Atomistry » Magnesium » PDB 4cgk-4cs3 » 4cn2
Atomistry »
  Magnesium »
    PDB 4cgk-4cs3 »
      4cn2 »

Magnesium in PDB 4cn2: Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element

Protein crystallography data

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element, PDB code: 4cn2 was solved by A.G.Mcewen, P.Poussin-Courmontagne, J.Osz, N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.898 / 2.07
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.234, 43.952, 63.316, 90.00, 106.02, 90.00
R / Rfree (%) 16.48 / 21.42

Other elements in 4cn2:

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element (pdb code 4cn2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element, PDB code: 4cn2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4cn2

Go back to Magnesium Binding Sites List in 4cn2
Magnesium binding site 1 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1035

b:34.3
occ:1.00
 O A:HOH2039 2.7 37.7 1.0
O C:LYS145 2.8 20.0 1.0
OP2 A:DG2 2.9 27.7 1.0
N C:LYS145 3.3 14.3 1.0
O5' A:DG2 3.3 27.6 1.0
C8 A:DG2 3.5 30.1 1.0
C C:GLY144 3.5 19.4 1.0
C2' A:DT1 3.5 26.0 1.0
CA C:GLY144 3.6 17.3 1.0
C2' A:DG2 3.7 26.6 1.0
P A:DG2 3.7 29.1 1.0
C C:LYS145 3.7 22.7 1.0
CE1 C:HIS146 3.8 26.7 1.0
CA C:LYS145 4.0 19.4 1.0
C3' A:DT1 4.0 26.8 1.0
ND1 C:HIS146 4.2 26.9 1.0
O C:GLY144 4.3 15.1 1.0
N C:GLY144 4.3 24.0 1.0
O3' A:DT1 4.3 26.9 1.0
NE2 C:HIS146 4.3 28.0 1.0
N9 A:DG2 4.4 30.4 1.0
N7 A:DG2 4.4 33.2 1.0
C1' A:DG2 4.4 25.3 1.0
C3' A:DG2 4.5 25.9 1.0
O C:SER143 4.5 31.7 1.0
C5' A:DG2 4.6 27.1 1.0
O4' A:DG2 4.6 26.9 1.0
C C:SER143 4.7 30.6 1.0
OG C:SER143 4.8 32.8 1.0
CB C:LYS145 4.8 27.7 1.0
O A:HOH2001 4.8 28.4 1.0
C4' A:DG2 4.8 28.8 1.0
CG C:HIS146 4.9 20.4 1.0
N C:HIS146 4.9 18.7 1.0
O A:HOH2010 4.9 38.8 1.0
CD2 C:HIS146 4.9 21.8 1.0
O A:HOH2003 5.0 37.5 1.0
C1' A:DT1 5.0 29.7 1.0

Magnesium binding site 2 out of 7 in 4cn2

Go back to Magnesium Binding Sites List in 4cn2
Magnesium binding site 2 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1036

b:36.5
occ:1.00
 OP2 A:DG10 2.7 23.2 1.0
O A:HOH2029 2.8 29.5 1.0
ND1 D:HIS146 2.8 30.2 1.0
O A:HOH2026 3.4 34.6 1.0
C8 A:DG10 3.5 35.0 1.0
CB D:HIS146 3.6 23.4 1.0
CG D:HIS146 3.6 33.5 1.0
CA D:HIS146 3.7 29.5 1.0
N7 A:DG10 3.7 23.9 1.0
C2' A:DA9 3.7 28.0 1.0
C5' A:DG10 3.8 23.6 1.0
CE1 D:HIS146 3.9 30.1 1.0
P A:DG10 3.9 25.4 1.0
O3' A:DA9 4.1 27.3 1.0
CD D:LYS156 4.1 39.2 1.0
O D:LYS145 4.3 33.4 1.0
CE D:LYS156 4.3 42.0 1.0
N D:TYR147 4.4 25.4 1.0
C3' A:DA9 4.4 30.3 1.0
O5' A:DG10 4.4 26.1 1.0
CZ D:TYR147 4.5 26.2 1.0
C D:HIS146 4.5 28.1 1.0
CE1 D:TYR147 4.5 20.5 1.0
C1' A:DA9 4.6 26.6 1.0
CG D:LYS156 4.7 30.2 1.0
CE2 D:TYR147 4.7 25.6 1.0
N9 A:DG10 4.8 32.3 1.0
OH D:TYR147 4.8 24.6 1.0
NZ D:LYS156 4.8 43.9 1.0
N D:HIS146 4.8 30.4 1.0
C4' A:DG10 4.8 21.0 1.0
CD2 D:HIS146 4.8 35.4 1.0
CD1 D:TYR147 4.9 20.0 1.0
O4' A:DG10 4.9 22.4 1.0
NE2 D:HIS146 5.0 37.6 1.0
OP2 A:DG11 5.0 21.9 1.0
C D:LYS145 5.0 36.3 1.0
C5 A:DG10 5.0 25.3 1.0

Magnesium binding site 3 out of 7 in 4cn2

Go back to Magnesium Binding Sites List in 4cn2
Magnesium binding site 3 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1035

b:40.3
occ:1.00
 O B:HOH2032 2.6 34.5 1.0
O B:HOH2031 2.9 44.6 1.0
OP2 B:DT9 2.9 42.4 1.0
O5' B:DT9 3.3 34.9 1.0
NZ C:LYS165 3.5 57.3 1.0
C2' B:DT9 3.5 19.3 1.0
P B:DT9 3.7 43.0 1.0
C6 B:DT9 3.8 28.6 1.0
C7 B:DT10 4.0 21.4 1.0
C3' B:DT9 4.0 25.5 1.0
CD C:ARG161 4.2 24.9 1.0
C7 B:DT9 4.4 26.3 1.0
OP1 B:DT9 4.4 35.9 1.0
C5 B:DT9 4.5 27.8 1.0
C5' B:DT9 4.5 27.9 1.0
C1' B:DT9 4.5 18.8 1.0
CE C:LYS165 4.5 54.8 1.0
N1 B:DT9 4.5 27.7 1.0
C4' B:DT9 4.6 28.0 1.0
O B:HOH2015 4.6 46.3 1.0
NE C:ARG161 4.7 20.5 1.0
O4' B:DT9 4.8 26.5 1.0
C2' B:DC8 4.9 28.8 1.0
O A:HOH2018 4.9 32.8 1.0
CD C:LYS165 4.9 46.3 1.0
O B:HOH2018 5.0 26.3 1.0

Magnesium binding site 4 out of 7 in 4cn2

Go back to Magnesium Binding Sites List in 4cn2
Magnesium binding site 4 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1215

b:29.3
occ:1.00
 OP2 B:DA12 2.7 26.5 1.0
N C:GLY154 2.9 14.4 1.0
OD2 C:ASP140 3.1 21.3 1.0
CB C:CYS152 3.4 14.7 1.0
SG C:CYS152 3.4 17.2 1.0
N C:GLU153 3.5 19.5 1.0
P B:DA12 3.6 24.7 1.0
CA C:GLY154 3.6 12.1 1.0
C3' B:DG11 3.6 20.8 1.0
MG C:MG1217 3.6 37.4 1.0
NH2 C:ARG184 3.7 22.3 1.0
O C:HOH2016 3.8 27.6 1.0
C C:GLU153 3.9 18.1 1.0
OP1 B:DA12 3.9 24.9 1.0
NH1 C:ARG184 3.9 20.4 1.0
O3' B:DG11 4.0 28.1 1.0
CA C:GLU153 4.1 15.9 1.0
CG C:ASP140 4.1 26.7 1.0
C C:CYS152 4.2 18.1 1.0
CZ C:ARG184 4.2 23.6 1.0
C2' B:DG11 4.2 19.5 1.0
CB C:GLU153 4.2 18.5 1.0
CA C:CYS152 4.4 10.6 1.0
CB C:ASP140 4.8 20.9 1.0
O5' B:DG11 4.9 17.8 1.0
C C:GLY154 4.9 19.5 1.0
C4' B:DG11 4.9 20.3 1.0
O C:GLU153 5.0 16.6 1.0
OD1 C:ASP140 5.0 20.2 1.0

Magnesium binding site 5 out of 7 in 4cn2

Go back to Magnesium Binding Sites List in 4cn2
Magnesium binding site 5 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1216

b:30.6
occ:1.00
 O C:LEU196 2.6 22.2 1.0
O C:MET200 2.9 25.7 1.0
C C:GLY199 3.3 25.7 1.0
NZ C:LYS201 3.3 49.3 1.0
CA C:GLY199 3.4 22.1 1.0
N C:MET200 3.5 17.7 1.0
C C:LEU196 3.6 21.4 1.0
O C:GLY199 3.7 24.9 1.0
C C:MET200 3.7 20.5 1.0
CA C:LEU196 3.8 19.0 1.0
N C:GLY199 3.9 16.8 1.0
CE C:LYS201 4.1 57.3 1.0
CA C:MET200 4.2 14.5 1.0
CD C:LYS201 4.3 55.7 1.0
O C:HOH2051 4.3 25.4 1.0
CB C:LEU196 4.3 18.3 1.0
CD2 C:LEU196 4.4 21.0 1.0
O C:CYS195 4.6 17.9 1.0
N C:LYS201 4.7 21.4 1.0
N C:ALA197 4.8 15.1 1.0
O C:HOH2052 4.9 35.1 1.0
N C:LEU196 5.0 19.0 1.0

Magnesium binding site 6 out of 7 in 4cn2

Go back to Magnesium Binding Sites List in 4cn2
Magnesium binding site 6 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1217

b:37.4
occ:1.00
 OD2 C:ASP140 2.6 21.3 1.0
O C:HOH2037 2.7 38.0 1.0
OP1 B:DA12 2.7 24.9 1.0
NH2 C:ARG184 3.3 22.3 1.0
CG C:ASP140 3.6 26.7 1.0
MG C:MG1215 3.6 29.3 1.0
CD C:LYS181 3.7 39.5 1.0
P B:DA12 3.8 24.7 1.0
OP2 B:DA12 3.8 26.5 1.0
OD1 C:ASP140 3.9 20.2 1.0
NH1 C:ARG184 4.0 20.4 1.0
CZ C:ARG184 4.0 23.6 1.0
CG C:LYS181 4.3 34.0 1.0
C3' B:DG11 4.8 20.8 1.0
CE C:LYS181 4.8 38.5 1.0
O B:HOH2006 4.8 50.0 1.0
O3' B:DG11 4.8 28.1 1.0
CB C:ASP140 4.9 20.9 1.0
O5' B:DA12 4.9 24.0 1.0
NZ C:LYS181 5.0 35.0 1.0

Magnesium binding site 7 out of 7 in 4cn2

Go back to Magnesium Binding Sites List in 4cn2
Magnesium binding site 7 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1218

b:36.3
occ:1.00
 O D:GLY154 2.7 23.5 1.0
NH2 D:ARG161 2.8 27.8 1.0
OP2 B:DG4 2.8 25.9 1.0
C2' B:DT3 3.2 23.9 1.0
N D:PHE158 3.4 18.9 1.0
C D:GLY154 3.4 25.8 1.0
C3' B:DT3 3.5 30.0 1.0
C8 B:DG4 3.5 26.3 1.0
CA D:GLY154 3.6 28.3 1.0
CZ D:ARG161 3.7 26.0 1.0
NH1 D:ARG161 3.8 22.6 1.0
P B:DG4 3.9 31.9 1.0
O5' B:DG4 3.9 31.8 1.0
CB D:PHE158 3.9 21.1 1.0
N7 B:DG4 3.9 21.0 1.0
CA D:PHE158 4.0 21.4 1.0
C D:GLY157 4.1 18.9 1.0
O3' B:DT3 4.1 29.7 1.0
NH1 D:ARG191 4.3 32.3 1.0
CA D:GLY157 4.3 24.1 1.0
O5' B:DT3 4.4 30.9 1.0
O D:GLU153 4.4 28.0 1.0
NH2 D:ARG191 4.5 27.1 1.0
N D:GLY157 4.6 25.1 1.0
N9 B:DG4 4.6 30.3 1.0
C1' B:DT3 4.7 25.2 1.0
N D:CYS155 4.7 25.9 1.0
C2' B:DG4 4.7 37.4 1.0
CZ D:ARG191 4.8 32.5 1.0
C4' B:DT3 4.8 30.9 1.0
N D:GLY154 4.8 27.6 1.0
O D:GLY157 4.9 19.2 1.0
NE D:ARG161 5.0 23.4 1.0

Reference:

J.Osz, A.G.Mcewen, P.Poussin-Courmontagne, E.Moutier, C.Birck, I.Davidson, D.Moras, N.Rochel. Structural Basis of Natural Promoter Recognition By the Retinoid X Nuclear Receptor. Sci.Rep. V. 5 8216 2015.
ISSN: ISSN 2045-2322
PubMed: 25645674
DOI: 10.1038/SREP08216
Page generated: Mon Dec 14 11:41:25 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy