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Fluorine 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:

Magnesium (Mg) 6 atoms
Zinc (Zn) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex, PDB code: 6mii:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 6mii

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Fluorine binding site 1 out of 9 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F2001

b:0.2
occ:1.00
 F1 A:08T2001 0.0 0.2 1.0
BE A:08T2001 1.5 0.0 1.0
MG A:MG2003 1.9 0.1 1.0
O3B A:08T2001 2.5 93.0 1.0
F2 A:08T2001 2.5 0.8 1.0
F3 A:08T2001 2.6 0.0 1.0
O A:HOH2101 2.7 79.0 1.0
O2B A:08T2001 2.7 93.6 1.0
O A:HOH2103 2.7 72.2 1.0
O A:HOH2102 2.9 78.3 1.0
PB A:08T2001 3.1 86.9 1.0
NH2 B:ARG473 3.3 89.0 1.0
NH2 B:ARG560 3.5 82.6 1.0
OE2 A:GLU405 3.8 0.8 1.0
NH1 B:ARG473 3.8 84.9 1.0
CZ B:ARG473 3.9 85.7 1.0
OG A:SER347 3.9 95.6 1.0
O3A A:08T2001 3.9 83.0 1.0
O1B A:08T2001 4.4 90.0 1.0
O1A A:08T2001 4.5 80.5 1.0
CD A:GLU405 4.5 0.5 1.0
CZ B:ARG560 4.6 78.6 1.0
ND2 A:ASN448 4.8 99.8 1.0
PA A:08T2001 4.8 77.5 1.0
NH1 B:ARG560 4.8 77.2 1.0
CB A:SER347 4.8 90.5 1.0
NE B:ARG473 5.0 87.7 1.0

Fluorine binding site 2 out of 9 in 6mii

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Fluorine binding site 2 out of 9 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


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Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
A:F2001

b:0.8
occ:1.00
 F2 A:08T2001 0.0 0.8 1.0
BE A:08T2001 1.5 0.0 1.0
O3B A:08T2001 2.4 93.0 1.0
F1 A:08T2001 2.5 0.2 1.0
F3 A:08T2001 2.6 0.0 1.0
NH1 B:ARG473 2.9 84.9 1.0
NH1 B:ARG560 3.4 77.2 1.0
NH2 B:ARG560 3.5 82.6 1.0
CA A:PRO342 3.6 84.9 1.0
CB A:PRO342 3.6 87.7 1.0
NH2 B:ARG473 3.7 89.0 1.0
CZ B:ARG473 3.7 85.7 1.0
N A:GLY343 3.9 81.9 1.0
CZ B:ARG560 3.9 78.6 1.0
ND2 A:ASN448 3.9 99.8 1.0
PB A:08T2001 3.9 86.9 1.0
CB B:THR469 4.2 0.3 1.0
C A:PRO342 4.3 83.5 1.0
O B:THR469 4.4 0.9 1.0
MG A:MG2003 4.4 0.1 1.0
O2B A:08T2001 4.4 93.6 1.0
CA B:THR469 4.5 0.9 1.0
OD1 A:ASN448 4.5 1.0 1.0
CG2 B:THR469 4.5 0.5 1.0
O3A A:08T2001 4.6 83.0 1.0
CG A:ASN448 4.6 0.9 1.0
O A:HOH2103 4.7 72.2 1.0
N A:PRO342 4.8 87.8 1.0
O1B A:08T2001 4.8 90.0 1.0
OE2 A:GLU405 4.8 0.8 1.0
O A:HOH2101 4.8 79.0 1.0
C B:THR469 4.9 0.1 1.0
NE B:ARG473 5.0 87.7 1.0
OG B:SER472 5.0 90.2 1.0

Fluorine binding site 3 out of 9 in 6mii

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Fluorine binding site 3 out of 9 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
A:F2001

b:0.0
occ:1.00
 F3 A:08T2001 0.0 0.0 1.0
BE A:08T2001 1.5 0.0 1.0
ND2 A:ASN448 2.3 99.8 1.0
O3B A:08T2001 2.5 93.0 1.0
F1 A:08T2001 2.6 0.2 1.0
F2 A:08T2001 2.6 0.8 1.0
O A:HOH2103 3.0 72.2 1.0
CE A:LYS346 3.3 78.6 1.0
CG A:ASN448 3.3 0.9 1.0
NZ A:LYS346 3.4 93.1 1.0
PB A:08T2001 3.4 86.9 1.0
O2B A:08T2001 3.5 93.6 1.0
OD1 A:ASN448 3.5 1.0 1.0
MG A:MG2003 3.6 0.1 1.0
O1B A:08T2001 4.0 90.0 1.0
CA A:PRO342 4.3 84.9 1.0
OE2 A:GLU405 4.4 0.8 1.0
O A:ASP341 4.4 85.1 1.0
OE1 A:GLU405 4.5 0.9 1.0
CD A:GLU405 4.7 0.5 1.0
CB A:ASN448 4.7 0.3 1.0
O A:HOH2102 4.7 78.3 1.0
N A:GLY343 4.7 81.9 1.0
O A:GLY340 4.8 90.9 1.0
CD A:LYS346 4.8 80.4 1.0
O3A A:08T2001 4.8 83.0 1.0
CB A:PRO342 4.9 87.7 1.0
N A:PRO342 5.0 87.8 1.0
O A:HOH2101 5.0 79.0 1.0

Fluorine binding site 4 out of 9 in 6mii

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Fluorine binding site 4 out of 9 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F2001

b:0.3
occ:1.00
 F1 B:08T2001 0.0 0.3 1.0
BE B:08T2001 1.5 97.7 1.0
MG B:MG2003 2.0 0.5 1.0
O3B B:08T2001 2.5 90.6 1.0
F2 B:08T2001 2.5 97.8 1.0
F3 B:08T2001 2.6 98.2 1.0
O2B B:08T2001 2.6 0.9 1.0
O C:HOH2101 2.7 84.8 1.0
O B:HOH2102 2.7 73.3 1.0
O B:HOH2101 2.9 76.3 1.0
PB B:08T2001 3.1 92.3 1.0
NH2 C:ARG473 3.1 0.4 1.0
NH2 C:ARG560 3.3 0.0 1.0
CZ C:ARG473 3.6 0.7 1.0
NH1 C:ARG473 3.6 94.3 1.0
OE2 B:GLU405 3.9 0.4 1.0
OG B:SER347 3.9 0.4 1.0
O3A B:08T2001 4.0 89.9 1.0
O1B B:08T2001 4.3 87.2 1.0
CZ C:ARG560 4.5 0.6 1.0
O1A B:08T2001 4.5 88.2 1.0
CD B:GLU405 4.5 0.6 1.0
NE C:ARG473 4.7 0.4 1.0
CB B:SER347 4.7 97.7 1.0
PA B:08T2001 4.8 84.2 1.0
NH1 C:ARG560 4.9 0.4 1.0
OE1 B:GLU405 5.0 0.3 1.0

Fluorine binding site 5 out of 9 in 6mii

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Fluorine binding site 5 out of 9 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F2001

b:97.8
occ:1.00
 F2 B:08T2001 0.0 97.8 1.0
BE B:08T2001 1.5 97.7 1.0
O3B B:08T2001 2.4 90.6 1.0
F1 B:08T2001 2.5 0.3 1.0
F3 B:08T2001 2.5 98.2 1.0
NH1 C:ARG473 2.6 94.3 1.0
NH2 C:ARG560 3.0 0.0 1.0
NH1 C:ARG560 3.2 0.4 1.0
CZ C:ARG473 3.5 0.7 1.0
CZ C:ARG560 3.5 0.6 1.0
CB B:PRO342 3.5 98.9 1.0
CA B:PRO342 3.6 99.8 1.0
NH2 C:ARG473 3.6 0.4 1.0
N B:GLY343 3.7 92.8 1.0
PB B:08T2001 3.9 92.3 1.0
C B:PRO342 4.1 99.5 1.0
O C:THR469 4.2 0.8 1.0
O2B B:08T2001 4.4 0.9 1.0
MG B:MG2003 4.4 0.5 1.0
ND2 B:ASN448 4.5 0.1 1.0
CB C:THR469 4.6 0.3 1.0
O3A B:08T2001 4.6 89.9 1.0
CA C:THR469 4.6 0.9 1.0
NE C:ARG473 4.7 0.4 1.0
OG C:SER472 4.7 0.9 1.0
O B:HOH2102 4.7 73.3 1.0
CA B:GLY343 4.7 93.9 1.0
O1B B:08T2001 4.8 87.2 1.0
NE C:ARG560 4.8 85.0 1.0
O C:HOH2101 4.8 84.8 1.0
C C:THR469 4.9 0.5 1.0
CG2 C:THR469 4.9 0.3 1.0
N B:PRO342 4.9 89.9 1.0
OD1 B:ASN448 4.9 96.5 1.0
CG B:PRO342 5.0 91.5 1.0

Fluorine binding site 6 out of 9 in 6mii

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Fluorine binding site 6 out of 9 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F2001

b:98.2
occ:1.00
 F3 B:08T2001 0.0 98.2 1.0
BE B:08T2001 1.5 97.7 1.0
O3B B:08T2001 2.4 90.6 1.0
F2 B:08T2001 2.5 97.8 1.0
F1 B:08T2001 2.6 0.3 1.0
ND2 B:ASN448 2.9 0.1 1.0
O B:HOH2102 3.0 73.3 1.0
NZ B:LYS346 3.3 0.8 1.0
CE B:LYS346 3.3 95.4 1.0
PB B:08T2001 3.3 92.3 1.0
O2B B:08T2001 3.5 0.9 1.0
O1B B:08T2001 3.6 87.2 1.0
MG B:MG2003 3.7 0.5 1.0
CG B:ASN448 3.8 94.2 1.0
OD1 B:ASN448 3.9 96.5 1.0
CA B:PRO342 3.9 99.8 1.0
N B:GLY343 4.3 92.8 1.0
O B:ASP341 4.3 86.1 1.0
CB B:PRO342 4.6 98.9 1.0
O3A B:08T2001 4.7 89.9 1.0
C B:PRO342 4.7 99.5 1.0
N B:PRO342 4.7 89.9 1.0
NH2 C:ARG560 4.7 0.0 1.0
CD B:LYS346 4.7 91.0 1.0
O B:GLY340 4.8 91.6 1.0
O B:HOH2101 4.8 76.3 1.0
C B:ASP341 4.8 87.0 1.0
NH1 C:ARG473 4.9 94.3 1.0
OE1 B:GLU405 4.9 0.3 1.0
OE2 B:GLU405 4.9 0.4 1.0
NH2 C:ARG473 4.9 0.4 1.0

Fluorine binding site 7 out of 9 in 6mii

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Fluorine binding site 7 out of 9 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:0.9
occ:1.00
 F1 C:08T2001 0.0 0.9 1.0
BE C:08T2001 1.5 0.9 1.0
MG C:MG2003 1.9 0.7 1.0
O3B C:08T2001 2.5 0.7 1.0
F2 C:08T2001 2.5 0.7 1.0
F3 C:08T2001 2.5 0.3 1.0
O2B C:08T2001 2.7 0.5 1.0
O D:HOH2102 2.7 95.9 1.0
O C:HOH2103 2.8 83.9 1.0
O C:HOH2102 2.9 92.6 1.0
NH2 D:ARG473 3.0 0.3 1.0
PB C:08T2001 3.2 0.6 1.0
NH2 D:ARG560 3.2 0.0 1.0
CZ D:ARG473 3.6 0.7 1.0
OG C:SER347 3.9 0.7 1.0
NH1 D:ARG473 3.9 0.1 1.0
OE2 C:GLU405 4.0 0.6 1.0
O3A C:08T2001 4.2 0.0 1.0
O2A C:08T2001 4.3 1.0 1.0
O1B C:08T2001 4.4 97.1 1.0
CZ D:ARG560 4.5 0.4 1.0
NE D:ARG473 4.5 0.4 1.0
CD C:GLU405 4.6 1.0 1.0
CB C:SER347 4.8 0.0 1.0
PA C:08T2001 4.9 0.1 1.0
OE1 C:GLU405 5.0 0.9 1.0

Fluorine binding site 8 out of 9 in 6mii

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Fluorine binding site 8 out of 9 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:0.7
occ:1.00
 F2 C:08T2001 0.0 0.7 1.0
BE C:08T2001 1.5 0.9 1.0
O3B C:08T2001 2.4 0.7 1.0
F1 C:08T2001 2.5 0.9 1.0
F3 C:08T2001 2.5 0.3 1.0
NH1 D:ARG473 2.6 0.1 1.0
NH2 D:ARG560 2.6 0.0 1.0
NH2 D:ARG473 3.1 0.3 1.0
CZ D:ARG473 3.2 0.7 1.0
NH1 D:ARG560 3.3 0.1 1.0
CZ D:ARG560 3.4 0.4 1.0
CB C:PRO342 3.6 0.5 1.0
CA C:PRO342 3.7 0.2 1.0
N C:GLY343 3.8 0.1 1.0
PB C:08T2001 3.9 0.6 1.0
C C:PRO342 4.3 0.7 1.0
ND2 C:ASN448 4.3 0.2 1.0
CB D:THR469 4.4 0.6 1.0
O2B C:08T2001 4.4 0.5 1.0
NE D:ARG473 4.4 0.4 1.0
MG C:MG2003 4.4 0.7 1.0
O D:THR469 4.4 0.6 1.0
CA D:THR469 4.6 0.6 1.0
CG2 D:THR469 4.6 0.5 1.0
NE D:ARG560 4.6 0.1 1.0
OD1 C:ASN448 4.6 0.4 1.0
O3A C:08T2001 4.7 0.0 1.0
OG D:SER472 4.7 0.8 1.0
O C:HOH2103 4.8 83.9 1.0
O1B C:08T2001 4.8 97.1 1.0
CA C:GLY343 4.9 0.3 1.0
O D:HOH2102 4.9 95.9 1.0
CG C:ASN448 4.9 0.6 1.0
C D:THR469 5.0 0.8 1.0
N C:PRO342 5.0 0.2 1.0

Fluorine binding site 9 out of 9 in 6mii

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Fluorine binding site 9 out of 9 in the Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Minichromosome Maintenance Protein Mcm/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:0.3
occ:1.00
 F3 C:08T2001 0.0 0.3 1.0
BE C:08T2001 1.5 0.9 1.0
O3B C:08T2001 2.5 0.7 1.0
F2 C:08T2001 2.5 0.7 1.0
F1 C:08T2001 2.5 0.9 1.0
ND2 C:ASN448 2.8 0.2 1.0
O C:HOH2103 2.9 83.9 1.0
PB C:08T2001 3.3 0.6 1.0
NZ C:LYS346 3.5 99.4 1.0
O2B C:08T2001 3.6 0.5 1.0
CG C:ASN448 3.6 0.6 1.0
OD1 C:ASN448 3.6 0.4 1.0
O1B C:08T2001 3.6 97.1 1.0
MG C:MG2003 3.6 0.7 1.0
CE C:LYS346 3.7 97.5 1.0
CA C:PRO342 4.2 0.2 1.0
NH2 D:ARG560 4.4 0.0 1.0
NH2 D:ARG473 4.5 0.3 1.0
N C:GLY343 4.6 0.1 1.0
O C:ASP341 4.6 0.8 1.0
O C:HOH2102 4.7 92.6 1.0
OE1 C:GLU405 4.7 0.9 1.0
O3A C:08T2001 4.7 0.0 1.0
CB C:PRO342 4.8 0.5 1.0
OE2 C:GLU405 4.8 0.6 1.0
O C:GLY340 4.9 0.7 1.0
CD C:GLU405 5.0 1.0 1.0
C C:PRO342 5.0 0.7 1.0
NH1 D:ARG473 5.0 0.1 1.0
N C:PRO342 5.0 0.2 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: Thu Aug 1 22:19:03 2024

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