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Zinc in PDB 2b0o: Crystal Structure of UPLC1 Gap Domain

Protein crystallography data

The structure of Crystal Structure of UPLC1 Gap Domain, PDB code: 2b0o was solved by S.Ismail, L.Shen, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.055, 106.716, 100.365, 90.00, 98.97, 90.00
R / Rfree (%) 18.3 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of UPLC1 Gap Domain (pdb code 2b0o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of UPLC1 Gap Domain, PDB code: 2b0o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2b0o

Go back to Zinc Binding Sites List in 2b0o
Zinc binding site 1 out of 4 in the Crystal Structure of UPLC1 Gap Domain


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 UPLC1 Gap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn698

b:17.0
occ:1.00
 SG E:CYS441 2.3 15.6 1.0
SG E:CYS464 2.3 13.5 1.0
SG E:CYS461 2.4 13.8 1.0
SG E:CYS444 2.4 17.5 1.0
CB E:CYS464 3.2 13.6 1.0
CB E:CYS444 3.2 17.1 1.0
CB E:CYS441 3.3 16.6 1.0
CB E:CYS461 3.5 16.1 1.0
N E:CYS444 3.7 14.4 1.0
N E:CYS461 3.9 16.3 1.0
CA E:CYS444 4.0 16.3 1.0
N E:CYS464 4.2 13.7 1.0
CA E:CYS461 4.3 17.3 1.0
CA E:CYS464 4.3 14.3 1.0
CB E:ALA446 4.5 20.4 1.0
O E:HOH835 4.6 31.9 1.0
C E:ASP443 4.6 15.4 1.0
C E:CYS444 4.7 17.8 1.0
CB E:ASP443 4.7 13.2 1.0
CA E:CYS441 4.7 16.6 1.0
N E:GLY445 4.8 18.5 1.0
C E:CYS461 4.8 17.8 1.0
O E:CYS461 4.9 17.4 1.0
N E:ALA446 4.9 20.1 1.0
N E:ASP443 4.9 11.9 1.0
CB E:THR460 5.0 15.1 1.0
CA E:ASP443 5.0 14.1 1.0

Zinc binding site 2 out of 4 in 2b0o

Go back to Zinc Binding Sites List in 2b0o
Zinc binding site 2 out of 4 in the Crystal Structure of UPLC1 Gap Domain


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 UPLC1 Gap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn698

b:16.8
occ:1.00
 SG F:CYS464 2.3 14.7 1.0
SG F:CYS441 2.3 15.6 1.0
SG F:CYS461 2.4 15.3 1.0
SG F:CYS444 2.4 16.4 1.0
CB F:CYS464 3.2 14.7 1.0
CB F:CYS441 3.2 16.3 1.0
CB F:CYS444 3.3 17.1 1.0
CB F:CYS461 3.5 14.3 1.0
NH1 F:ARG527 3.7 16.2 1.0
N F:CYS444 3.7 17.7 1.0
N F:CYS461 3.9 15.9 1.0
CA F:CYS444 4.0 18.5 1.0
N F:CYS464 4.1 16.6 1.0
CA F:CYS464 4.3 16.8 1.0
CA F:CYS461 4.3 15.7 1.0
CB F:ALA446 4.5 18.2 1.0
C F:ASP443 4.6 16.6 1.0
O F:HOH796 4.6 28.7 1.0
CA F:CYS441 4.6 16.8 1.0
C F:CYS444 4.7 19.6 1.0
CB F:ASP443 4.8 15.2 1.0
C F:CYS461 4.9 16.1 1.0
O F:CYS461 4.9 16.1 1.0
N F:ALA446 4.9 18.8 1.0
N F:GLY445 4.9 18.9 1.0
CZ F:ARG527 4.9 19.4 1.0
N F:ASP443 5.0 14.3 1.0
CA F:ASP443 5.0 15.3 1.0
CB F:THR460 5.0 15.8 1.0

Zinc binding site 3 out of 4 in 2b0o

Go back to Zinc Binding Sites List in 2b0o
Zinc binding site 3 out of 4 in the Crystal Structure of UPLC1 Gap Domain


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 UPLC1 Gap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn698

b:16.6
occ:1.00
 SG G:CYS464 2.2 17.9 1.0
SG G:CYS444 2.3 14.6 1.0
SG G:CYS461 2.4 15.6 1.0
SG G:CYS441 2.4 13.0 1.0
CB G:CYS464 3.2 14.4 1.0
CB G:CYS444 3.3 16.0 1.0
CB G:CYS441 3.3 13.1 1.0
CB G:CYS461 3.5 15.8 1.0
NH1 G:ARG527 3.6 18.8 1.0
N G:CYS444 3.8 15.1 1.0
N G:CYS461 3.9 15.4 1.0
CA G:CYS444 4.0 15.8 1.0
N G:CYS464 4.3 15.2 1.0
CA G:CYS461 4.3 16.0 1.0
CA G:CYS464 4.4 15.8 1.0
O G:HOH798 4.5 21.1 1.0
C G:ASP443 4.6 14.4 1.0
CB G:ALA446 4.6 19.9 1.0
C G:CYS444 4.7 17.9 1.0
CA G:CYS441 4.8 13.3 1.0
C G:CYS461 4.8 16.9 1.0
O G:CYS461 4.8 15.7 1.0
CB G:ASP443 4.9 12.8 1.0
CZ G:ARG527 4.9 20.3 1.0
N G:GLY445 4.9 17.4 1.0
N G:ASP443 4.9 13.2 1.0
CB G:THR460 5.0 14.9 1.0
CA G:ASP443 5.0 13.4 1.0
N G:ALA446 5.0 19.5 1.0

Zinc binding site 4 out of 4 in 2b0o

Go back to Zinc Binding Sites List in 2b0o
Zinc binding site 4 out of 4 in the Crystal Structure of UPLC1 Gap Domain


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 UPLC1 Gap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn698

b:22.9
occ:1.00
 SG H:CYS464 2.3 23.5 1.0
SG H:CYS461 2.3 21.8 1.0
SG H:CYS441 2.3 22.0 1.0
SG H:CYS444 2.4 22.5 1.0
CB H:CYS464 3.1 22.7 1.0
CB H:CYS441 3.3 23.4 1.0
CB H:CYS444 3.4 21.1 1.0
CB H:CYS461 3.5 20.4 1.0
NH2 H:ARG527 3.6 41.4 1.0
N H:CYS444 3.7 20.9 1.0
N H:CYS461 3.9 20.8 1.0
CA H:CYS444 4.0 23.0 1.0
N H:CYS464 4.3 24.6 1.0
CA H:CYS461 4.3 22.1 1.0
CA H:CYS464 4.3 23.7 1.0
NE H:ARG527 4.6 40.4 1.0
CB H:ALA446 4.6 24.4 1.0
CZ H:ARG527 4.6 39.1 1.0
C H:ASP443 4.6 20.5 1.0
C H:CYS444 4.7 23.3 1.0
CA H:CYS441 4.8 23.6 1.0
N H:ALA446 4.8 25.3 1.0
O H:CYS461 4.8 22.5 1.0
C H:CYS461 4.8 22.2 1.0
CB H:ASP443 4.8 20.1 1.0
N H:GLY445 4.8 24.7 1.0
N H:ASP443 4.9 19.7 1.0
CB H:THR460 5.0 20.6 1.0
CA H:ASP443 5.0 19.6 1.0

Reference:

S.Ismail, L.Shen, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park. Structural Analysis of Gap and Ankyrin Domains of UPLC1 To Be Published.
Page generated: Wed Oct 16 21:51:46 2024

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