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Zinc in PDB 4ywm: Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring

Protein crystallography data

The structure of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring, PDB code: 4ywm was solved by C.A.Froelich, E.J.Enemark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.709, 210.709, 209.638, 90.00, 90.00, 120.00
R / Rfree (%) 23.7 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring (pdb code 4ywm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring, PDB code: 4ywm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4ywm

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Zinc binding site 1 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:0.4
occ:1.00
 SG A:CYS142 2.3 87.3 1.0
SG A:CYS139 2.3 0.3 1.0
SG A:CYS165 2.3 0.3 1.0
SG A:CYS162 2.4 0.3 1.0
CB A:CYS139 3.0 0.3 1.0
CB A:CYS165 3.2 0.3 1.0
CB A:CYS142 3.2 87.3 1.0
CB A:CYS162 3.3 0.3 1.0
N A:CYS142 3.6 91.2 1.0
CA A:CYS142 3.9 91.2 1.0
N A:CYS165 4.0 0.5 1.0
CA A:CYS165 4.1 0.5 1.0
CB A:SER167 4.2 96.7 1.0
CB A:HIS144 4.2 0.5 1.0
CA A:CYS139 4.5 0.9 1.0
C A:CYS165 4.6 0.5 1.0
N A:HIS144 4.6 0.8 1.0
CB A:ASP141 4.7 0.3 1.0
N A:SER167 4.7 0.7 1.0
C A:CYS142 4.7 91.2 1.0
N A:GLY143 4.7 0.6 1.0
CA A:CYS162 4.8 0.4 1.0
C A:ASP141 4.8 0.4 1.0
N A:GLY166 4.9 0.7 1.0

Zinc binding site 2 out of 10 in 4ywm

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Zinc binding site 2 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:0.3
occ:1.00
 SG B:CYS142 2.3 91.3 1.0
SG B:CYS162 2.3 0.3 1.0
SG B:CYS165 2.3 0.1 1.0
SG B:CYS139 2.3 0.4 1.0
CB B:CYS139 3.1 0.4 1.0
CB B:CYS165 3.2 0.1 1.0
CB B:CYS142 3.3 91.3 1.0
CB B:CYS162 3.3 0.3 1.0
N B:CYS142 3.8 0.1 1.0
N B:CYS165 3.9 0.3 1.0
CA B:CYS165 4.0 0.3 1.0
CA B:CYS142 4.0 0.1 1.0
CB B:HIS144 4.1 0.6 1.0
CB B:SER167 4.3 0.4 1.0
CA B:CYS139 4.5 0.3 1.0
N B:HIS144 4.5 0.2 1.0
C B:CYS165 4.6 0.3 1.0
C B:CYS142 4.7 0.1 1.0
N B:SER167 4.7 0.4 1.0
CA B:CYS162 4.7 0.3 1.0
N B:GLY143 4.7 0.9 1.0
N B:GLY166 4.9 0.9 1.0
CB B:ASP141 4.9 96.1 1.0
C B:ASP141 4.9 0.2 1.0
CA B:HIS144 5.0 0.2 1.0

Zinc binding site 3 out of 10 in 4ywm

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Zinc binding site 3 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:70.3
occ:1.00
 SG C:CYS165 2.3 80.3 1.0
SG C:CYS139 2.3 63.5 1.0
SG C:CYS142 2.3 86.8 1.0
SG C:CYS162 2.3 60.1 1.0
CB C:CYS139 3.1 63.5 1.0
CB C:CYS165 3.1 80.3 1.0
CB C:CYS162 3.3 60.1 1.0
CB C:CYS142 3.3 86.8 1.0
N C:CYS142 3.6 70.0 1.0
CA C:CYS142 4.0 70.0 1.0
N C:CYS165 4.0 73.6 1.0
CA C:CYS165 4.0 73.6 1.0
CB C:SER167 4.1 81.1 1.0
CB C:HIS144 4.3 58.3 1.0
C C:CYS165 4.5 73.6 1.0
CA C:CYS139 4.6 64.0 1.0
N C:SER167 4.6 1.0 1.0
CB C:ASP141 4.6 76.9 1.0
C C:CYS142 4.7 70.0 1.0
CA C:CYS162 4.7 59.1 1.0
N C:HIS144 4.7 72.1 1.0
N C:GLY143 4.7 61.0 1.0
C C:ASP141 4.8 96.8 1.0
N C:GLY166 4.8 79.4 1.0
CA C:SER167 5.0 1.0 1.0

Zinc binding site 4 out of 10 in 4ywm

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Zinc binding site 4 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:0.6
occ:1.00
 SG D:CYS142 2.3 72.7 1.0
SG D:CYS162 2.3 1.0 1.0
SG D:CYS139 2.3 0.1 1.0
SG D:CYS165 2.3 0.6 1.0
CB D:CYS139 3.0 0.1 1.0
CB D:CYS165 3.2 0.6 1.0
CB D:CYS142 3.2 72.7 1.0
CB D:CYS162 3.3 1.0 1.0
N D:CYS142 3.7 85.6 1.0
N D:CYS165 4.0 0.1 1.0
CA D:CYS142 4.0 85.6 1.0
CA D:CYS165 4.1 0.1 1.0
CB D:HIS144 4.1 0.1 1.0
CB D:SER167 4.4 96.9 1.0
N D:HIS144 4.5 0.6 1.0
CA D:CYS139 4.5 0.4 1.0
C D:CYS165 4.6 0.1 1.0
C D:CYS142 4.7 85.6 1.0
N D:GLY143 4.7 0.6 1.0
CA D:CYS162 4.7 0.7 1.0
N D:SER167 4.7 0.6 1.0
CB D:ASP141 4.8 0.0 1.0
N D:GLY166 4.9 1.0 1.0
C D:ASP141 4.9 0.3 1.0
CA D:HIS144 4.9 0.6 1.0

Zinc binding site 5 out of 10 in 4ywm

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Zinc binding site 5 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:68.0
occ:1.00
 SG E:CYS165 2.3 88.0 1.0
SG E:CYS139 2.3 75.4 1.0
SG E:CYS162 2.3 57.8 1.0
SG E:CYS142 2.4 78.6 1.0
CB E:CYS139 3.1 75.4 1.0
CB E:CYS165 3.1 88.0 1.0
CB E:CYS162 3.2 57.8 1.0
CB E:CYS142 3.4 78.6 1.0
N E:CYS142 3.6 80.2 1.0
CB E:SER167 4.0 68.2 1.0
CA E:CYS165 4.0 67.6 1.0
N E:CYS165 4.1 67.6 1.0
CA E:CYS142 4.1 80.2 1.0
N E:SER167 4.4 0.2 1.0
C E:CYS165 4.5 67.6 1.0
CB E:HIS144 4.5 56.3 1.0
CB E:ASP141 4.5 96.9 1.0
CA E:CYS139 4.6 73.2 1.0
CA E:CYS162 4.7 70.1 1.0
C E:ASP141 4.8 89.8 1.0
N E:GLY166 4.8 87.2 1.0
CA E:SER167 4.8 0.2 1.0
C E:CYS142 4.8 80.2 1.0
N E:GLY143 4.8 54.0 1.0
N E:HIS144 4.9 51.9 1.0
O E:CYS165 5.0 67.6 1.0
OG E:SER167 5.0 68.2 1.0

Zinc binding site 6 out of 10 in 4ywm

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Zinc binding site 6 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:73.0
occ:1.00
 SG F:CYS165 2.3 47.5 1.0
SG F:CYS162 2.3 64.2 1.0
SG F:CYS142 2.3 70.4 1.0
SG F:CYS139 2.4 59.7 1.0
CB F:CYS139 3.2 59.7 1.0
CB F:CYS162 3.2 64.2 1.0
CB F:CYS165 3.2 47.5 1.0
CB F:CYS142 3.3 70.4 1.0
N F:CYS165 3.7 57.0 1.0
N F:CYS142 4.0 95.0 1.0
CA F:CYS165 4.0 57.0 1.0
CA F:CYS142 4.2 95.0 1.0
CB F:HIS144 4.5 71.5 1.0
CB F:SER167 4.6 69.3 1.0
C F:CYS165 4.6 57.0 1.0
CA F:CYS139 4.7 55.0 1.0
CA F:CYS162 4.7 69.6 1.0
N F:GLY143 4.7 66.1 1.0
CB F:GLN164 4.7 92.8 1.0
N F:HIS144 4.8 79.7 1.0
C F:GLN164 4.9 60.2 1.0
N F:GLY166 4.9 75.2 1.0
N F:SER167 4.9 72.8 1.0
C F:CYS142 4.9 95.0 1.0

Zinc binding site 7 out of 10 in 4ywm

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Zinc binding site 7 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:0.6
occ:1.00
 SG G:CYS165 2.3 63.4 1.0
SG G:CYS142 2.3 77.2 1.0
SG G:CYS139 2.3 69.2 1.0
SG G:CYS162 2.3 89.0 1.0
CB G:CYS139 3.1 69.2 1.0
CB G:CYS162 3.2 89.0 1.0
CB G:CYS142 3.3 77.2 1.0
CB G:CYS165 3.3 63.4 1.0
N G:CYS165 3.8 79.2 1.0
N G:CYS142 3.9 68.4 1.0
CA G:CYS165 4.1 79.2 1.0
CA G:CYS142 4.2 68.4 1.0
CB G:HIS144 4.5 90.6 1.0
CB G:SER167 4.5 63.6 1.0
CA G:CYS139 4.6 69.9 1.0
N G:GLY143 4.6 64.1 1.0
C G:CYS165 4.7 79.2 1.0
CA G:CYS162 4.7 0.0 1.0
CB G:GLN164 4.8 0.6 1.0
N G:HIS144 4.8 67.3 1.0
C G:CYS142 4.9 68.4 1.0
N G:SER167 5.0 0.3 1.0
CB G:ASP141 5.0 97.4 1.0
N G:GLY166 5.0 0.3 1.0

Zinc binding site 8 out of 10 in 4ywm

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Zinc binding site 8 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:65.5
occ:1.00
 SG H:CYS165 2.3 56.4 1.0
SG H:CYS162 2.3 68.1 1.0
SG H:CYS142 2.4 72.1 1.0
SG H:CYS139 2.4 59.0 1.0
CB H:CYS162 3.1 68.1 1.0
CB H:CYS139 3.2 59.0 1.0
CB H:CYS165 3.2 56.4 1.0
CB H:CYS142 3.4 72.1 1.0
N H:CYS165 3.7 63.6 1.0
N H:CYS142 4.0 80.8 1.0
CA H:CYS165 4.0 63.6 1.0
CA H:CYS142 4.3 80.8 1.0
CB H:SER167 4.5 80.0 1.0
CB H:HIS144 4.5 77.9 1.0
CA H:CYS162 4.6 65.4 1.0
C H:CYS165 4.6 63.6 1.0
CA H:CYS139 4.6 55.1 1.0
N H:GLY143 4.7 52.5 1.0
CB H:GLN164 4.8 92.9 1.0
N H:SER167 4.8 74.1 1.0
N H:GLY166 4.8 62.7 1.0
N H:HIS144 4.9 59.4 1.0
C H:GLN164 4.9 81.3 1.0
C H:CYS142 5.0 80.8 1.0

Zinc binding site 9 out of 10 in 4ywm

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Zinc binding site 9 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:1.0
occ:1.00
 SG I:CYS165 2.3 61.5 1.0
SG I:CYS139 2.3 77.1 1.0
SG I:CYS142 2.3 88.8 1.0
SG I:CYS162 2.3 83.3 1.0
CB I:CYS139 3.1 77.1 1.0
CB I:CYS162 3.2 83.3 1.0
CB I:CYS142 3.3 88.8 1.0
CB I:CYS165 3.3 61.5 1.0
N I:CYS142 3.9 0.7 1.0
N I:CYS165 3.9 71.7 1.0
CA I:CYS165 4.1 71.7 1.0
CA I:CYS142 4.2 0.7 1.0
CB I:SER167 4.4 91.5 1.0
CA I:CYS139 4.5 81.6 1.0
CB I:HIS144 4.6 0.8 1.0
N I:GLY143 4.7 81.0 1.0
CA I:CYS162 4.7 82.3 1.0
C I:CYS165 4.7 71.7 1.0
CB I:ASP141 4.9 92.9 1.0
N I:SER167 4.9 0.6 1.0
N I:HIS144 4.9 99.0 1.0
C I:CYS142 4.9 0.7 1.0
CB I:GLN164 5.0 0.6 1.0
N I:GLY166 5.0 0.2 1.0

Zinc binding site 10 out of 10 in 4ywm

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Zinc binding site 10 out of 10 in the Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Pyrococcus Furiosus Mcm N-Terminal Domain Beta-Turn Triple Mutant Pentameric Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:0.4
occ:1.00
 SG J:CYS165 2.3 68.1 1.0
SG J:CYS162 2.3 95.7 1.0
SG J:CYS139 2.3 74.5 1.0
SG J:CYS142 2.3 0.6 1.0
CB J:CYS139 3.1 74.5 1.0
CB J:CYS162 3.2 95.7 1.0
CB J:CYS165 3.3 68.1 1.0
CB J:CYS142 3.4 0.6 1.0
N J:CYS165 3.8 91.8 1.0
N J:CYS142 4.0 0.9 1.0
CA J:CYS165 4.0 91.8 1.0
CA J:CYS142 4.2 0.9 1.0
CB J:SER167 4.5 0.7 1.0
CB J:HIS144 4.6 0.9 1.0
CA J:CYS139 4.6 75.3 1.0
C J:CYS165 4.7 91.8 1.0
CA J:CYS162 4.7 0.8 1.0
N J:GLY143 4.7 81.5 1.0
CB J:GLN164 4.8 0.7 1.0
N J:SER167 4.9 0.8 1.0
N J:HIS144 4.9 95.7 1.0
N J:GLY166 4.9 0.3 1.0
C J:CYS142 4.9 0.9 1.0
CB J:ASP141 5.0 96.5 1.0
C J:GLN164 5.0 0.0 1.0

Reference:

C.A.Froelich, A.Nourse, E.J.Enemark. Mcm Ring Hexamerization Is A Prerequisite For Dna-Binding. Nucleic Acids Res. V. 43 9553 2015.
ISSN: ESSN 1362-4962
PubMed: 26365238
DOI: 10.1093/NAR/GKV914
Page generated: Wed Aug 20 23:55:29 2025

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