Zinc in PDB 6mii: Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex

Enzymatic activity of Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex

All present enzymatic activity of Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex, PDB code: 6mii was solved by E.J.Enemark, M.Meagher, L.B.Epling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.70 / 3.15
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 186.665, 186.665, 281.489, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.1

Other elements in 6mii:

The structure of Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex (pdb code 6mii). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex, PDB code: 6mii:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6mii

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Zinc binding site 1 out of 6 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


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 Minichromosome Maintenance Protein Mcm/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:0.5
occ:1.00
 SG A:CYS174 2.1 0.4 1.0
SG A:CYS149 2.1 0.8 1.0
SG A:CYS171 2.1 0.4 1.0
ND1 A:HIS144 2.1 0.3 1.0
CB A:CYS149 2.8 0.8 1.0
CB A:CYS171 2.9 0.1 1.0
CE1 A:HIS144 3.1 0.3 1.0
CG A:HIS144 3.1 0.8 1.0
CB A:HIS144 3.4 0.0 1.0
CB A:CYS174 3.5 0.6 1.0
NE2 A:HIS144 4.2 0.2 1.0
CD2 A:HIS144 4.2 0.9 1.0
N A:CYS174 4.2 0.8 1.0
CA A:CYS149 4.3 0.3 1.0
CA A:CYS171 4.3 1.0 1.0
O A:LYS176 4.3 0.2 1.0
CA A:CYS174 4.5 0.0 1.0
C A:CYS171 4.8 0.5 1.0
N A:LYS176 4.9 0.0 1.0
C A:LYS173 4.9 0.4 1.0
CA A:HIS144 4.9 0.8 1.0
O A:CYS171 4.9 0.0 1.0
N A:GLY175 4.9 0.6 1.0
CB A:LYS176 5.0 0.5 1.0

Zinc binding site 2 out of 6 in 6mii

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Zinc binding site 2 out of 6 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


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 Minichromosome Maintenance Protein Mcm/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:0.1
occ:1.00
 SG B:CYS174 2.1 0.0 1.0
SG B:CYS171 2.1 0.7 1.0
SG B:CYS149 2.1 0.7 1.0
ND1 B:HIS144 2.1 0.9 1.0
CB B:CYS149 2.9 0.6 1.0
CB B:CYS171 3.0 0.9 1.0
CE1 B:HIS144 3.0 0.1 1.0
CG B:HIS144 3.1 0.5 1.0
CB B:HIS144 3.5 0.5 1.0
CB B:CYS174 3.6 1.0 1.0
N B:CYS174 4.1 0.5 1.0
NE2 B:HIS144 4.2 0.5 1.0
CD2 B:HIS144 4.2 0.2 1.0
CA B:CYS149 4.3 1.0 1.0
CA B:CYS171 4.4 0.1 1.0
CA B:CYS174 4.4 0.5 1.0
O B:LYS176 4.4 0.8 1.0
C B:LYS173 4.7 0.7 1.0
CB B:LYS173 4.7 0.3 1.0
N B:GLY175 4.9 0.1 1.0
CA B:HIS144 5.0 0.1 1.0

Zinc binding site 3 out of 6 in 6mii

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Zinc binding site 3 out of 6 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


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 Minichromosome Maintenance Protein Mcm/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2002

b:0.6
occ:1.00
 SG C:CYS174 2.1 1.0 1.0
SG C:CYS149 2.1 0.9 1.0
ND1 C:HIS144 2.1 0.4 1.0
SG C:CYS171 2.1 0.8 1.0
CB C:CYS171 2.9 0.9 1.0
CG C:HIS144 3.0 0.6 1.0
CB C:CYS149 3.1 0.4 1.0
CE1 C:HIS144 3.1 0.9 1.0
CB C:HIS144 3.3 1.0 1.0
CB C:CYS174 3.4 0.2 1.0
N C:CYS174 4.2 0.9 1.0
CD2 C:HIS144 4.2 0.8 1.0
O C:LYS176 4.2 0.0 1.0
NE2 C:HIS144 4.2 0.4 1.0
CA C:CYS174 4.4 1.0 1.0
CA C:CYS171 4.4 0.2 1.0
CA C:CYS149 4.5 0.1 1.0
CA C:HIS144 4.8 0.6 1.0
N C:GLY175 4.9 0.8 1.0
C C:LYS173 4.9 0.2 1.0
N C:LYS176 4.9 0.6 1.0
C C:CYS171 4.9 0.6 1.0

Zinc binding site 4 out of 6 in 6mii

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Zinc binding site 4 out of 6 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


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 Minichromosome Maintenance Protein Mcm/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.3
occ:1.00
 ND1 D:HIS144 2.1 0.0 1.0
SG D:CYS171 2.1 0.4 1.0
SG D:CYS149 2.1 0.5 1.0
SG D:CYS174 2.1 0.4 1.0
CB D:CYS149 2.7 1.0 1.0
CE1 D:HIS144 2.9 0.5 1.0
CG D:HIS144 3.2 0.2 1.0
CB D:CYS171 3.2 0.1 1.0
CB D:CYS174 3.5 0.0 1.0
CB D:HIS144 3.6 0.8 1.0
N D:CYS174 4.0 0.7 1.0
NE2 D:HIS144 4.1 0.9 1.0
CA D:CYS149 4.1 0.6 1.0
CD2 D:HIS144 4.2 0.5 1.0
CA D:CYS174 4.3 0.1 1.0
CB D:LYS173 4.5 0.0 1.0
O D:LYS176 4.5 0.4 1.0
C D:LYS173 4.6 0.6 1.0
CA D:CYS171 4.6 0.0 1.0
N D:GLY175 4.9 0.6 1.0
N D:LYS173 4.9 0.9 1.0
CA D:LYS173 4.9 1.0 1.0
N D:CYS149 4.9 0.5 1.0

Zinc binding site 5 out of 6 in 6mii

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Zinc binding site 5 out of 6 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn2002

b:0.4
occ:1.00
 ND1 E:HIS144 2.1 0.3 1.0
SG E:CYS149 2.1 0.7 1.0
SG E:CYS171 2.1 0.0 1.0
SG E:CYS174 2.1 0.2 1.0
CB E:CYS149 2.7 0.0 1.0
CB E:CYS171 2.9 0.7 1.0
CE1 E:HIS144 3.0 1.0 1.0
CG E:HIS144 3.1 0.8 1.0
CB E:HIS144 3.4 0.6 1.0
CB E:CYS174 3.6 0.0 1.0
CA E:CYS149 4.1 0.2 1.0
N E:CYS174 4.1 0.4 1.0
NE2 E:HIS144 4.1 0.6 1.0
CD2 E:HIS144 4.2 0.5 1.0
CA E:CYS171 4.3 0.7 1.0
CA E:CYS174 4.5 0.1 1.0
CB E:LYS173 4.6 0.8 1.0
C E:LYS173 4.7 0.6 1.0
C E:CYS171 4.8 0.4 1.0
O E:LYS176 4.8 0.6 1.0
N E:CYS149 4.9 0.7 1.0
O E:CYS171 4.9 0.9 1.0
CA E:HIS144 4.9 0.5 1.0
N E:LYS173 5.0 0.2 1.0
C E:CYS149 5.0 0.0 1.0

Zinc binding site 6 out of 6 in 6mii

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Zinc binding site 6 out of 6 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2002

b:0.3
occ:1.00
 SG F:CYS149 2.1 0.1 1.0
ND1 F:HIS144 2.1 0.3 1.0
SG F:CYS171 2.1 0.7 1.0
SG F:CYS174 2.1 0.8 1.0
CB F:CYS171 2.9 0.9 1.0
CB F:CYS149 3.0 0.7 1.0
CG F:HIS144 3.1 0.1 1.0
CE1 F:HIS144 3.1 0.8 1.0
CB F:HIS144 3.4 0.9 1.0
CB F:CYS174 3.5 0.4 1.0
N F:CYS174 4.1 0.0 1.0
NE2 F:HIS144 4.2 0.8 1.0
CD2 F:HIS144 4.2 0.3 1.0
O F:LYS176 4.2 0.7 1.0
CA F:CYS149 4.4 0.4 1.0
CA F:CYS171 4.4 0.3 1.0
CA F:CYS174 4.4 0.2 1.0
C F:LYS173 4.8 0.8 1.0
CA F:HIS144 4.9 0.7 1.0
CB F:LYS173 4.9 0.7 1.0
C F:CYS171 4.9 0.2 1.0
N F:GLY175 4.9 0.9 1.0

Reference:

M.Meagher, L.B.Epling, E.J.Enemark. Dna Translocation Mechanism of the Mcm Complex and Implications For Replication Initiation. Nat Commun V. 10 3117 2019.
ISSN: ESSN 2041-1723
PubMed: 31308367
DOI: 10.1038/S41467-019-11074-3
Page generated: Wed Dec 16 12:19:49 2020

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