Atomistry » Zinc » PDB 5jwl-5k8c » 5k6v
Atomistry »
  Zinc »
    PDB 5jwl-5k8c »
      5k6v »

Zinc in PDB 5k6v: Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2

Protein crystallography data

The structure of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2, PDB code: 5k6v was solved by X.Jin, K.M.Goodman, S.Mannepalli, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.74 / 3.21
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.189, 158.189, 53.525, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 (pdb code 5k6v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2, PDB code: 5k6v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5k6v

Go back to Zinc Binding Sites List in 5k6v
Zinc binding site 1 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:81.9
occ:1.00
ND1 A:HIS18 2.6 54.9 1.0
CE1 A:HIS18 3.1 63.5 1.0
CG A:HIS18 3.6 57.6 1.0
NE2 A:HIS18 4.1 67.7 1.0
CB A:HIS18 4.2 38.7 1.0
CD2 A:HIS18 4.4 64.1 1.0
ND2 A:ASN22 4.6 57.5 1.0
CA A:HIS18 4.9 38.0 1.0

Zinc binding site 2 out of 6 in 5k6v

Go back to Zinc Binding Sites List in 5k6v
Zinc binding site 2 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:0.7
occ:1.00
O A:HOH603 2.6 37.9 1.0
OD2 A:ASP376 2.6 65.1 1.0
OD1 A:ASP376 3.0 74.9 1.0
CG A:ASP376 3.1 70.0 1.0
CB A:ASP376 4.5 62.3 1.0

Zinc binding site 3 out of 6 in 5k6v

Go back to Zinc Binding Sites List in 5k6v
Zinc binding site 3 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:1.0
occ:1.00
OD2 A:ASP186 2.4 0.3 1.0
CD2 A:HIS190 2.9 1.0 1.0
CG A:ASP186 3.1 1.0 1.0
CB A:HIS190 3.3 0.9 1.0
CG A:HIS190 3.4 0.6 1.0
OD1 A:ASP186 3.6 0.0 1.0
N A:HIS190 3.7 0.8 1.0
O A:THR187 3.8 1.0 1.0
CA A:HIS190 4.0 0.3 1.0
CB A:ASP186 4.1 0.9 1.0
NE2 A:HIS190 4.1 0.4 1.0
CE1 A:HIS108 4.2 0.9 1.0
O A:GLN106 4.2 84.8 1.0
N A:THR189 4.5 0.9 1.0
O A:ASP186 4.6 0.7 1.0
C A:THR189 4.6 0.0 1.0
ND1 A:HIS190 4.7 0.6 1.0
CB A:THR189 4.7 0.3 1.0
C A:ASP186 4.7 0.7 1.0
ND1 A:HIS108 4.8 0.4 1.0
C A:THR187 4.8 0.1 1.0
CA A:THR189 4.9 0.7 1.0

Zinc binding site 4 out of 6 in 5k6v

Go back to Zinc Binding Sites List in 5k6v
Zinc binding site 4 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:0.4
occ:1.00
CD2 A:HIS108 3.0 0.3 1.0
CG A:HIS108 3.6 0.5 1.0
CB A:HIS108 3.6 85.9 1.0
CA A:HIS108 3.8 76.0 1.0
N A:ALA109 3.8 55.5 1.0
ND2 A:ASN220 4.0 72.3 1.0
CE A:MET193 4.2 88.6 1.0
NE2 A:HIS108 4.2 0.5 1.0
C A:HIS108 4.4 56.5 1.0
CG2 A:ILE196 4.4 81.2 1.0
CG A:ASN220 4.7 60.6 1.0
ND1 A:HIS108 4.8 0.4 1.0
CB A:ALA109 4.9 53.2 1.0
CD1 A:ILE196 4.9 74.0 1.0
CA A:ALA109 5.0 51.9 1.0

Zinc binding site 5 out of 6 in 5k6v

Go back to Zinc Binding Sites List in 5k6v
Zinc binding site 5 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn511

b:81.2
occ:1.00
NE2 A:HIS180 2.3 49.1 1.0
OD2 A:ASP99 2.4 80.7 1.0
CE1 A:HIS180 3.0 49.4 1.0
CG A:ASP99 3.1 70.5 1.0
CD2 A:HIS180 3.4 58.5 1.0
CB A:ASP99 3.5 48.8 1.0
OD1 A:ASP99 4.2 87.5 1.0
ND1 A:HIS180 4.2 48.7 1.0
CD2 A:PHE178 4.4 45.0 1.0
CG A:HIS180 4.4 48.1 1.0
CB A:PHE178 4.5 42.1 1.0
CG A:PHE178 4.9 42.6 1.0
CA A:ASP99 5.0 48.2 1.0

Zinc binding site 6 out of 6 in 5k6v

Go back to Zinc Binding Sites List in 5k6v
Zinc binding site 6 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn512

b:0.3
occ:1.00
CE1 A:HIS243 3.1 0.1 1.0
NE2 A:HIS243 3.4 0.1 1.0
ND1 A:HIS243 4.0 0.2 1.0
CD2 A:HIS243 4.5 0.6 1.0
CG A:HIS243 4.8 87.5 1.0

Reference:

K.M.Goodman, M.Yamagata, X.Jin, S.Mannepalli, P.S.Katsamba, G.Ahlsen, A.P.Sergeeva, B.Honig, J.R.Sanes, L.Shapiro. Molecular Basis of Sidekick-Mediated Cell-Cell Adhesion and Specificity. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27644106
DOI: 10.7554/ELIFE.19058
Page generated: Wed Dec 16 06:26:23 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy