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Zinc in PDB 1enq: Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site

Protein crystallography data

The structure of Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site, PDB code: 1enq was solved by J.Bouckaert, R.Loris, F.Poortmans, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.230, 113.030, 122.140, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 28.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site (pdb code 1enq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site, PDB code: 1enq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1enq

Go back to Zinc Binding Sites List in 1enq
Zinc binding site 1 out of 4 in the Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn238

b:38.2
occ:1.00
O A:HOH257 1.9 25.6 1.0
O A:HOH270 2.0 20.6 1.0
NE2 A:HIS24 2.1 21.8 1.0
OD2 A:ASP10 2.2 29.9 1.0
O A:HOH264 2.2 30.7 1.0
OE2 A:GLU8 2.3 31.6 1.0
CE1 A:HIS24 3.0 16.4 1.0
CD A:GLU8 3.1 32.0 1.0
CG A:ASP10 3.2 32.1 1.0
OE1 A:GLU8 3.2 33.8 1.0
CD2 A:HIS24 3.2 20.4 1.0
O A:HOH266 3.4 43.5 1.0
CB A:ASP10 3.6 29.5 1.0
OG A:SER34 3.8 40.4 1.0
O A:HOH282 4.1 44.5 1.0
ND1 A:HIS24 4.2 20.5 1.0
OD1 A:ASP10 4.3 33.4 1.0
CG A:HIS24 4.3 18.5 1.0
O A:VAL32 4.5 38.1 1.0
CG A:GLU8 4.6 31.5 1.0
OD1 A:ASP19 4.6 55.6 1.0
O A:HOH299 4.6 74.3 1.0
CD A:PRO20 4.7 56.5 1.0
ND2 A:ASN14 4.7 94.2 0.0
OD1 A:ASN14 4.8 96.3 0.0

Zinc binding site 2 out of 4 in 1enq

Go back to Zinc Binding Sites List in 1enq
Zinc binding site 2 out of 4 in the Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn238

b:24.9
occ:1.00
NE2 B:HIS24 1.9 20.0 1.0
O B:HOH274 2.0 24.7 1.0
OE2 B:GLU8 2.1 39.9 1.0
OD2 B:ASP10 2.1 36.5 1.0
O B:HOH273 2.1 20.2 1.0
O B:HOH294 2.5 39.9 1.0
CE1 B:HIS24 2.8 25.6 1.0
CD2 B:HIS24 3.0 26.3 1.0
CG B:ASP10 3.0 35.1 1.0
CD B:GLU8 3.0 34.9 1.0
OE1 B:GLU8 3.3 33.1 1.0
CB B:ASP10 3.3 34.1 1.0
OG B:SER34 3.9 42.6 1.0
O B:HOH239 3.9 25.9 1.0
ND1 B:HIS24 4.0 27.5 1.0
O B:HOH275 4.1 53.4 1.0
CG B:HIS24 4.1 26.4 1.0
OD1 B:ASP10 4.2 33.6 1.0
CG B:GLU8 4.5 33.1 1.0
O B:HOH277 4.7 40.2 1.0
O B:VAL32 4.8 33.4 1.0
CA B:ASP10 4.9 30.6 1.0
ND2 B:ASN14 5.0 0.9 0.0

Zinc binding site 3 out of 4 in 1enq

Go back to Zinc Binding Sites List in 1enq
Zinc binding site 3 out of 4 in the Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn238

b:52.5
occ:1.00
O C:HOH263 1.9 31.8 1.0
NE2 C:HIS24 1.9 32.6 1.0
OD2 C:ASP10 2.0 42.2 1.0
OE2 C:GLU8 2.3 49.4 1.0
CE1 C:HIS24 2.7 42.4 1.0
CG C:ASP10 3.0 48.1 1.0
CD2 C:HIS24 3.2 40.0 1.0
CD C:GLU8 3.2 46.1 1.0
O C:HOH239 3.3 53.2 1.0
CB C:ASP10 3.4 44.3 1.0
OE1 C:GLU8 3.4 47.8 1.0
ND1 C:HIS24 4.0 40.2 1.0
OG C:SER34 4.0 48.0 1.0
OD1 C:ASP10 4.1 56.0 1.0
CG C:HIS24 4.2 39.8 1.0
OD1 C:ASP19 4.4 0.2 1.0
ND2 C:ASN14 4.6 96.7 0.0
CG C:GLU8 4.6 36.6 1.0
OD1 C:ASN14 4.6 96.9 0.0
CD C:PRO20 4.7 92.1 1.0
O C:VAL32 4.8 38.3 1.0
CA C:ASP10 4.9 42.6 1.0
CG C:ASP19 5.0 0.3 1.0

Zinc binding site 4 out of 4 in 1enq

Go back to Zinc Binding Sites List in 1enq
Zinc binding site 4 out of 4 in the Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Co-Crystals of Demetallized Concanavalin A with Zinc Having A Zinc Ion Bound in the S1 Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn238

b:51.0
occ:1.00
NE2 D:HIS24 2.0 24.8 1.0
OD2 D:ASP10 2.2 44.5 1.0
OE2 D:GLU8 2.2 37.5 1.0
O D:HOH261 2.3 65.3 1.0
CE1 D:HIS24 3.0 28.0 1.0
CD D:GLU8 3.0 39.7 1.0
OE1 D:GLU8 3.2 33.5 1.0
CG D:ASP10 3.2 45.0 1.0
CD2 D:HIS24 3.2 28.6 1.0
CB D:ASP10 3.5 43.0 1.0
O D:HOH273 3.6 58.6 1.0
OG D:SER34 3.8 41.8 1.0
ND1 D:HIS24 4.2 25.4 1.0
OD1 D:ASP10 4.3 44.0 1.0
CG D:HIS24 4.3 29.1 1.0
CG D:GLU8 4.5 35.5 1.0
O D:VAL32 4.5 53.7 1.0
OD1 D:ASN14 4.9 91.3 0.0

Reference:

J.Bouckaert, F.Poortmans, L.Wyns, R.Loris. Sequential Structural Changes Upon Zinc and Calcium Binding to Metal-Free Concanavalin A. J.Biol.Chem. V. 271 16144 1996.
ISSN: ISSN 0021-9258
PubMed: 8663112
DOI: 10.1074/JBC.271.27.16144
Page generated: Wed Dec 16 02:48:26 2020

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