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Magnesium 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
Zinc (Zn) 6 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 6mii

Go back to Magnesium Binding Sites List in 6mii
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2003

b:0.1
occ:1.00
 O A:HOH2101 1.9 79.0 1.0
O A:HOH2103 1.9 72.2 1.0
OG A:SER347 1.9 95.6 1.0
F1 A:08T2001 1.9 0.2 1.0
O2B A:08T2001 1.9 93.6 1.0
O A:HOH2102 2.0 78.3 1.0
CB A:SER347 3.0 90.5 1.0
BE A:08T2001 3.1 0.0 1.0
PB A:08T2001 3.2 86.9 1.0
O3B A:08T2001 3.5 93.0 1.0
F3 A:08T2001 3.6 0.0 1.0
OD2 A:ASP404 3.8 84.8 1.0
N A:SER347 3.9 80.8 1.0
CA A:SER347 4.0 86.7 1.0
O3A A:08T2001 4.0 83.0 1.0
OE1 B:GLN423 4.1 0.8 1.0
O1A A:08T2001 4.1 80.5 1.0
OE2 A:GLU405 4.3 0.8 1.0
OD1 A:ASP404 4.4 79.0 1.0
PA A:08T2001 4.4 77.5 1.0
F2 A:08T2001 4.4 0.8 1.0
CG A:ASP404 4.4 79.1 1.0
O1B A:08T2001 4.5 90.0 1.0
NH2 B:ARG560 4.5 82.6 1.0
O2A A:08T2001 4.6 75.8 1.0
NH2 B:ARG473 4.7 89.0 1.0
NE2 B:GLN423 4.8 72.2 1.0
CD A:GLU405 4.8 0.5 1.0
CD B:GLN423 4.8 84.3 1.0

Magnesium binding site 2 out of 6 in 6mii

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2003

b:0.5
occ:1.00
 O B:HOH2101 1.9 76.3 1.0
O2B B:08T2001 1.9 0.9 1.0
O C:HOH2101 1.9 84.8 1.0
F1 B:08T2001 2.0 0.3 1.0
O B:HOH2102 2.0 73.3 1.0
OG B:SER347 2.0 0.4 1.0
CB B:SER347 2.9 97.7 1.0
BE B:08T2001 3.2 97.7 1.0
PB B:08T2001 3.3 92.3 1.0
O3B B:08T2001 3.6 90.6 1.0
F3 B:08T2001 3.7 98.2 1.0
N B:SER347 3.9 94.4 1.0
OE1 C:GLN423 4.0 99.6 1.0
OD2 B:ASP404 4.0 94.0 1.0
CA B:SER347 4.0 90.3 1.0
O3A B:08T2001 4.2 89.9 1.0
OE2 B:GLU405 4.3 0.4 1.0
O1A B:08T2001 4.3 88.2 1.0
OD1 B:ASP404 4.3 96.3 1.0
NH2 C:ARG473 4.4 0.4 1.0
O1B B:08T2001 4.4 87.2 1.0
F2 B:08T2001 4.4 97.8 1.0
CG B:ASP404 4.5 97.7 1.0
NH2 C:ARG560 4.6 0.0 1.0
PA B:08T2001 4.6 84.2 1.0
CD B:GLU405 4.6 0.6 1.0
O2A B:08T2001 4.7 81.4 1.0
CD C:GLN423 4.8 87.4 1.0
NE2 C:GLN423 4.9 87.7 1.0
CG B:GLU405 4.9 89.9 1.0

Magnesium binding site 3 out of 6 in 6mii

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2003

b:0.7
occ:1.00
 OG C:SER347 1.9 0.7 1.0
F1 C:08T2001 1.9 0.9 1.0
O C:HOH2103 1.9 83.9 1.0
O C:HOH2102 2.0 92.6 1.0
O2B C:08T2001 2.0 0.5 1.0
O D:HOH2102 2.0 95.9 1.0
CB C:SER347 3.0 0.0 1.0
BE C:08T2001 3.1 0.9 1.0
PB C:08T2001 3.3 0.6 1.0
O3B C:08T2001 3.6 0.7 1.0
F3 C:08T2001 3.6 0.3 1.0
OD2 C:ASP404 3.9 0.2 1.0
O2A C:08T2001 4.0 1.0 1.0
N C:SER347 4.0 0.9 1.0
CA C:SER347 4.0 0.2 1.0
OE1 D:GLN423 4.0 0.8 1.0
O3A C:08T2001 4.3 0.0 1.0
OD1 C:ASP404 4.4 95.8 1.0
O1B C:08T2001 4.4 97.1 1.0
F2 C:08T2001 4.4 0.7 1.0
OE2 C:GLU405 4.5 0.6 1.0
CG C:ASP404 4.5 0.8 1.0
NH2 D:ARG560 4.5 0.0 1.0
PA C:08T2001 4.6 0.1 1.0
NH2 D:ARG473 4.6 0.3 1.0
CD C:GLU405 4.8 1.0 1.0
CD D:GLN423 4.9 0.8 1.0
NE2 D:GLN423 4.9 0.1 1.0
O1A C:08T2001 4.9 0.1 1.0
CG C:GLU405 5.0 0.1 1.0

Magnesium binding site 4 out of 6 in 6mii

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2003

b:0.7
occ:1.00
 O D:HOH2101 1.9 73.4 1.0
OG D:SER347 1.9 0.5 1.0
O3B D:ADP2001 1.9 0.8 1.0
O D:HOH2103 2.0 79.7 1.0
O D:HOH2104 2.0 76.4 1.0
PB D:ADP2001 3.1 0.0 1.0
CB D:SER347 3.1 1.0 1.0
O1B D:ADP2001 3.2 0.6 1.0
OE1 E:GLN423 3.8 0.6 1.0
OD2 D:ASP404 3.8 0.9 1.0
N D:SER347 4.0 0.9 1.0
O1A D:ADP2001 4.1 0.5 1.0
CA D:SER347 4.1 1.0 1.0
OD1 D:ASP404 4.2 0.0 1.0
O3A D:ADP2001 4.2 0.1 1.0
O2B D:ADP2001 4.3 0.1 1.0
OE2 D:GLU405 4.4 0.8 1.0
CG D:ASP404 4.4 0.7 1.0
PA D:ADP2001 4.5 1.0 1.0
NH2 E:ARG473 4.5 1.0 1.0
CD D:GLU405 4.7 0.4 1.0
CD E:GLN423 4.7 0.4 1.0
NH2 E:ARG560 4.7 0.9 1.0
NE2 E:GLN423 4.8 0.2 1.0
O2A D:ADP2001 4.8 0.2 1.0
CG D:GLU405 5.0 0.6 1.0
CB D:LYS346 5.0 0.4 1.0

Magnesium binding site 5 out of 6 in 6mii

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2003

b:0.4
occ:1.00
 O E:HOH2102 1.9 71.8 1.0
O E:HOH2101 1.9 69.5 1.0
OG E:SER347 1.9 0.5 1.0
O2B E:ADP2001 1.9 0.4 1.0
O E:HOH2103 1.9 78.5 1.0
PB E:ADP2001 2.9 0.9 1.0
CB E:SER347 3.0 0.6 1.0
O3B E:ADP2001 3.0 0.1 1.0
N E:SER347 3.7 0.2 1.0
OD2 E:ASP404 3.8 0.6 1.0
CA E:SER347 3.9 0.8 1.0
O3A E:ADP2001 4.0 0.6 1.0
NH2 F:ARG473 4.1 0.0 1.0
O1B E:ADP2001 4.1 0.5 1.0
O1A E:ADP2001 4.1 0.8 1.0
OD1 E:ASP404 4.2 0.5 1.0
PA E:ADP2001 4.4 0.5 1.0
CG E:ASP404 4.4 0.9 1.0
OE1 F:GLN423 4.4 0.5 1.0
O2A E:ADP2001 4.4 0.2 1.0
NH2 F:ARG560 4.5 0.2 1.0
OE2 E:GLU405 4.6 0.7 1.0
CB E:LYS346 4.7 0.5 1.0
C E:LYS346 4.9 0.8 1.0
CD E:GLU405 4.9 0.1 1.0

Magnesium binding site 6 out of 6 in 6mii

Go back to Magnesium Binding Sites List in 6mii
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2003

b:0.7
occ:1.00
 O F:HOH2102 1.9 86.6 1.0
O F:HOH2101 1.9 85.8 1.0
OG F:SER347 1.9 0.1 1.0
O2B F:ADP2001 2.0 0.5 1.0
O F:HOH2103 2.0 86.3 1.0
CB F:SER347 3.1 0.5 1.0
PB F:ADP2001 3.2 0.2 1.0
O3B F:ADP2001 3.4 0.4 1.0
OD2 F:ASP404 3.8 0.8 1.0
N F:SER347 3.9 0.6 1.0
OD1 F:ASP404 4.0 0.6 1.0
CA F:SER347 4.0 0.2 1.0
O2A F:ADP2001 4.2 0.8 1.0
O3A F:ADP2001 4.2 0.9 1.0
O1B F:ADP2001 4.3 98.5 1.0
CG F:ASP404 4.3 0.2 1.0
NH2 A:ARG473 4.3 0.7 1.0
NH2 A:ARG560 4.4 0.2 1.0
PA F:ADP2001 4.5 1.0 1.0
O1A F:ADP2001 4.6 0.3 1.0
OE2 F:GLU405 4.6 0.9 1.0
CB F:LYS346 4.8 93.7 1.0
CE F:LYS346 4.8 0.9 1.0
CD F:GLU405 4.8 0.8 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: Tue Oct 1 11:39:49 2024

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