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Magnesium in PDB 9e2y: Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3

Enzymatic activity of Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3

All present enzymatic activity of Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3:
3.6.4.12;

Other elements in 9e2y:

The structure of Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3 also contains other interesting chemical elements:

Zinc (Zn) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3 (pdb code 9e2y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3, PDB code: 9e2y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 9e2y

Go back to Magnesium Binding Sites List in 9e2y
Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1002

b:52.3
occ:1.00
 O2B 2:ADP1001 1.9 84.2 1.0
HG 2:SER550 2.0 59.4 1.0
OG 2:SER550 2.3 65.9 1.0
PB 2:ADP1001 3.0 84.0 1.0
O3B 2:ADP1001 3.3 73.2 1.0
HB2 2:SER550 3.3 59.4 1.0
CB 2:SER550 3.4 59.4 1.0
OE2 2:GLU608 3.6 76.5 1.0
H 2:SER550 3.6 50.1 1.0
OD2 2:ASP607 3.6 61.2 1.0
HH22 6:ARG708 3.7 81.7 1.0
OD1 2:ASP607 3.9 61.5 1.0
HE21 6:GLN658 3.9 69.0 1.0
HH21 6:ARG708 3.9 81.7 1.0
HB3 2:SER550 4.0 59.4 1.0
O1B 2:ADP1001 4.1 56.1 1.0
O3A 2:ADP1001 4.1 85.0 1.0
NH2 6:ARG708 4.2 81.7 1.0
CG 2:ASP607 4.2 60.1 1.0
O2A 2:ADP1001 4.2 75.7 1.0
N 2:SER550 4.2 50.1 1.0
HB2 2:LYS549 4.3 50.4 1.0
CA 2:SER550 4.3 51.6 1.0
NE2 6:GLN658 4.5 69.0 1.0
HA 2:SER550 4.5 51.6 1.0
HE22 6:GLN658 4.6 69.0 1.0
PA 2:ADP1001 4.6 76.7 1.0
HE2 2:LYS549 4.7 56.8 1.0
HH22 6:ARG798 4.8 73.1 1.0
CD 2:GLU608 4.9 76.0 1.0
O1A 2:ADP1001 4.9 61.7 1.0
HH21 6:ARG798 4.9 73.1 1.0

Magnesium binding site 2 out of 6 in 9e2y

Go back to Magnesium Binding Sites List in 9e2y
Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1001

b:61.4
occ:1.00
 HG 3:SER416 1.7 58.2 1.0
O2G 5:ATP801 2.1 83.8 1.0
OG 3:SER416 2.1 70.8 1.0
O1B 5:ATP801 2.3 71.5 1.0
HH22 5:ARG549 3.2 70.0 1.0
CB 3:SER416 3.3 58.2 1.0
HB2 3:SER416 3.4 58.2 1.0
PG 5:ATP801 3.4 76.3 1.0
PB 5:ATP801 3.4 60.3 1.0
O3B 5:ATP801 3.5 64.9 1.0
HH21 5:ARG549 3.7 70.0 1.0
H 3:SER416 3.8 53.3 1.0
NH2 5:ARG549 3.8 70.0 1.0
HB3 3:SER416 3.8 58.2 1.0
OD1 3:ASP473 3.9 68.7 1.0
OD2 3:ASP473 4.1 74.2 1.0
O2A 5:ATP801 4.1 61.4 1.0
O3G 5:ATP801 4.3 69.1 1.0
CA 3:SER416 4.3 50.6 1.0
N 3:SER416 4.3 53.3 1.0
O1G 5:ATP801 4.3 69.4 1.0
CG 3:ASP473 4.4 69.7 1.0
O3A 5:ATP801 4.4 62.4 1.0
HA 3:SER416 4.5 50.6 1.0
O2B 5:ATP801 4.5 62.9 1.0
HB2 3:LYS415 4.5 56.0 1.0
OE1 5:GLN499 4.5 60.6 1.0
HH22 5:ARG651 4.6 74.1 1.0
HZ1 3:LYS415 4.7 64.2 1.0
HG2 3:GLU474 4.7 72.0 1.0
HE2 3:LYS415 4.8 58.2 1.0
OE2 3:GLU474 4.8 92.0 1.0
HH21 5:ARG651 4.8 74.1 1.0
HZ3 3:LYS415 4.8 64.2 1.0
PA 5:ATP801 4.9 57.6 1.0

Magnesium binding site 3 out of 6 in 9e2y

Go back to Magnesium Binding Sites List in 9e2y
Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg1002

b:104.1
occ:1.00
 O3B 4:ATP1001 1.9 118.3 1.0
HG 4:SER575 2.4 89.6 1.0
O2B 4:ATP1001 2.5 110.3 1.0
OG 4:SER575 2.6 90.9 1.0
O3G 4:ATP1001 2.7 130.9 1.0
PB 4:ATP1001 2.7 120.6 1.0
PG 4:ATP1001 2.8 129.4 1.0
O2A 4:ATP1001 3.1 109.2 1.0
O3A 4:ATP1001 3.5 112.4 1.0
H 4:SER575 3.6 90.0 1.0
O1G 4:ATP1001 3.6 128.9 1.0
HB2 4:SER575 3.7 89.6 1.0
CB 4:SER575 3.7 89.6 1.0
HH21 7:ARG593 3.8 145.3 1.0
PA 4:ATP1001 3.9 115.3 1.0
HZ3 4:LYS574 3.9 94.8 1.0
O1B 4:ATP1001 4.0 116.0 1.0
O2G 4:ATP1001 4.0 118.5 1.0
OD1 4:ASP632 4.2 96.5 1.0
HB2 4:LYS574 4.2 88.1 1.0
N 4:SER575 4.2 90.0 1.0
HZ1 4:LYS574 4.3 94.8 1.0
HB3 4:SER575 4.4 89.6 1.0
NH2 7:ARG593 4.4 145.3 1.0
HH22 7:ARG593 4.5 145.3 1.0
O1A 4:ATP1001 4.5 123.5 1.0
CA 4:SER575 4.6 88.3 1.0
NZ 4:LYS574 4.6 94.8 1.0
OE1 7:GLU542 4.6 148.5 1.0
H 4:LYS574 4.7 88.5 1.0
HA 4:SER575 4.9 88.3 1.0
OD1 4:ASN676 4.9 104.4 1.0
OD2 4:ASP632 4.9 109.7 1.0
CG 4:ASP632 5.0 99.8 1.0

Magnesium binding site 4 out of 6 in 9e2y

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Mg803

b:47.8
occ:1.00
 HG 5:SER423 1.5 64.0 1.0
OG 5:SER423 1.9 69.1 1.0
O3B 5:ATP802 2.8 56.0 1.0
CB 5:SER423 3.1 64.0 1.0
HB2 5:SER423 3.1 64.0 1.0
O1B 5:ATP802 3.3 89.9 1.0
HH22 2:ARG676 3.4 61.9 1.0
PB 5:ATP802 3.5 52.1 1.0
O1G 5:ATP802 3.6 78.9 1.0
HB3 5:SER423 3.6 64.0 1.0
H 5:SER423 3.7 51.4 1.0
PG 5:ATP802 3.8 75.3 1.0
OE1 5:GLU481 3.8 77.8 1.0
O3A 5:ATP802 3.9 57.3 1.0
HH21 2:ARG676 3.9 61.9 1.0
OD2 5:ASP480 3.9 74.3 1.0
NH2 2:ARG676 4.0 61.9 1.0
OD1 5:ASP480 4.1 65.4 1.0
CA 5:SER423 4.1 53.5 1.0
OE1 2:GLN626 4.2 56.0 1.0
N 5:SER423 4.2 51.4 1.0
HA 5:SER423 4.3 53.5 1.0
HH22 2:ARG808 4.4 54.4 1.0
CG 5:ASP480 4.4 66.6 1.0
O2A 5:ATP802 4.5 76.2 1.0
HH21 2:ARG808 4.6 54.4 1.0
O3G 5:ATP802 4.7 76.7 1.0
HB2 5:LYS422 4.7 60.7 1.0
HE22 2:GLN626 4.8 60.2 1.0
CD 5:GLU481 4.9 79.9 1.0
PA 5:ATP802 4.9 70.5 1.0
O2G 5:ATP802 4.9 70.7 1.0
NH2 2:ARG808 4.9 54.4 1.0
O2B 5:ATP802 4.9 76.3 1.0

Magnesium binding site 5 out of 6 in 9e2y

Go back to Magnesium Binding Sites List in 9e2y
Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg1102

b:62.8
occ:1.00
 HG 6:SER582 1.8 75.7 1.0
O3G 6:ATP1101 1.8 87.2 1.0
OG 6:SER582 2.0 77.9 1.0
O2B 6:ATP1101 2.1 83.6 1.0
O3B 6:ATP1101 2.7 76.7 1.0
PG 6:ATP1101 2.8 94.1 1.0
PB 6:ATP1101 3.0 90.0 1.0
CB 6:SER582 3.1 75.7 1.0
H 6:SER582 3.1 72.9 1.0
HB2 6:SER582 3.2 75.7 1.0
HH21 4:ARG701 3.6 96.7 1.0
O2G 6:ATP1101 3.7 108.5 1.0
N 6:SER582 3.8 72.9 1.0
HB3 6:SER582 3.8 75.7 1.0
HB2 6:LYS581 3.9 77.2 1.0
HH22 4:ARG701 3.9 96.7 1.0
O1G 6:ATP1101 4.0 104.0 1.0
CA 6:SER582 4.0 73.2 1.0
NH2 4:ARG701 4.0 96.7 1.0
O1B 6:ATP1101 4.0 107.9 1.0
OD1 6:ASP639 4.0 66.6 1.0
O3A 6:ATP1101 4.1 81.5 1.0
O1A 6:ATP1101 4.2 91.4 1.0
OE2 4:GLU650 4.3 98.0 1.0
HA 6:SER582 4.4 73.2 1.0
HH21 4:ARG796 4.4 80.5 1.0
HZ3 6:LYS581 4.4 87.8 1.0
HE2 6:LYS581 4.5 77.6 1.0
HZ1 6:LYS581 4.5 87.8 1.0
PA 6:ATP1101 4.6 81.1 1.0
HB3 6:LYS581 4.7 77.2 1.0
CB 6:LYS581 4.7 77.2 1.0
OD2 6:ASP639 4.8 101.0 1.0
O2A 6:ATP1101 4.8 85.0 1.0
C 6:LYS581 4.8 68.3 1.0
CG 6:ASP639 4.8 84.7 1.0
NZ 6:LYS581 4.9 87.8 1.0
CD 4:GLU650 4.9 94.1 1.0
H 6:LYS581 4.9 78.8 1.0
HH22 4:ARG796 5.0 80.5 1.0

Magnesium binding site 6 out of 6 in 9e2y

Go back to Magnesium Binding Sites List in 9e2y
Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Yeast Cmg Helicase Stalled at G4-Containing Dna Template, State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Mg1002

b:91.3
occ:1.00
 HG 7:SER467 2.0 122.8 1.0
OG 7:SER467 2.1 128.2 1.0
O3B 7:ATP1001 2.3 138.4 1.0
O3G 7:ATP1001 2.4 148.8 1.0
PG 7:ATP1001 2.6 165.0 1.0
O2G 7:ATP1001 2.7 164.9 1.0
CB 7:SER467 3.5 122.8 1.0
O3A 7:ATP1001 3.5 132.5 1.0
H 7:SER467 3.5 116.7 1.0
PB 7:ATP1001 3.6 139.2 1.0
HB2 7:SER467 3.7 122.8 1.0
O1A 7:ATP1001 3.7 131.2 1.0
HB2 7:LYS466 3.9 115.8 1.0
HE3 7:LYS466 4.0 120.9 1.0
PA 7:ATP1001 4.0 133.0 1.0
OD2 7:ASP524 4.1 136.5 1.0
HB3 7:SER467 4.1 122.8 1.0
N 7:SER467 4.1 116.7 1.0
O1G 7:ATP1001 4.1 148.7 1.0
CA 7:SER467 4.3 119.4 1.0
O2B 7:ATP1001 4.4 147.5 1.0
HA 7:SER467 4.4 119.4 1.0
O2A 7:ATP1001 4.5 134.6 1.0
OE2 7:GLU525 4.5 146.3 1.0
OD1 7:ASP524 4.6 134.5 1.0
O1B 7:ATP1001 4.6 140.7 1.0
HH22 3:ARG700 4.7 108.8 1.0
CG 7:ASP524 4.7 138.0 1.0
HH22 3:ARG542 4.8 103.6 1.0
CB 7:LYS466 4.9 115.8 1.0
CE 7:LYS466 4.9 120.9 1.0
HH21 3:ARG542 5.0 103.6 1.0

Reference:

S.Batra, B.Allwein, C.Kumar, S.Devbhandari, J.G.Bruning, S.Bahng, C.M.Lee, K.J.Marians, R.K.Hite, D.Remus. G-Quadruplex-Stalled Eukaryotic Replisome Structure Reveals Helical Inchworm Dna Translocation. Science V. 387 T1978 2025.
ISSN: ESSN 1095-9203
PubMed: 40048517
DOI: 10.1126/SCIENCE.ADT1978
Page generated: Sat Aug 16 00:54:10 2025

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