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Zinc in PDB 4pof: Pfmcm N-Terminal Domain Without Dna

Protein crystallography data

The structure of Pfmcm N-Terminal Domain Without Dna, PDB code: 4pof was solved by C.A.Froelich, S.Kang, L.B.Epling, S.P.Bell, E.J.Enemark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.33 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 122.849, 103.064, 122.435, 90.00, 119.85, 90.00
R / Rfree (%) 25.9 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the Pfmcm N-Terminal Domain Without Dna (pdb code 4pof). 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 Without Dna, PDB code: 4pof:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4pof

Go back to Zinc Binding Sites List in 4pof
Zinc binding site 1 out of 6 in the Pfmcm N-Terminal Domain Without Dna


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 Without Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:0.3
occ:1.00
SG A:CYS142 2.3 0.7 1.0
SG A:CYS139 2.3 0.6 1.0
SG A:CYS165 2.3 0.7 1.0
SG A:CYS162 2.4 1.0 1.0
CB A:CYS139 3.2 0.1 1.0
CB A:CYS142 3.3 0.8 1.0
CB A:CYS162 3.4 0.9 1.0
CB A:CYS165 3.4 0.4 1.0
OG A:SER167 3.5 0.9 1.0
N A:CYS142 3.7 0.3 1.0
CA A:CYS142 4.0 0.5 1.0
N A:CYS165 4.0 0.8 1.0
CA A:CYS165 4.2 0.9 1.0
C A:CYS142 4.6 0.2 1.0
CB A:HIS144 4.6 0.6 1.0
CB A:SER167 4.6 1.0 1.0
N A:GLY166 4.6 0.4 1.0
CA A:CYS139 4.7 0.4 1.0
N A:SER167 4.7 0.7 1.0
N A:GLY143 4.7 0.5 1.0
C A:CYS165 4.8 0.5 1.0
CA A:CYS162 4.8 1.0 1.0
N A:HIS144 4.8 0.6 1.0
C A:ASP141 4.9 0.9 1.0
CB A:ASP141 5.0 0.8 1.0

Zinc binding site 2 out of 6 in 4pof

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Zinc binding site 2 out of 6 in the Pfmcm N-Terminal Domain Without Dna


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 Without Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:0.8
occ:1.00
SG B:CYS162 2.3 0.4 1.0
SG B:CYS142 2.3 0.5 1.0
SG B:CYS165 2.4 0.7 1.0
SG B:CYS139 2.4 0.8 1.0
CB B:CYS162 3.2 0.5 1.0
CB B:CYS139 3.3 0.0 1.0
CB B:CYS142 3.4 0.3 1.0
CB B:CYS165 3.4 0.6 1.0
OG B:SER167 3.7 0.2 1.0
N B:CYS165 3.8 0.2 1.0
N B:CYS142 4.0 0.5 1.0
CA B:CYS165 4.1 0.7 1.0
CA B:CYS142 4.2 0.9 1.0
CB B:HIS144 4.3 0.9 1.0
N B:GLY166 4.6 0.7 1.0
C B:CYS142 4.6 0.2 1.0
CA B:CYS162 4.7 0.9 1.0
N B:HIS144 4.7 0.3 1.0
CA B:CYS139 4.7 0.1 1.0
C B:CYS165 4.7 0.1 1.0
N B:GLY143 4.8 0.3 1.0
N B:SER167 4.8 0.4 1.0
CB B:SER167 4.9 0.7 1.0
CB B:GLN164 4.9 0.1 1.0
C B:GLN164 4.9 0.3 1.0

Zinc binding site 3 out of 6 in 4pof

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Zinc binding site 3 out of 6 in the Pfmcm N-Terminal Domain Without Dna


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 Without Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:0.1
occ:1.00
SG C:CYS139 2.3 0.6 1.0
SG C:CYS165 2.3 0.1 1.0
SG C:CYS142 2.3 0.2 1.0
SG C:CYS162 2.3 0.7 1.0
OG C:SER167 3.2 0.6 1.0
CB C:CYS139 3.3 0.6 1.0
CB C:CYS162 3.3 0.6 1.0
CB C:CYS142 3.3 0.6 1.0
CB C:CYS165 3.4 0.7 1.0
N C:CYS142 3.7 0.4 1.0
N C:CYS165 4.0 0.6 1.0
CA C:CYS142 4.0 0.2 1.0
CA C:CYS165 4.2 0.1 1.0
CB C:SER167 4.4 0.6 1.0
N C:SER167 4.5 0.6 1.0
N C:GLY166 4.5 0.5 1.0
C C:CYS142 4.7 0.8 1.0
C C:CYS165 4.7 0.5 1.0
CA C:CYS139 4.7 0.5 1.0
CA C:CYS162 4.8 0.4 1.0
CB C:HIS144 4.8 0.7 1.0
N C:GLY143 4.8 0.1 1.0
CB C:ASP141 4.9 0.8 1.0
C C:ASP141 4.9 0.6 1.0
N C:HIS144 5.0 1.0 1.0

Zinc binding site 4 out of 6 in 4pof

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Zinc binding site 4 out of 6 in the Pfmcm N-Terminal Domain Without Dna


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 Without Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:0.8
occ:1.00
SG D:CYS142 2.3 0.6 1.0
SG D:CYS165 2.3 0.1 1.0
SG D:CYS162 2.3 0.4 1.0
SG D:CYS139 2.3 1.0 1.0
CB D:CYS139 3.3 0.3 1.0
CB D:CYS162 3.3 0.4 1.0
CB D:CYS142 3.3 0.5 1.0
CB D:CYS165 3.4 0.3 1.0
OG D:SER167 3.5 0.3 1.0
N D:CYS142 3.8 0.2 1.0
N D:CYS165 3.9 0.8 1.0
CA D:CYS142 4.1 0.1 1.0
CA D:CYS165 4.1 0.7 1.0
N D:GLY166 4.6 0.4 1.0
CB D:HIS144 4.6 0.6 1.0
C D:CYS142 4.6 0.7 1.0
CB D:SER167 4.6 0.1 1.0
N D:SER167 4.7 0.9 1.0
C D:CYS165 4.7 0.3 1.0
CA D:CYS139 4.7 0.9 1.0
N D:GLY143 4.8 0.5 1.0
CA D:CYS162 4.8 0.7 1.0
N D:HIS144 4.8 0.9 1.0

Zinc binding site 5 out of 6 in 4pof

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Zinc binding site 5 out of 6 in the Pfmcm N-Terminal Domain Without Dna


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 Without Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:0.8
occ:1.00
SG E:CYS139 2.3 0.3 1.0
SG E:CYS142 2.3 0.9 1.0
SG E:CYS162 2.3 0.5 1.0
SG E:CYS165 2.3 0.7 1.0
CB E:CYS139 3.3 0.0 1.0
CB E:CYS162 3.3 0.9 1.0
CB E:CYS142 3.3 0.3 1.0
CB E:CYS165 3.4 0.2 1.0
OG E:SER167 3.5 0.1 1.0
N E:CYS142 3.8 0.3 1.0
N E:CYS165 3.9 0.8 1.0
CA E:CYS142 4.0 0.6 1.0
CA E:CYS165 4.1 0.6 1.0
N E:GLY166 4.6 0.8 1.0
CB E:HIS144 4.6 0.3 1.0
C E:CYS142 4.6 0.4 1.0
CB E:SER167 4.6 0.5 1.0
N E:SER167 4.7 0.6 1.0
C E:CYS165 4.7 0.8 1.0
CA E:CYS139 4.7 0.4 1.0
N E:GLY143 4.7 0.0 1.0
CA E:CYS162 4.8 0.0 1.0
N E:HIS144 4.8 0.2 1.0

Zinc binding site 6 out of 6 in 4pof

Go back to Zinc Binding Sites List in 4pof
Zinc binding site 6 out of 6 in the Pfmcm N-Terminal Domain Without Dna


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 Without Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:0.6
occ:1.00
SG F:CYS142 2.3 0.3 1.0
SG F:CYS139 2.3 0.9 1.0
SG F:CYS162 2.3 0.1 1.0
SG F:CYS165 2.3 0.3 1.0
CB F:CYS139 3.2 0.2 1.0
CB F:CYS162 3.3 0.0 1.0
CB F:CYS142 3.3 0.7 1.0
CB F:CYS165 3.4 0.6 1.0
OG F:SER167 3.5 0.5 1.0
N F:CYS142 3.8 0.9 1.0
N F:CYS165 3.9 0.1 1.0
CA F:CYS142 4.1 0.7 1.0
CA F:CYS165 4.2 0.3 1.0
CB F:HIS144 4.5 0.9 1.0
N F:GLY166 4.6 1.0 1.0
C F:CYS142 4.6 0.4 1.0
CB F:SER167 4.7 0.8 1.0
CA F:CYS139 4.7 0.2 1.0
C F:CYS165 4.7 0.7 1.0
N F:SER167 4.7 0.7 1.0
N F:GLY143 4.7 0.1 1.0
CA F:CYS162 4.8 0.8 1.0
N F:HIS144 4.8 0.6 1.0

Reference:

C.A.Froelich, S.Kang, L.B.Epling, S.P.Bell, E.J.Enemark. A Conserved Mcm Single-Stranded Dna Binding Element Is Essential For Replication Initiation Elife V. 3 01993 2014.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.01993
Page generated: Wed Dec 16 05:41:02 2020

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