.0
C A:ASP102 4.6 5.0 1.0
CA A:ASP102 4.6 5.3 1.0
N A:ILE105 4.7 5.5 1.0
C A:SER104 4.7 6.3 1.0
C A:GLN103 4.9 5.6 1.0

Zinc binding site 2 out of 4 in 5t7k

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Zinc binding site 2 out of 4 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:Zn403

b:10.8
occ:0.30
 O A:HOH664 1.7 26.8 0.7
O A:HOH531 1.7 4.9 0.3
OD1 A:ASP36 2.0 10.9 0.7
OD1 A:ASP38 2.0 9.9 0.3
CG A:ASP36 2.7 8.7 0.7
OD2 A:ASP36 2.7 14.8 0.7
OD1 A:ASP36 2.8 7.8 0.3
CG A:ASP38 3.1 7.4 0.3
OD2 A:ASP38 3.7 4.8 0.3
CG A:ASP36 3.8 6.6 0.3
CB A:ASP38 3.8 9.9 0.7
N A:ALA39 3.8 6.8 1.0
N A:ASP38 3.9 5.4 0.7
N A:ASP38 3.9 5.8 0.3
C A:ASP38 4.0 6.5 0.7
C A:ASP38 4.0 6.9 0.3
CA A:ASP38 4.0 6.4 0.7
O A:HOH834 4.1 55.4 1.0
CA A:ASP38 4.2 7.0 0.3
CB A:ASP38 4.2 8.6 0.3
CB A:ASP36 4.2 8.1 0.7
O A:HOH621 4.2 22.6 1.0
OD2 A:ASP36 4.3 8.8 0.3
O A:HOH788 4.4 14.5 0.5
CA A:ALA39 4.4 7.7 1.0
CB A:ALA39 4.6 10.9 1.0
O A:ASP38 4.6 8.1 0.3
O A:ASP38 4.6 8.8 0.7
C A:ASP36 4.7 6.2 0.7
C A:ASP36 4.7 6.5 0.3
CA A:ASP36 4.8 6.8 0.7
N A:LEU37 4.8 6.0 1.0
CB A:ASP36 4.8 6.1 0.3
CA A:ASP36 4.9 6.7 0.3
CG A:ASP38 4.9 13.0 0.7
OD2 A:ASP38 5.0 15.7 0.7

Zinc binding site 3 out of 4 in 5t7k

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Zinc binding site 3 out of 4 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:Zn404

b:17.2
occ:0.20
 ND1 A:HIC1 1.2 13.7 0.8
CE1 A:HIC1 1.9 25.6 0.8
N A:HIC1 2.0 12.7 0.2
ND1 A:HIC1 2.1 9.5 0.2
NE2 A:HIS91 2.1 12.4 0.2
N A:HIC1 2.2 9.8 0.8
CG A:HIC1 2.5 13.7 0.8
O A:HOH649 2.8 6.5 0.8
OH A:TYR224 2.9 17.9 1.0
CA A:HIC1 3.0 7.0 0.8
CG A:HIC1 3.0 12.2 0.2
CA A:HIC1 3.0 9.1 0.2
CE1 A:HIS91 3.0 10.9 0.2
NE2 A:HIC1 3.1 25.6 0.8
CE1 A:HIC1 3.1 6.7 0.2
CD2 A:HIS91 3.1 11.9 0.2
O A:GLY89 3.1 8.6 0.2
CD2 A:HIC1 3.4 22.9 0.8
CB A:HIC1 3.4 10.1 0.8
CB A:HIC1 3.4 10.6 0.2
CZ A:TYR224 3.6 11.7 1.0
O A:GLY89 3.7 7.3 0.8
CA A:GLY89 3.8 4.9 0.2
C A:GLY89 3.8 6.3 0.2
CE1 A:TYR224 3.9 9.5 1.0
O A:HOH679 3.9 12.5 0.2
NE2 A:GLN222 4.0 9.3 1.0
O A:HOH504 4.1 24.1 0.8
OE1 A:GLN222 4.2 17.0 1.0
ND1 A:HIS91 4.2 15.6 0.2
CD2 A:HIC1 4.2 13.4 0.2
O A:HOH594 4.2 27.2 1.0
NE2 A:HIC1 4.2 12.7 0.2
CG A:HIS91 4.2 12.2 0.2
C A:GLY89 4.3 8.5 0.8
C A:HIC1 4.3 6.2 0.2
CZ A:HIC1 4.4 40.2 0.8
C A:HIC1 4.4 6.4 0.8
CD A:GLN222 4.4 9.7 1.0
CA A:GLY89 4.5 15.0 0.8
CE2 A:TYR224 4.5 10.3 1.0
CH2 A:TRP215 4.8 7.1 1.0
O A:HIC1 4.8 7.2 0.2
O A:HOH512 4.8 41.7 1.0
O A:HIC1 4.9 8.2 0.8
N A:GLY89 4.9 3.2 0.2
O A:HOH767 4.9 12.9 0.2
CZ3 A:TRP215 4.9 6.4 1.0
O A:ASN88 5.0 20.8 0.8

Zinc binding site 4 out of 4 in 5t7k

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Zinc binding site 4 out of 4 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:11.6
occ:0.10
 O A:HOH803 0.5 76.1 0.9
O A:HOH637 2.8 63.1 0.5
O A:HOH545 3.1 21.6 1.0
O A:HOH637 3.4 38.5 0.5
O A:HOH782 3.9 32.7 1.0
O A:LEU110 4.0 7.7 1.0
O A:SER67 4.1 22.7 0.7
O A:SER67 4.6 11.4 0.3
O A:HOH532 4.6 34.9 1.0
O A:HOH722 4.6 61.9 1.0

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 10:55:22 2020

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