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Zinc in PDB 5iy0: Pfmcm N-Terminal Domain Double Hexamer

Protein crystallography data

The structure of Pfmcm N-Terminal Domain Double Hexamer, PDB code: 5iy0 was solved by M.Meagher, E.J.Enemark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 211.427, 122.610, 111.892, 90.00, 92.35, 90.00
R / Rfree (%) 20.5 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Pfmcm N-Terminal Domain Double Hexamer (pdb code 5iy0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Pfmcm N-Terminal Domain Double Hexamer, PDB code: 5iy0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5iy0

Go back to Zinc Binding Sites List in 5iy0
Zinc binding site 1 out of 6 in the Pfmcm N-Terminal Domain Double Hexamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pfmcm N-Terminal Domain Double Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:76.4
occ:1.00
 SG A:CYS142 2.2 74.4 1.0
SG A:CYS165 2.2 68.0 1.0
SG A:CYS139 2.4 73.6 1.0
SG A:CYS162 2.4 68.7 1.0
CB A:CYS165 3.1 67.6 1.0
CB A:CYS162 3.2 66.5 1.0
CB A:CYS139 3.2 73.9 1.0
CB A:CYS142 3.2 75.5 1.0
N A:CYS142 3.7 68.7 1.0
N A:CYS165 3.7 70.7 1.0
CA A:CYS165 4.0 69.3 1.0
CA A:CYS142 4.0 70.5 1.0
CB A:HIS144 4.5 72.6 1.0
OG A:SER167 4.6 78.7 1.0
C A:ASP141 4.6 70.4 1.0
C A:CYS142 4.6 72.0 1.0
CA A:CYS162 4.7 71.0 1.0
CA A:CYS139 4.7 71.0 1.0
CB A:ASP141 4.7 70.5 1.0
CB A:GLN164 4.7 79.3 1.0
C A:CYS165 4.8 70.8 1.0
N A:HIS144 4.9 76.0 1.0
C A:GLN164 4.9 76.1 1.0
N A:GLY143 4.9 75.7 1.0
N A:GLY166 4.9 70.7 1.0

Zinc binding site 2 out of 6 in 5iy0

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Zinc binding site 2 out of 6 in the Pfmcm N-Terminal Domain Double Hexamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pfmcm N-Terminal Domain Double Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:70.3
occ:1.00
 SG B:CYS165 2.3 64.6 1.0
SG B:CYS142 2.3 69.4 1.0
SG B:CYS139 2.3 67.0 1.0
SG B:CYS162 2.5 66.2 1.0
CB B:CYS165 3.1 65.8 1.0
CB B:CYS139 3.2 67.7 1.0
CB B:CYS162 3.2 61.5 1.0
CB B:CYS142 3.3 71.4 1.0
N B:CYS142 3.7 67.9 1.0
N B:CYS165 3.8 69.9 1.0
CA B:CYS142 4.0 69.2 1.0
CA B:CYS165 4.0 67.4 1.0
OG B:SER167 4.5 71.3 1.0
C B:ASP141 4.5 67.0 1.0
CB B:HIS144 4.6 72.9 1.0
CA B:CYS139 4.6 69.4 1.0
CB B:ASP141 4.6 64.3 1.0
CA B:CYS162 4.7 64.2 1.0
C B:CYS142 4.7 71.3 1.0
C B:CYS165 4.9 67.4 1.0
CB B:GLN164 4.9 76.8 1.0
N B:HIS144 4.9 74.4 1.0
N B:GLY143 4.9 75.1 1.0
CA B:ASP141 4.9 66.9 1.0
N B:GLY166 5.0 64.5 1.0
C B:GLN164 5.0 74.6 1.0

Zinc binding site 3 out of 6 in 5iy0

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Zinc binding site 3 out of 6 in the Pfmcm N-Terminal Domain Double Hexamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pfmcm N-Terminal Domain Double Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:70.3
occ:1.00
 SG C:CYS165 2.2 68.3 1.0
SG C:CYS142 2.2 70.5 1.0
SG C:CYS162 2.3 74.6 1.0
SG C:CYS139 2.4 66.1 1.0
CB C:CYS165 3.0 72.3 1.0
CB C:CYS162 3.1 68.4 1.0
CB C:CYS139 3.2 66.8 1.0
CB C:CYS142 3.4 71.3 1.0
N C:CYS165 3.6 69.8 1.0
N C:CYS142 3.9 66.8 1.0
CA C:CYS165 3.9 72.0 1.0
CA C:CYS142 4.1 68.8 1.0
CB C:HIS144 4.5 71.3 1.0
CA C:CYS162 4.5 67.0 1.0
OG C:SER167 4.6 84.8 1.0
CB C:GLN164 4.6 72.6 1.0
CA C:CYS139 4.7 67.1 1.0
C C:CYS165 4.8 74.2 1.0
C C:ASP141 4.8 68.5 1.0
C C:CYS142 4.8 70.6 1.0
C C:GLN164 4.8 72.3 1.0
CB C:ASP141 4.8 72.6 1.0
N C:GLY166 4.8 76.9 1.0
N C:HIS144 4.9 75.4 1.0

Zinc binding site 4 out of 6 in 5iy0

Go back to Zinc Binding Sites List in 5iy0
Zinc binding site 4 out of 6 in the Pfmcm N-Terminal Domain Double Hexamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pfmcm N-Terminal Domain Double Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:70.3
occ:1.00
 SG D:CYS165 2.2 70.8 1.0
SG D:CYS139 2.2 72.5 1.0
SG D:CYS142 2.3 74.2 1.0
SG D:CYS162 2.5 72.1 1.0
CB D:CYS165 3.1 68.7 1.0
CB D:CYS162 3.1 67.3 1.0
CB D:CYS139 3.2 72.5 1.0
CB D:CYS142 3.3 71.1 1.0
N D:CYS142 3.7 67.3 1.0
N D:CYS165 3.8 72.3 1.0
CA D:CYS165 4.0 69.3 1.0
CA D:CYS142 4.0 69.0 1.0
OG D:SER167 4.4 78.9 1.0
C D:ASP141 4.5 67.6 1.0
CB D:ASP141 4.5 66.5 1.0
CA D:CYS139 4.6 71.8 1.0
CA D:CYS162 4.6 69.2 1.0
CB D:HIS144 4.7 69.2 1.0
C D:CYS142 4.7 70.4 1.0
C D:CYS165 4.8 68.7 1.0
CA D:ASP141 4.9 69.1 1.0
N D:GLY166 4.9 69.8 1.0
CB D:GLN164 4.9 76.4 1.0
N D:GLY143 5.0 73.7 1.0
N D:HIS144 5.0 71.9 1.0
N D:ASP141 5.0 76.2 1.0

Zinc binding site 5 out of 6 in 5iy0

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Zinc binding site 5 out of 6 in the Pfmcm N-Terminal Domain Double Hexamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pfmcm N-Terminal Domain Double Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:74.5
occ:1.00
 SG E:CYS165 2.1 70.2 1.0
SG E:CYS139 2.3 67.8 1.0
SG E:CYS142 2.4 70.8 1.0
SG E:CYS162 2.4 68.7 1.0
CB E:CYS165 3.0 68.5 1.0
CB E:CYS162 3.1 63.0 1.0
CB E:CYS139 3.2 66.6 1.0
CB E:CYS142 3.4 71.1 1.0
N E:CYS142 3.7 66.0 1.0
N E:CYS165 3.8 70.1 1.0
CA E:CYS165 3.9 67.5 1.0
CA E:CYS142 4.1 68.2 1.0
OG E:SER167 4.3 72.9 1.0
CB E:ASP141 4.5 68.1 1.0
C E:ASP141 4.6 69.8 1.0
CA E:CYS162 4.6 64.8 1.0
CA E:CYS139 4.7 65.0 1.0
C E:CYS165 4.7 66.3 1.0
CB E:HIS144 4.7 66.8 1.0
C E:CYS142 4.8 67.0 1.0
N E:GLY166 4.8 67.0 1.0
CB E:GLN164 4.9 77.6 1.0
CA E:ASP141 4.9 71.0 1.0
C E:GLN164 5.0 75.2 1.0

Zinc binding site 6 out of 6 in 5iy0

Go back to Zinc Binding Sites List in 5iy0
Zinc binding site 6 out of 6 in the Pfmcm N-Terminal Domain Double Hexamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pfmcm N-Terminal Domain Double Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:72.2
occ:1.00
 SG F:CYS142 2.2 79.5 1.0
SG F:CYS165 2.3 68.5 1.0
SG F:CYS162 2.3 67.0 1.0
SG F:CYS139 2.3 72.6 1.0
CB F:CYS165 3.1 70.2 1.0
CB F:CYS162 3.2 68.3 1.0
CB F:CYS139 3.2 73.1 1.0
CB F:CYS142 3.3 76.3 1.0
N F:CYS165 3.7 71.3 1.0
N F:CYS142 3.8 70.0 1.0
CA F:CYS142 4.0 72.3 1.0
CA F:CYS165 4.0 69.7 1.0
CB F:HIS144 4.4 74.6 1.0
CA F:CYS139 4.6 74.6 1.0
CA F:CYS162 4.6 68.4 1.0
OG F:SER167 4.6 74.9 1.0
C F:CYS142 4.7 73.3 1.0
C F:ASP141 4.7 70.3 1.0
CB F:GLN164 4.7 76.7 1.0
CB F:ASP141 4.8 73.2 1.0
N F:HIS144 4.8 73.3 1.0
C F:CYS165 4.9 69.0 1.0
C F:GLN164 4.9 77.6 1.0
N F:GLY143 4.9 77.8 1.0
N F:GLY166 5.0 66.2 1.0

Reference:

M.Meagher, E.J.Enemark. Structure of A Double Hexamer of the Pyrococcus Furiosus Minichromosome Maintenance Protein N-Terminal Domain. Acta Crystallogr.,Sect.F V. 72 545 2016.
ISSN: ESSN 2053-230X
PubMed: 27380371
DOI: 10.1107/S2053230X1600858X
Page generated: Wed Dec 16 06:22:58 2020

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