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Zinc in PDB 3n0i: Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide

Protein crystallography data

The structure of Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide, PDB code: 3n0i was solved by E.C.Nilsson, R.J.Storm, J.Bauer, S.M.C.Johansson, A.Lookene, J.Angstroem, M.Hedenstroem, L.Fraengsmyr, S.Rinaldi, H.Willison, F.P.Domelloef, T.Stehle, N.Arnberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.90 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.990, 69.770, 74.900, 90.00, 94.92, 90.00
R / Rfree (%) 16 / 18.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide (pdb code 3n0i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide, PDB code: 3n0i:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3n0i

Go back to Zinc Binding Sites List in 3n0i
Zinc binding site 1 out of 3 in the Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn10

b:23.8
occ:0.75
NE2 A:HIS231 1.8 22.6 1.0
OE2 A:GLU351 1.8 29.1 1.0
O A:HOH537 2.2 10.5 1.0
O A:HOH536 2.3 10.5 1.0
CE1 A:HIS231 2.7 29.1 1.0
CD A:GLU351 2.8 27.0 1.0
CD2 A:HIS231 2.9 28.0 1.0
CG A:GLU351 3.3 23.9 1.0
O B:HOH504 3.4 11.8 1.0
ND1 A:HIS231 3.9 28.1 1.0
OE1 A:GLU351 4.0 26.5 1.0
CG A:HIS231 4.0 27.3 1.0
O A:VAL225 4.2 24.8 1.0
O B:HOH454 4.3 17.8 1.0
CE B:LYS300 4.3 31.8 1.0
O A:HOH538 4.3 18.6 1.0
CA A:VAL226 4.6 29.5 1.0
NZ B:LYS300 4.6 30.3 1.0
O A:VAL226 4.6 32.1 1.0
CB A:GLU351 4.7 22.8 1.0
CD1 A:ILE232 4.8 26.6 1.0
C A:VAL226 4.9 31.4 1.0

Zinc binding site 2 out of 3 in 3n0i

Go back to Zinc Binding Sites List in 3n0i
Zinc binding site 2 out of 3 in the Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn10

b:30.9
occ:1.00
NE2 B:HIS231 2.0 25.2 1.0
OE2 B:GLU351 2.1 38.6 1.0
O B:HOH505 2.3 9.6 1.0
O B:HOH538 2.5 20.2 1.0
CE1 B:HIS231 2.9 26.9 1.0
CD B:GLU351 3.1 31.1 1.0
CD2 B:HIS231 3.1 28.8 1.0
O C:HOH462 3.8 20.4 1.0
CG B:GLU351 3.8 28.9 1.0
OE1 B:GLU351 4.0 26.3 1.0
O B:HOH537 4.0 17.3 1.0
ND1 B:HIS231 4.1 29.2 1.0
CG B:HIS231 4.2 25.5 1.0
CE C:LYS300 4.2 33.2 1.0
O B:VAL225 4.2 24.9 1.0
O B:VAL226 4.4 30.5 1.0
NZ C:LYS300 4.5 30.9 1.0
CA B:VAL226 4.6 30.7 1.0
O B:HOH502 4.7 33.0 1.0
C B:VAL226 4.8 30.9 1.0

Zinc binding site 3 out of 3 in 3n0i

Go back to Zinc Binding Sites List in 3n0i
Zinc binding site 3 out of 3 in the Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of AD37 Fiber Knob in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn10

b:37.6
occ:1.00
NE2 C:HIS231 2.2 18.1 1.0
CE1 C:HIS231 3.0 20.9 1.0
CD2 C:HIS231 3.2 22.9 1.0
O C:HOH496 3.9 33.6 1.0
ND1 C:HIS231 4.2 16.9 1.0
CG C:HIS231 4.3 17.4 1.0
CD1 C:ILE232 4.3 26.1 1.0
OE2 C:GLU351 4.6 24.3 1.0
CG1 C:ILE232 4.7 25.6 1.0

Reference:

E.C.Nilsson, R.J.Storm, J.Bauer, S.M.Johansson, A.Lookene, J.Angstrom, M.Hedenstrom, T.L.Eriksson, L.Frangsmyr, S.Rinaldi, H.J.Willison, F.P.Domellof, T.Stehle, N.Arnberg. The GD1A Glycan Is A Cellular Receptor For Adenoviruses Causing Epidemic Keratoconjunctivitis. Nat.Med. (N.Y.) V. 17 105 2011.
ISSN: ISSN 1078-8956
PubMed: 21151139
DOI: 10.1038/NM.2267
Page generated: Sat Sep 26 11:51:59 2020
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