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Zinc in PDB 4nqa: Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna

Protein crystallography data

The structure of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna, PDB code: 4nqa was solved by X.H.Lou, G.Toresson, C.Benod, J.H.Suh, K.J.Phillips, P.Webb, J.A.Gustafsson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.97 / 3.10
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 85.783, 85.783, 238.577, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.8

Other elements in 4nqa:

The structure of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna (pdb code 4nqa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna, PDB code: 4nqa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4nqa

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Zinc binding site 1 out of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:53.3
occ:1.00
 SG A:CYS138 2.3 0.1 1.0
SG A:CYS155 2.3 53.6 1.0
SG A:CYS152 2.3 82.0 1.0
SG A:CYS135 2.3 49.4 1.0
CB A:CYS155 3.4 53.6 1.0
CB A:CYS135 3.4 49.4 1.0
CB A:CYS138 3.7 0.1 1.0
NH1 A:ARG184 3.7 87.7 1.0
N A:CYS152 3.8 82.0 1.0
CB A:CYS152 3.8 82.0 1.0
N A:CYS138 4.0 0.1 1.0
N A:CYS155 4.0 53.6 1.0
CA A:CYS152 4.3 82.0 1.0
CA A:CYS155 4.3 53.6 1.0
CA A:CYS138 4.4 0.1 1.0
CB A:SER151 4.7 28.2 1.0
CB A:ILE137 4.7 69.4 1.0
C A:SER151 4.8 28.2 1.0
CB A:ASP140 4.8 41.1 1.0
CA A:CYS135 4.8 49.4 1.0
O A:CYS152 4.8 82.0 1.0
C A:CYS152 4.8 82.0 1.0
CA A:SER151 4.9 28.2 1.0
CZ A:ARG184 4.9 87.7 1.0
NH2 A:ARG191 5.0 63.3 1.0

Zinc binding site 2 out of 8 in 4nqa

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Zinc binding site 2 out of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:83.5
occ:1.00
 SG A:CYS177 2.3 95.1 1.0
SG A:CYS190 2.3 60.6 1.0
SG A:CYS187 2.3 0.0 1.0
SG A:CYS171 2.3 0.5 1.0
CB A:CYS177 3.1 95.1 1.0
CB A:CYS190 3.4 60.6 1.0
CB A:CYS171 3.4 0.5 1.0
CB A:CYS187 3.6 0.0 1.0
N A:CYS190 4.1 60.6 1.0
CA A:CYS190 4.4 60.6 1.0
CA A:CYS177 4.4 95.1 1.0
N A:CYS177 4.5 95.1 1.0
CD2 A:TYR189 4.5 0.7 1.0
CB A:ASP173 4.7 64.2 1.0
N A:LYS175 4.7 99.9 1.0
CA A:CYS171 4.8 0.5 1.0
CB A:TYR189 4.9 0.7 1.0
CA A:LYS175 5.0 99.9 1.0
CA A:CYS187 5.0 0.0 1.0

Zinc binding site 3 out of 8 in 4nqa

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Zinc binding site 3 out of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:68.5
occ:1.00
 SG B:CYS90 2.2 83.3 1.0
SG B:CYS104 2.3 71.2 1.0
SG B:CYS107 2.3 57.7 1.0
SG B:CYS87 2.4 58.0 1.0
CB B:CYS87 3.4 58.0 1.0
CB B:CYS90 3.5 83.3 1.0
CB B:CYS107 3.6 57.7 1.0
N B:CYS90 3.7 83.3 1.0
N B:CYS104 3.9 71.2 1.0
CB B:CYS104 4.0 71.2 1.0
CA B:CYS90 4.1 83.3 1.0
N B:GLY91 4.3 90.9 1.0
CB B:VAL89 4.3 37.1 1.0
CB B:SER103 4.5 98.7 1.0
N B:ASP92 4.5 32.4 1.0
CA B:CYS104 4.5 71.2 1.0
CB B:ASP92 4.5 32.4 1.0
N B:CYS107 4.6 57.7 1.0
NH1 B:ARG138 4.7 96.3 1.0
CA B:CYS107 4.7 57.7 1.0
C B:CYS90 4.8 83.3 1.0
CA B:SER103 4.8 98.7 1.0
C B:VAL89 4.8 37.1 1.0
C B:SER103 4.8 98.7 1.0
CA B:CYS87 4.9 58.0 1.0
CG1 B:VAL89 5.0 37.1 1.0
CA B:VAL89 5.0 37.1 1.0

Zinc binding site 4 out of 8 in 4nqa

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Zinc binding site 4 out of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:0.8
occ:1.00
 SG B:CYS125 2.3 0.7 1.0
SG B:CYS144 2.3 78.3 1.0
SG B:CYS141 2.4 89.0 1.0
SG B:CYS131 2.4 0.3 1.0
CB B:CYS125 3.1 0.7 1.0
CB B:CYS141 3.3 89.0 1.0
CB B:CYS131 3.5 0.3 1.0
CB B:CYS144 3.7 78.3 1.0
O B:GLY128 3.8 1.0 1.0
CA B:CYS125 4.1 0.7 1.0
N B:CYS144 4.7 78.3 1.0
CA B:CYS141 4.7 89.0 1.0
C B:GLY128 4.7 1.0 1.0
CA B:CYS144 4.8 78.3 1.0
CA B:CYS131 4.8 0.3 1.0
C B:CYS125 4.9 0.7 1.0
NH2 B:ARG147 4.9 54.1 1.0

Zinc binding site 5 out of 8 in 4nqa

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Zinc binding site 5 out of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn502

b:48.8
occ:1.00
 SG H:CYS138 2.2 58.6 1.0
SG H:CYS155 2.3 50.5 1.0
SG H:CYS152 2.3 62.9 1.0
SG H:CYS135 2.3 50.6 1.0
CB H:CYS155 3.4 50.5 1.0
CB H:CYS138 3.5 58.6 1.0
CB H:CYS135 3.6 50.6 1.0
CB H:CYS152 3.8 62.9 1.0
N H:CYS152 3.8 62.9 1.0
N H:CYS138 3.9 58.6 1.0
NH1 H:ARG184 3.9 91.1 1.0
N H:CYS155 4.0 50.5 1.0
CA H:CYS138 4.2 58.6 1.0
CG2 H:ILE137 4.2 0.2 1.0
CA H:CYS152 4.3 62.9 1.0
CA H:CYS155 4.3 50.5 1.0
CB H:ASP140 4.3 58.5 1.0
N H:ASP140 4.8 58.5 1.0
C H:CYS152 4.8 62.9 1.0
O H:CYS152 4.8 62.9 1.0
C H:CYS138 4.8 58.6 1.0
CG1 H:ILE137 4.8 0.2 1.0
CB H:SER151 4.9 32.7 1.0
N H:GLY139 4.9 41.5 1.0
C H:SER151 4.9 32.7 1.0
CA H:CYS135 5.0 50.6 1.0
CA H:SER151 5.0 32.7 1.0
CB H:ILE137 5.0 0.2 1.0

Zinc binding site 6 out of 8 in 4nqa

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Zinc binding site 6 out of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn503

b:0.2
occ:1.00
 SG H:CYS187 2.2 0.9 1.0
SG H:CYS190 2.3 99.1 1.0
SG H:CYS177 2.3 89.2 1.0
SG H:CYS171 2.4 0.6 1.0
CB H:CYS190 3.2 99.1 1.0
CB H:CYS187 3.5 0.9 1.0
CB H:CYS177 3.5 89.2 1.0
CB H:CYS171 3.8 0.6 1.0
O H:ASN174 3.8 0.5 1.0
N H:CYS190 4.0 99.1 1.0
CA H:LYS175 4.1 0.5 1.0
CA H:CYS190 4.2 99.1 1.0
N H:ASP176 4.4 0.8 1.0
CB H:LYS175 4.5 0.5 1.0
N H:CYS177 4.6 89.2 1.0
CA H:CYS177 4.7 89.2 1.0
C H:ASN174 4.7 0.5 1.0
C H:ASP176 4.8 0.8 1.0
C H:LYS175 4.8 0.5 1.0
CA H:CYS187 4.8 0.9 1.0
CA H:CYS171 4.9 0.6 1.0
N H:LYS175 4.9 0.5 1.0
O H:ASP176 5.0 0.8 1.0

Zinc binding site 7 out of 8 in 4nqa

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Zinc binding site 7 out of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn502

b:73.4
occ:1.00
 SG I:CYS104 2.3 73.2 1.0
SG I:CYS90 2.3 62.4 1.0
SG I:CYS107 2.3 56.2 1.0
SG I:CYS87 2.4 95.0 1.0
CB I:CYS107 3.6 56.2 1.0
CB I:CYS87 3.7 95.0 1.0
CB I:CYS90 3.7 62.4 1.0
CB I:CYS104 3.7 73.2 1.0
NH1 I:ARG138 3.8 47.2 1.0
N I:CYS90 3.9 62.4 1.0
N I:CYS104 4.1 73.2 1.0
CB I:VAL89 4.3 52.0 1.0
CA I:CYS90 4.4 62.4 1.0
N I:CYS107 4.4 56.2 1.0
CA I:CYS104 4.5 73.2 1.0
N I:GLY91 4.5 71.4 1.0
N I:ASP92 4.5 95.9 1.0
CB I:ASP92 4.5 95.9 1.0
N I:VAL89 4.6 52.0 1.0
CA I:CYS107 4.6 56.2 1.0
O I:CYS87 4.8 95.0 1.0
CG2 I:VAL89 4.9 52.0 1.0
CA I:VAL89 4.9 52.0 1.0
C I:VAL89 4.9 52.0 1.0
C I:CYS87 4.9 95.0 1.0
CA I:CYS87 5.0 95.0 1.0
C I:CYS90 5.0 62.4 1.0

Zinc binding site 8 out of 8 in 4nqa

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Zinc binding site 8 out of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn503

b:0.2
occ:1.00
 SG I:CYS144 2.3 0.6 1.0
SG I:CYS141 2.3 0.8 1.0
SG I:CYS125 2.3 0.8 1.0
SG I:CYS131 2.3 0.4 1.0
CB I:CYS141 3.4 0.8 1.0
CB I:CYS144 3.4 0.6 1.0
CB I:CYS131 3.4 0.4 1.0
CB I:CYS125 3.7 0.8 1.0
N I:ARG126 4.2 92.5 1.0
N I:GLY127 4.2 95.4 1.0
N I:CYS144 4.3 0.6 1.0
CA I:CYS144 4.4 0.6 1.0
CA I:CYS125 4.4 0.8 1.0
CA I:GLY129 4.5 41.8 1.0
N I:GLY129 4.5 41.8 1.0
C I:GLY129 4.7 41.8 1.0
CA I:CYS131 4.7 0.4 1.0
CA I:GLY127 4.8 95.4 1.0
CA I:CYS141 4.8 0.8 1.0
O I:GLY129 4.8 41.8 1.0
C I:CYS125 4.9 0.8 1.0
C I:GLY127 4.9 95.4 1.0
N I:CYS131 4.9 0.4 1.0
O I:GLY127 4.9 95.4 1.0

Reference:

X.Lou, G.Toresson, C.Benod, J.H.Suh, K.J.Philips, P.Webb, J.A.Gustafsson. Structure of the Retinoid X Receptor Alpha-Liver X Receptor Beta (Rxr Alpha-Lxr Beta ) Heterodimer on Dna. Nat.Struct.Mol.Biol. V. 21 277 2014.
ISSN: ISSN 1545-9993
PubMed: 24561505
DOI: 10.1038/NSMB.2778
Page generated: Sun Oct 27 03:18:20 2024

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