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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

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Zinc binding site 1 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


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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

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Zinc binding site 2 out of 23 in the Zn-Mediated Polymer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


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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

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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

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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

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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

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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

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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

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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

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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

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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: Wed Dec 16 04:50:05 2020

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