Atomistry » Magnesium » PDB 8dk2-8dtp » 8dqz
Atomistry »
  Magnesium »
    PDB 8dk2-8dtp »
      8dqz »

Magnesium in PDB 8dqz: Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (pdb code 8dqz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction, PDB code: 8dqz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8dqz

Go back to Magnesium Binding Sites List in 8dqz
Magnesium binding site 1 out of 4 in the Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:56.5
occ:1.00
HG1 A:THR360 1.9 77.8 1.0
O2G A:AGS901 2.2 76.7 1.0
O1B A:AGS901 2.3 74.7 1.0
OG1 A:THR360 2.3 82.7 1.0
O3G A:AGS901 2.9 73.3 1.0
PG A:AGS901 2.9 63.4 1.0
HOG2 A:AGS901 3.0 74.6 1.0
PB A:AGS901 3.3 68.6 1.0
HB A:THR360 3.3 76.7 1.0
CB A:THR360 3.4 75.5 1.0
O3B A:AGS901 3.4 71.4 1.0
H A:THR360 3.5 77.7 1.0
OD2 A:ASP424 3.6 81.8 1.0
H21 A:AGS901 3.7 75.0 1.0
HH21 B:ARG128 3.8 59.5 1.0
OD1 A:ASP424 3.8 84.9 1.0
O3A A:AGS901 4.0 72.8 1.0
HH22 B:ARG157 4.1 56.9 1.0
CG A:ASP424 4.2 80.5 1.0
N A:THR360 4.2 77.1 1.0
HG21 A:THR360 4.2 77.4 1.0
HG21 A:ILE454 4.2 86.4 1.0
HB2 A:LYS359 4.3 75.7 1.0
O1A A:AGS901 4.3 78.1 1.0
HH21 B:ARG157 4.4 55.6 1.0
CG2 A:THR360 4.4 76.3 1.0
CA A:THR360 4.4 75.1 1.0
HH22 A:ARG515 4.4 66.1 1.0
HE2 A:LYS359 4.4 75.8 1.0
NH2 B:ARG128 4.5 61.8 1.0
HH22 B:ARG128 4.5 60.5 1.0
NH2 B:ARG157 4.6 55.3 1.0
O2B A:AGS901 4.6 80.5 1.0
PA A:AGS901 4.7 69.1 1.0
S1G A:AGS901 4.7 66.6 1.0
HA A:THR360 4.8 77.6 1.0
HD3 B:ARG129 4.8 60.8 1.0
HG23 A:THR360 4.8 77.7 1.0
HZ1 A:LYS359 4.8 75.4 1.0
O2A A:AGS901 4.9 71.6 1.0
HG3 A:GLU425 4.9 79.9 1.0
HG22 A:ILE454 4.9 86.2 1.0
HZ3 A:LYS359 5.0 75.8 1.0
HG2 A:GLU425 5.0 79.2 1.0

Magnesium binding site 2 out of 4 in 8dqz

Go back to Magnesium Binding Sites List in 8dqz
Magnesium binding site 2 out of 4 in the Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:38.3
occ:1.00
HG1 B:THR56 1.8 46.7 1.0
O2G B:AGS402 2.3 56.1 1.0
OG1 B:THR56 2.4 53.1 1.0
HOG2 B:AGS402 2.8 52.5 1.0
O2B B:AGS402 2.9 45.0 1.0
HH22 C:ARG160 3.0 40.9 1.0
HB B:THR56 3.1 44.7 1.0
CB B:THR56 3.3 37.5 1.0
PG B:AGS402 3.6 39.4 1.0
O3B B:AGS402 3.6 45.9 1.0
NH2 C:ARG160 3.6 39.4 1.0
HH21 C:ARG160 3.6 40.9 1.0
HG21 B:THR56 3.7 45.7 1.0
HH21 C:ARG131 3.8 40.8 1.0
OD2 B:ASP114 3.8 55.0 1.0
OE2 B:GLU115 3.8 47.4 1.0
PB B:AGS402 3.9 25.8 1.0
HD3 C:ARG132 4.0 43.0 1.0
O2A B:AGS402 4.0 58.9 1.0
H B:THR56 4.0 45.7 1.0
CG2 B:THR56 4.1 44.1 1.0
OE1 C:GLU135 4.1 54.4 1.0
HH11 C:ARG132 4.2 42.8 1.0
OD1 B:ASP114 4.2 44.4 1.0
HH22 B:ARG203 4.4 47.4 1.0
CG B:ASP114 4.5 50.3 1.0
NH2 C:ARG131 4.5 36.0 1.0
CA B:THR56 4.6 35.0 1.0
HD2 C:ARG132 4.6 43.3 1.0
N B:THR56 4.6 40.3 1.0
HG22 B:THR56 4.7 46.4 1.0
O3G B:AGS402 4.7 53.6 1.0
HG23 B:THR56 4.7 46.6 1.0
HH22 C:ARG131 4.7 40.4 1.0
CD C:ARG132 4.8 45.8 1.0
O3A B:AGS402 4.8 56.8 1.0
PA B:AGS402 4.8 45.7 1.0
HH21 B:ARG203 4.8 47.4 1.0
S1G B:AGS402 4.8 52.3 1.0
CZ C:ARG160 4.9 43.0 1.0
HH12 C:ARG160 4.9 42.2 1.0
O1A B:AGS402 4.9 46.3 1.0
NH2 B:ARG203 4.9 48.3 1.0
HA B:THR56 4.9 45.7 1.0
O1B B:AGS402 5.0 44.7 1.0
NH1 C:ARG132 5.0 46.1 1.0

Magnesium binding site 3 out of 4 in 8dqz

Go back to Magnesium Binding Sites List in 8dqz
Magnesium binding site 3 out of 4 in the Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:30.3
occ:1.00
HOG2 C:AGS402 2.1 61.3 1.0
OG1 C:THR60 2.4 48.6 1.0
O2G C:AGS402 2.4 61.7 1.0
O2B C:AGS402 2.4 65.5 1.0
HG1 C:THR60 2.8 49.6 1.0
HH22 D:ARG183 3.0 39.4 1.0
OE2 C:GLU118 3.1 50.2 1.0
OD2 C:ASP117 3.3 54.5 1.0
HB C:THR60 3.5 48.4 1.0
CB C:THR60 3.5 41.0 1.0
HD3 D:ARG155 3.6 43.2 1.0
OD1 C:ASP117 3.6 44.2 1.0
PB C:AGS402 3.7 43.1 1.0
NH2 D:ARG183 3.7 34.7 1.0
PG C:AGS402 3.7 31.1 1.0
HH21 D:ARG183 3.8 39.0 1.0
HH21 D:ARG154 3.8 34.5 1.0
CG C:ASP117 3.9 42.2 1.0
O3B C:AGS402 3.9 52.8 1.0
HG21 C:THR60 4.0 47.8 1.0
H C:THR60 4.1 48.0 1.0
CD C:GLU118 4.3 46.9 1.0
CG2 C:THR60 4.4 42.6 1.0
CD D:ARG155 4.4 44.8 1.0
NH2 D:ARG154 4.5 24.1 1.0
HH11 D:ARG155 4.5 44.2 1.0
HG3 C:GLU118 4.5 42.5 1.0
HD2 D:ARG155 4.5 44.1 1.0
HD22 C:LEU146 4.6 39.8 1.0
O3G C:AGS402 4.6 66.2 1.0
HH22 D:ARG154 4.6 35.5 1.0
CA C:THR60 4.6 40.1 1.0
N C:THR60 4.7 39.9 1.0
O1B C:AGS402 4.7 21.3 1.0
O3A C:AGS402 4.7 62.8 1.0
HA C:THR60 4.8 48.1 1.0
OE1 D:GLU158 4.8 46.9 1.0
HH12 D:ARG183 4.8 40.4 1.0
HD23 C:LEU146 4.9 39.2 1.0
HB2 C:LYS59 4.9 36.5 1.0
HG2 D:ARG155 4.9 44.4 1.0
HG23 C:THR60 4.9 48.9 1.0
CZ D:ARG183 4.9 28.7 1.0
HE2 C:LYS59 5.0 34.9 1.0
CG C:GLU118 5.0 42.0 1.0

Magnesium binding site 4 out of 4 in 8dqz

Go back to Magnesium Binding Sites List in 8dqz
Magnesium binding site 4 out of 4 in the Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Intermediate State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:43.8
occ:1.00
HOG2 D:AGS402 1.9 61.2 1.0
O2G D:AGS402 2.2 50.6 1.0
O2B D:AGS402 2.4 62.0 1.0
OG1 D:THR72 2.6 43.2 1.0
HH22 E:ARG184 3.0 41.3 1.0
HG1 D:THR72 3.2 46.4 1.0
HB D:THR72 3.4 44.6 1.0
HH21 E:ARG184 3.5 40.3 1.0
HD3 E:ARG156 3.5 47.9 1.0
HH21 E:ARG155 3.5 38.6 1.0
NH2 E:ARG184 3.6 40.0 1.0
CB D:THR72 3.6 32.5 1.0
PG D:AGS402 3.6 38.2 1.0
PB D:AGS402 3.7 33.2 1.0
O3B D:AGS402 3.9 59.6 1.0
H D:THR72 4.0 45.3 1.0
OD1 D:ASP140 4.1 44.4 1.0
OD2 D:ASP140 4.1 52.2 1.0
O2A D:AGS402 4.2 60.9 1.0
HG21 D:THR72 4.2 46.4 1.0
NH2 E:ARG155 4.2 34.5 1.0
OE2 E:GLU159 4.3 58.2 1.0
HH22 E:ARG155 4.3 38.5 1.0
HH22 D:ARG229 4.4 37.3 1.0
CD E:ARG156 4.5 48.4 1.0
CG D:ASP140 4.5 46.9 1.0
CG2 D:THR72 4.5 44.9 1.0
OE2 D:GLU141 4.6 50.0 1.0
O1B D:AGS402 4.6 48.8 1.0
N D:THR72 4.6 37.9 1.0
HD2 E:ARG156 4.7 48.3 1.0
O3G D:AGS402 4.7 68.5 1.0
CA D:THR72 4.7 39.1 1.0
H21 D:AGS402 4.7 60.2 1.0
HE2 D:LYS71 4.7 37.5 1.0
HG21 D:ILE169 4.8 37.4 1.0
HG2 E:ARG156 4.8 48.0 1.0
HB2 D:LYS71 4.8 35.9 1.0
S1G D:AGS402 4.8 38.6 1.0
O3A D:AGS402 4.8 56.3 1.0
CZ E:ARG184 4.9 32.9 1.0
HH11 E:ARG156 4.9 48.6 1.0
HG3 D:GLU141 4.9 37.6 1.0
PA D:AGS402 5.0 32.3 1.0
HH21 D:ARG229 5.0 37.5 1.0

Reference:

M.Schrecker, J.C.Castaneda, S.Devbhandari, C.Kumar, D.Remus, R.K.Hite. Multistep Loading of A Dna Sliding Clamp Onto Dna By Replication Factor C. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35939393
DOI: 10.7554/ELIFE.78253
Page generated: Fri Oct 4 00:50:16 2024

Last articles

Na in 2QZ7
Na in 2QZI
Na in 2R20
Na in 2R1S
Na in 2R22
Na in 2R21
Na in 2QFP
Na in 2R0W
Na in 2QWM
Na in 2QWP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy