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Zinc in PDB 3qnd: Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor

Protein crystallography data

The structure of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor, PDB code: 3qnd was solved by T.Stehle, J.Bauer, M.Elofsson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.47 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.190, 108.645, 112.511, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor (pdb code 3qnd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor, PDB code: 3qnd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3qnd

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Zinc binding site 1 out of 7 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor


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 Trivalent Sialic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn7

b:28.9
occ:0.75
 OE2 A:GLU351 1.8 33.3 1.0
O A:HOH13 2.0 22.4 1.0
NE2 A:HIS231 2.0 34.6 1.0
CD A:GLU351 3.0 32.2 1.0
CE1 A:HIS231 3.0 35.1 1.0
CD2 A:HIS231 3.0 34.4 1.0
CG A:GLU351 3.6 30.8 1.0
OE1 A:GLU351 4.0 31.9 1.0
ND1 A:HIS231 4.1 34.8 1.0
CG A:HIS231 4.2 34.4 1.0
O A:VAL225 4.3 29.9 1.0
O A:VAL226 4.3 32.6 1.0
CE B:LYS300 4.4 41.7 1.0
CA A:VAL226 4.5 31.6 1.0
NZ B:LYS300 4.7 42.1 1.0
CD1 A:ILE232 4.7 36.1 1.0
C A:VAL226 4.8 32.1 1.0
CB A:GLU351 4.8 30.4 1.0

Zinc binding site 2 out of 7 in 3qnd

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Zinc binding site 2 out of 7 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor


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 Trivalent Sialic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8

b:56.0
occ:1.00
 OE2 B:GLU351 1.9 32.6 1.0
NE2 B:HIS231 2.1 39.7 1.0
O C:HOH452 2.8 35.1 1.0
O B:HOH78 2.9 34.0 1.0
CE1 B:HIS231 3.0 40.8 1.0
CD B:GLU351 3.0 31.9 1.0
CD2 B:HIS231 3.1 39.0 1.0
CG B:GLU351 3.6 30.9 1.0
OE1 B:GLU351 4.0 32.1 1.0
ND1 B:HIS231 4.1 40.9 1.0
O B:VAL226 4.2 36.9 1.0
O B:VAL225 4.2 32.7 1.0
CG B:HIS231 4.2 39.6 1.0
CA B:VAL226 4.5 34.8 1.0
CE C:LYS300 4.6 45.0 1.0
C B:VAL226 4.7 36.0 1.0
NZ C:LYS300 4.8 46.1 1.0
CB B:GLU351 4.9 30.9 1.0
CD1 B:ILE232 5.0 42.5 1.0

Zinc binding site 3 out of 7 in 3qnd

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Zinc binding site 3 out of 7 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor


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 Trivalent Sialic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn9

b:72.8
occ:1.00
 OE2 C:GLU351 1.9 52.4 1.0
NE2 C:HIS231 2.1 70.4 1.0
CD2 C:HIS231 3.0 69.0 1.0
CD C:GLU351 3.0 50.8 1.0
CE1 C:HIS231 3.1 72.0 1.0
CG C:GLU351 3.6 49.7 1.0
OE1 C:GLU351 3.9 50.1 1.0
O C:VAL226 4.1 63.5 1.0
CG C:HIS231 4.1 69.7 1.0
O C:VAL225 4.2 56.8 1.0
ND1 C:HIS231 4.2 71.6 1.0
CE A:LYS300 4.3 56.6 1.0
CA C:VAL226 4.4 60.3 1.0
C C:VAL226 4.7 62.1 1.0
NZ A:LYS300 4.9 56.8 1.0

Zinc binding site 4 out of 7 in 3qnd

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Zinc binding site 4 out of 7 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn10

b:81.9
occ:1.00
 OE1 E:GLU281 3.1 63.9 1.0
CD E:GLU281 3.3 63.5 1.0
OE2 E:GLU281 3.6 64.0 1.0
CG E:GLU281 4.1 62.1 1.0

Zinc binding site 5 out of 7 in 3qnd

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Zinc binding site 5 out of 7 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn7

b:27.5
occ:0.75
 OE2 E:GLU351 1.9 31.8 1.0
O E:HOH89 2.0 30.3 1.0
NE2 E:HIS231 2.1 33.5 1.0
O E:HOH6 2.1 21.4 1.0
CD E:GLU351 2.9 31.4 1.0
CE1 E:HIS231 3.0 33.9 1.0
CD2 E:HIS231 3.1 33.5 1.0
CG E:GLU351 3.4 30.9 1.0
OE1 E:GLU351 4.0 31.3 1.0
ND1 E:HIS231 4.2 34.1 1.0
O E:VAL225 4.2 31.5 1.0
CG E:HIS231 4.2 34.0 1.0
CE F:LYS300 4.3 40.8 1.0
O E:VAL226 4.5 33.8 1.0
CA E:VAL226 4.6 33.0 1.0
CD1 E:ILE232 4.8 34.8 1.0
CB E:GLU351 4.8 30.7 1.0
NZ F:LYS300 4.8 40.8 1.0
C E:VAL226 4.9 33.5 1.0

Zinc binding site 6 out of 7 in 3qnd

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Zinc binding site 6 out of 7 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn8

b:36.9
occ:1.00
 OE2 F:GLU351 1.9 27.1 1.0
NE2 F:HIS231 2.1 30.1 1.0
O F:HOH390 2.6 37.9 1.0
O G:HOH12 2.9 26.4 1.0
CD F:GLU351 3.0 26.3 1.0
CE1 F:HIS231 3.1 30.9 1.0
CD2 F:HIS231 3.1 30.1 1.0
CG F:GLU351 3.6 25.3 1.0
OE1 F:GLU351 4.0 26.7 1.0
CE G:LYS300 4.1 36.4 1.0
O F:VAL225 4.1 30.4 1.0
ND1 F:HIS231 4.2 31.1 1.0
CG F:HIS231 4.3 30.3 1.0
O F:VAL226 4.3 33.1 1.0
NZ G:LYS300 4.6 36.7 1.0
CA F:VAL226 4.6 32.0 1.0
C F:VAL226 4.8 32.6 1.0
CB F:GLU351 4.9 25.0 1.0
CD1 F:ILE232 4.9 30.6 1.0

Zinc binding site 7 out of 7 in 3qnd

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Zinc binding site 7 out of 7 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn9

b:53.6
occ:1.00
 OE2 G:GLU351 1.8 39.5 1.0
NE2 G:HIS231 2.2 47.3 1.0
O G:HOH82 2.3 37.7 1.0
O E:HOH166 2.8 31.3 1.0
CD G:GLU351 2.9 38.8 1.0
CE1 G:HIS231 3.1 48.2 1.0
CD2 G:HIS231 3.2 46.4 1.0
CG G:GLU351 3.6 37.7 1.0
OE1 G:GLU351 3.9 38.8 1.0
O G:VAL225 4.2 37.4 1.0
O G:VAL226 4.2 41.8 1.0
ND1 G:HIS231 4.3 48.2 1.0
CG G:HIS231 4.3 46.8 1.0
CE E:LYS300 4.4 44.3 1.0
CA G:VAL226 4.5 39.7 1.0
C G:VAL226 4.7 41.0 1.0
CD1 G:ILE232 4.9 47.5 1.0
CB G:GLU351 4.9 37.6 1.0
NZ E:LYS300 4.9 44.9 1.0

Reference:

S.Spjut, W.Qian, J.Bauer, R.Storm, L.Frangsmyr, T.Stehle, N.Arnberg, M.Elofsson. A Potent Trivalent Sialic Acid Inhibitor of Adenovirus Type 37 Infection of Human Corneal Cells. Angew.Chem.Int.Ed.Engl. V. 50 6519 2011.
ISSN: ISSN 1433-7851
PubMed: 21648036
DOI: 10.1002/ANIE.201101559
Page generated: Sat Oct 26 12:14:34 2024

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