Atomistry » Zinc » PDB 3sci-3sjb » 3sey
Atomistry »
  Zinc »
    PDB 3sci-3sjb »
      3sey »

Zinc in PDB 3sey: Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)

Protein crystallography data

The structure of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II), PDB code: 3sey was solved by M.Zhao, A.B.Soriaga, A.Laganowsky, M.R.Sawaya, D.Cascio, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.09 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.660, 63.650, 221.830, 90.00, 90.06, 90.00
R / Rfree (%) 20.8 / 24.7

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Zinc atom in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) (pdb code 3sey). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 23 binding sites of Zinc where determined in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II), PDB code: 3sey:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 1 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn373

b:18.0
occ:1.00
OE2 A:GLU222 1.9 13.4 1.0
NE2 A:HIS216 2.0 13.2 1.0
CD A:GLU222 2.7 16.9 1.0
OE1 A:GLU222 2.9 16.9 1.0
CE1 A:HIS216 3.0 17.6 1.0
CD2 A:HIS216 3.1 16.8 1.0
ND1 A:HIS216 4.1 15.6 1.0
CG A:GLU222 4.1 20.9 1.0
CG A:HIS216 4.2 13.3 1.0
CB A:HIS220 4.8 20.2 0.5

Zinc binding site 2 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 2 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn374

b:25.8
occ:1.00
NE2 A:HIS204 2.0 15.6 1.0
O A:ACT384 2.0 21.3 1.0
O A:ACT383 2.1 25.1 1.0
O A:HOH574 2.3 34.1 1.0
CE1 A:HIS204 2.9 20.6 1.0
CD2 A:HIS204 3.1 15.1 1.0
C A:ACT384 3.1 24.7 1.0
C A:ACT383 3.2 32.8 1.0
OXT A:ACT383 3.5 35.5 1.0
OXT A:ACT384 3.6 19.3 1.0
CB A:PRO134 3.8 20.4 1.0
ND1 A:HIS204 4.0 16.5 1.0
O A:HOH526 4.1 27.8 1.0
CG A:HIS204 4.1 16.0 1.0
CH3 A:ACT384 4.4 26.2 1.0
CH3 A:ACT383 4.5 23.3 1.0
CB A:ASN202 4.5 30.6 1.0
CA A:PRO134 4.6 22.4 1.0
O A:PRO134 4.7 19.9 1.0
C A:PRO134 4.7 25.2 1.0
O A:HOH470 4.7 19.2 1.0
OD1 A:ASN202 4.8 38.9 1.0
CG A:PRO134 4.8 16.1 1.0
CG A:ASN202 4.9 34.8 1.0

Zinc binding site 3 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 3 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:21.0
occ:0.50
OD1 A:ASP165 2.2 35.6 1.0
CG A:ASP165 3.0 31.5 1.0
OD2 A:ASP165 3.2 28.2 1.0
O A:ASP165 3.9 33.2 1.0
NE2 A:GLN254 3.9 29.1 1.0
NZ A:LYS252 4.0 33.8 1.0
CE A:LYS252 4.2 34.6 1.0
CB A:ASP165 4.4 30.2 1.0
OE1 A:GLN254 4.6 32.9 1.0
CD A:GLN254 4.7 20.0 1.0
C A:ASP165 4.7 32.0 1.0
CA A:ASP165 4.7 28.2 1.0
CD A:LYS252 4.9 30.0 1.0

Zinc binding site 4 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 4 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:30.8
occ:0.80
ND1 C:HIS220 2.2 18.5 0.5
N A:LYS2 2.4 66.7 1.0
CD2 C:HIS220 2.5 18.0 0.5
O A:LYS2 2.5 58.8 1.0
O A:HOH540 2.5 28.9 1.0
C A:MET1 2.6 69.1 1.0
CA A:MET1 2.6 71.5 1.0
CG A:MET1 2.9 71.3 1.0
CG C:HIS220 3.1 19.2 0.5
CE1 C:HIS220 3.2 17.6 0.5
CB A:MET1 3.3 72.2 1.0
C A:LYS2 3.3 56.9 1.0
CG C:HIS220 3.3 19.1 0.5
CB C:HIS220 3.4 18.0 0.5
CA A:LYS2 3.4 63.3 1.0
O A:MET1 3.5 69.0 1.0
NE2 C:HIS220 3.6 19.8 0.5
CB C:HIS220 3.7 18.2 0.5
N A:MET1 3.9 70.4 1.0
ZN C:ZN378 4.0 39.6 0.5
CA C:HIS220 4.0 14.9 0.5
CA C:HIS220 4.0 15.1 0.5
O A:ACT385 4.2 38.2 1.0
O A:HOH550 4.2 30.8 1.0
SD A:MET1 4.3 1.0 1.0
NE2 C:HIS220 4.3 14.0 0.5
CD2 C:HIS220 4.3 17.8 0.5
ND1 C:HIS220 4.5 18.1 0.5
CB A:LYS2 4.6 64.2 1.0
N A:ILE3 4.6 49.7 1.0
CE1 C:HIS220 4.6 19.2 0.5
O C:HIS220 4.7 17.7 1.0
C C:HIS220 4.8 19.5 1.0
O C:ASN219 4.8 15.5 1.0
O A:HOH495 4.8 43.2 1.0

Zinc binding site 5 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 5 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn377

b:30.8
occ:0.80
ND1 A:HIS220 2.1 13.7 0.5
O A:HOH600 2.5 42.7 1.0
CD2 A:HIS220 2.6 19.9 0.5
CG A:HIS220 3.1 20.4 0.5
CE1 A:HIS220 3.1 18.4 0.5
CG A:HIS220 3.3 21.0 0.5
CB A:HIS220 3.3 19.3 0.5
CB A:HIS220 3.6 20.2 0.5
NE2 A:HIS220 3.6 23.2 0.5
CA A:HIS220 4.0 14.3 0.5
CA A:HIS220 4.0 15.6 0.5
ZN A:ZN381 4.1 45.7 0.5
O A:HOH562 4.2 32.4 1.0
CD2 A:HIS220 4.2 20.5 0.5
NE2 A:HIS220 4.2 17.9 0.5
ND1 A:HIS220 4.4 21.7 0.5
CE1 A:HIS220 4.5 22.5 0.5
O A:HIS220 4.7 22.5 1.0
O A:ASN219 4.8 14.5 1.0
C A:HIS220 4.8 20.5 1.0

Zinc binding site 6 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 6 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn378

b:43.4
occ:1.00
O A:HIS40 2.1 17.4 1.0
ND1 A:HIS40 2.2 24.4 1.0
O A:HOH514 2.3 26.8 1.0
O A:HOH566 2.7 42.6 1.0
CE1 A:HIS40 3.0 25.7 1.0
CG A:HIS40 3.2 20.2 1.0
C A:HIS40 3.3 12.1 1.0
CB A:HIS40 3.6 11.1 1.0
O A:HOH527 4.0 21.8 1.0
CA A:HIS40 4.0 13.3 1.0
NE2 A:HIS40 4.1 21.8 1.0
CD2 A:HIS40 4.3 17.2 1.0
N A:PRO41 4.3 14.3 1.0
O A:HOH421 4.3 17.4 1.0
C A:PRO41 4.4 26.2 1.0
CA A:PRO41 4.4 21.0 1.0
N A:ASP42 4.6 27.9 1.0
N A:HIS40 4.6 12.7 1.0
O A:PRO41 4.7 21.0 1.0

Zinc binding site 7 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 7 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn379

b:51.3
occ:1.00
OD2 A:ASP83 2.3 29.1 1.0
O A:HOH558 2.5 41.5 1.0
CG A:ASP83 3.1 32.7 1.0
OD1 A:ASP83 3.2 28.7 1.0
O A:HOH524 4.5 29.2 1.0
O A:HOH449 4.5 22.8 1.0
CB A:ALA85 4.5 36.0 1.0
CB A:ASP83 4.6 32.9 1.0

Zinc binding site 8 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 8 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn380

b:85.7
occ:1.00
O A:HOH451 2.6 44.1 1.0
O A:HOH452 2.9 46.1 1.0
OE2 A:GLU329 3.0 49.0 1.0
OE1 A:GLU329 3.3 39.8 1.0
CD A:GLU329 3.5 43.7 1.0
O A:GLY328 4.0 24.0 1.0
O A:HOH508 4.5 28.1 1.0
O A:GLN326 4.8 23.9 1.0
CG A:GLU329 4.8 35.5 1.0
CE A:LYS257 4.9 32.2 1.0
NZ A:LYS257 4.9 38.8 1.0

Zinc binding site 9 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 9 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn381

b:45.7
occ:0.50
O A:HOH560 2.0 25.6 1.0
NE2 A:HIS220 2.2 23.2 0.5
O A:HOH562 2.3 32.4 1.0
CE1 A:HIS220 2.4 18.4 0.5
CD2 A:HIS220 3.0 19.9 0.5
NE2 A:HIS220 3.0 17.9 0.5
ND1 A:HIS220 3.2 13.7 0.5
CE1 A:HIS220 3.4 22.5 0.5
O A:HOH501 4.0 18.7 1.0
CD2 A:HIS220 4.0 20.5 0.5
CG A:HIS220 4.1 20.4 0.5
ZN A:ZN377 4.1 30.8 0.8
CG A:HIS220 4.2 21.0 0.5
ND1 A:HIS220 4.4 21.7 0.5
O A:HOH600 4.6 42.7 1.0
CE1 A:HIS216 4.9 17.6 1.0

Zinc binding site 10 out of 23 in 3sey

Go back to Zinc Binding Sites List in 3sey
Zinc binding site 10 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn382

b:38.8
occ:0.50
O A:HOH563 2.4 32.8 1.0
O A:HOH564 2.4 45.4 1.0
O C:HOH544 2.5 52.0 1.0
O A:HOH503 2.5 24.0 1.0
OD1 C:ASP208 3.6 55.3 1.0
OD1 A:ASN19 4.1 15.5 1.0
O A:HOH565 4.2 33.5 1.0
CB A:ALA22 4.2 13.1 1.0
CG C:ASP208 4.5 43.3 1.0
CB C:ASP208 4.5 23.1 1.0
CG A:ASN19 4.9 22.1 1.0
O A:ASN19 4.9 15.2 1.0
O C:HOH494 4.9 53.4 1.0

Reference:

A.Laganowsky, M.Zhao, A.B.Soriaga, M.R.Sawaya, D.Cascio, T.O.Yeates. An Approach to Crystallizing Proteins By Metal-Mediated Synthetic Symmetrization. Protein Sci. V. 20 1876 2011.
ISSN: ISSN 0961-8368
PubMed: 21898649
DOI: 10.1002/PRO.727
Page generated: Sat Oct 26 15:43:49 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy