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Magnesium in PDB 7pbs: Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset]

Enzymatic activity of Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset]

All present enzymatic activity of Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset]:
3.6.4.12;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset] (pdb code 7pbs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset], PDB code: 7pbs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7pbs

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Magnesium binding site 1 out of 5 in the Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset]


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:62.3
occ:1.00
 O2B A:AGS401 1.9 64.2 1.0
O2G A:AGS401 1.9 64.2 1.0
OG1 A:THR66 1.9 61.9 1.0
HOG2 A:AGS401 2.3 64.2 1.0
HG1 A:THR66 2.4 61.9 1.0
HB A:THR66 2.9 61.9 1.0
CB A:THR66 2.9 61.9 1.0
PB A:AGS401 3.3 64.2 1.0
PG A:AGS401 3.3 64.2 1.0
H A:THR66 3.4 61.9 1.0
O3B A:AGS401 3.6 64.2 1.0
HG21 A:THR66 3.6 61.9 1.0
O2A A:AGS401 3.8 64.2 1.0
OD2 A:ASP110 3.8 65.0 1.0
CG2 A:THR66 3.9 61.9 1.0
O1B A:AGS401 3.9 64.2 1.0
N A:THR66 4.0 61.9 1.0
CA A:THR66 4.0 61.9 1.0
HH22 F:ARG171 4.1 70.7 1.0
O3G A:AGS401 4.3 64.2 1.0
O3A A:AGS401 4.3 64.2 1.0
HH21 F:ARG171 4.3 70.7 1.0
OD1 A:ASP110 4.4 65.0 1.0
HA A:THR66 4.4 61.9 1.0
HG23 A:THR66 4.4 61.9 1.0
OE2 A:GLU111 4.5 66.2 1.0
PA A:AGS401 4.5 64.2 1.0
CG A:ASP110 4.5 65.0 1.0
S1G A:AGS401 4.5 64.2 1.0
HH22 A:ARG218 4.5 65.4 1.0
NH2 F:ARG171 4.6 70.7 1.0
HB2 A:LYS65 4.6 61.1 1.0
HG22 A:THR66 4.6 61.9 1.0
O1A A:AGS401 4.6 64.2 1.0
H21 A:AGS401 4.9 64.2 1.0
HH22 A:ARG21 5.0 65.1 1.0

Magnesium binding site 2 out of 5 in 7pbs

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Magnesium binding site 2 out of 5 in the Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset]


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:55.4
occ:1.00
 OG1 B:THR66 1.9 58.5 1.0
O2G B:AGS401 2.2 58.1 1.0
HG1 B:THR66 2.3 58.5 1.0
HOG2 B:AGS401 2.4 58.1 1.0
O2B B:AGS401 2.5 58.1 1.0
CB B:THR66 3.2 58.5 1.0
HB B:THR66 3.3 58.5 1.0
OD2 B:ASP110 3.4 63.7 1.0
H B:THR66 3.6 58.5 1.0
PG B:AGS401 3.6 58.1 1.0
PB B:AGS401 3.8 58.1 1.0
HG21 B:THR66 3.9 58.5 1.0
OD1 B:ASP110 4.0 63.7 1.0
HH22 A:ARG171 4.0 55.7 1.0
CG2 B:THR66 4.1 58.5 1.0
O3B B:AGS401 4.1 58.1 1.0
CG B:ASP110 4.1 63.7 1.0
N B:THR66 4.1 58.5 1.0
CA B:THR66 4.2 58.5 1.0
O2A B:AGS401 4.2 58.1 1.0
HA B:THR66 4.4 58.5 1.0
O1B B:AGS401 4.4 58.1 1.0
HG23 B:THR66 4.4 58.5 1.0
HB2 B:LYS65 4.4 57.4 1.0
OE2 B:GLU111 4.5 63.3 1.0
S1G B:AGS401 4.6 58.1 1.0
O3G B:AGS401 4.7 58.1 1.0
HE2 B:LYS65 4.7 57.4 1.0
NH2 A:ARG171 4.7 55.7 1.0
HH21 A:ARG171 4.8 55.7 1.0
HG22 B:THR66 4.9 58.5 1.0
O3A B:AGS401 4.9 58.1 1.0
PA B:AGS401 5.0 58.1 1.0

Magnesium binding site 3 out of 5 in 7pbs

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Magnesium binding site 3 out of 5 in the Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset]


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset] within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:53.5
occ:1.00
 OG1 C:THR66 1.9 59.9 1.0
O2G C:AGS401 2.1 58.8 1.0
O2B C:AGS401 2.2 58.8 1.0
HG1 C:THR66 2.3 59.9 1.0
HOG2 C:AGS401 2.3 58.8 1.0
CB C:THR66 3.0 59.9 1.0
HB C:THR66 3.0 59.9 1.0
PB C:AGS401 3.5 58.8 1.0
H C:THR66 3.5 59.9 1.0
PG C:AGS401 3.5 58.8 1.0
HG21 C:THR66 3.7 59.9 1.0
OD2 C:ASP110 3.7 68.8 1.0
O3B C:AGS401 3.9 58.8 1.0
CG2 C:THR66 3.9 59.9 1.0
HH22 B:ARG171 4.0 59.4 1.0
O1B C:AGS401 4.0 58.8 1.0
CA C:THR66 4.1 59.9 1.0
O2A C:AGS401 4.1 58.8 1.0
N C:THR66 4.1 59.9 1.0
O3G C:AGS401 4.2 58.8 1.0
OD1 C:ASP110 4.3 68.8 1.0
HG23 C:THR66 4.4 59.9 1.0
HA C:THR66 4.4 59.9 1.0
CG C:ASP110 4.4 68.8 1.0
HB2 C:LYS65 4.5 59.5 1.0
O3A C:AGS401 4.6 58.8 1.0
OE2 C:GLU111 4.7 68.8 1.0
NH2 B:ARG171 4.7 59.4 1.0
HG22 C:THR66 4.7 59.9 1.0
HH21 B:ARG171 4.7 59.4 1.0
PA C:AGS401 4.8 58.8 1.0
O1A C:AGS401 4.8 58.8 1.0
HE2 C:LYS65 4.8 59.5 1.0
HH22 C:ARG218 4.9 57.4 1.0
S1G C:AGS401 5.0 58.8 1.0

Magnesium binding site 4 out of 5 in 7pbs

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Magnesium binding site 4 out of 5 in the Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset]


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:93.9
occ:1.00
 O2B D:AGS401 1.8 91.0 1.0
O2A D:AGS401 1.9 91.0 1.0
O3B D:AGS401 2.0 91.0 1.0
O2G D:AGS401 2.0 91.0 1.0
PB D:AGS401 2.2 91.0 1.0
PG D:AGS401 2.3 91.0 1.0
HOG2 D:AGS401 2.5 91.0 1.0
HH22 D:ARG218 2.8 79.4 1.0
O3A D:AGS401 2.9 91.0 1.0
PA D:AGS401 2.9 91.0 1.0
O3G D:AGS401 2.9 91.0 1.0
NH2 D:ARG218 3.6 79.4 1.0
OG1 D:THR66 3.6 98.5 1.0
O1B D:AGS401 3.6 91.0 1.0
O1A D:AGS401 3.7 91.0 1.0
H21 D:AGS401 3.7 91.0 1.0
HH21 D:ARG218 3.9 79.4 1.0
HH12 D:ARG218 4.1 79.4 1.0
HH22 C:ARG171 4.1 75.9 1.0
HB D:THR66 4.1 98.5 1.0
S1G D:AGS401 4.1 91.0 1.0
H5'2 D:AGS401 4.2 91.0 1.0
O5' D:AGS401 4.2 91.0 1.0
HG1 D:THR66 4.2 98.5 1.0
H D:THR66 4.3 98.5 1.0
HA2 D:GLY62 4.3 85.2 1.0
CB D:THR66 4.4 98.5 1.0
H5'1 D:AGS401 4.4 91.0 1.0
H D:GLY62 4.4 85.2 1.0
HH21 C:ARG171 4.4 75.9 1.0
NH2 C:ARG171 4.5 75.9 1.0
C5' D:AGS401 4.5 91.0 1.0
CZ D:ARG218 4.5 79.4 1.0
HH12 D:ARG21 4.6 94.4 1.0
HH22 D:ARG21 4.6 94.4 1.0
NH1 D:ARG218 4.6 79.4 1.0

Magnesium binding site 5 out of 5 in 7pbs

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Magnesium binding site 5 out of 5 in the Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset]


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ruvab Branch Migration Motor Complexed to the Holliday Junction - Ruvb Aaa+ State S0+A [T1 Dataset] within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:80.5
occ:1.00
 OG1 F:THR66 1.9 77.2 1.0
HG1 F:THR66 2.2 77.2 1.0
HG21 F:THR66 2.4 77.2 1.0
O2G F:AGS401 2.6 81.7 1.0
HOG2 F:AGS401 2.7 81.7 1.0
O2B F:AGS401 2.8 81.7 1.0
CB F:THR66 2.8 77.2 1.0
CG2 F:THR66 3.0 77.2 1.0
HB F:THR66 3.0 77.2 1.0
HG23 F:THR66 3.4 77.2 1.0
O2A F:AGS401 3.5 81.7 1.0
HG22 F:THR66 3.8 77.2 1.0
PG F:AGS401 4.1 81.7 1.0
HH22 E:ARG171 4.1 92.5 1.0
CA F:THR66 4.2 77.2 1.0
PB F:AGS401 4.2 81.7 1.0
OD2 F:ASP110 4.2 79.2 1.0
H F:THR66 4.3 77.2 1.0
HE2 F:PHE108 4.3 73.7 1.0
HA F:THR66 4.4 77.2 1.0
HH12 F:ARG218 4.4 85.6 1.0
O3B F:AGS401 4.5 81.7 1.0
HH21 E:ARG171 4.6 92.5 1.0
NH2 E:ARG171 4.6 92.5 1.0
N F:THR66 4.7 77.2 1.0
PA F:AGS401 4.8 81.7 1.0
HZ F:PHE108 4.9 73.7 1.0
CE2 F:PHE108 4.9 73.7 1.0

Reference:

J.Wald, D.Fahrenkamp, N.Goessweiner-Mohr, W.Lugmayr, L.Ciccarelli, O.Vesper, T.C.Marlovits. Mechanism of Aaa+ Atpase-Mediated Ruvab-Holliday Junction Branch Migration. Nature V. 609 630 2022.
ISSN: ESSN 1476-4687
PubMed: 36002576
DOI: 10.1038/S41586-022-05121-1
Page generated: Thu Oct 3 04:06:29 2024

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