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Zinc in PDB 6lc1: Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter

Protein crystallography data

The structure of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter, PDB code: 6lc1 was solved by L.Jiang, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.65 / 3.12
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.822, 63.210, 91.762, 109.98, 90.21, 89.54
R / Rfree (%) 20.9 / 26.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter (pdb code 6lc1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter, PDB code: 6lc1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6lc1

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Zinc binding site 1 out of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn401

b:96.1
occ:1.00
SG J:CYS303 2.4 93.9 1.0
SG J:CYS319 2.4 97.8 1.0
SG J:CYS309 2.5 94.4 1.0
SG J:CYS322 2.5 97.4 1.0
CB J:CYS303 3.2 90.5 1.0
CB J:CYS309 3.3 98.0 1.0
CB J:CYS319 3.3 93.9 1.0
CB J:CYS322 3.6 94.9 1.0
CA J:CYS303 4.1 90.3 1.0
CA J:CYS309 4.4 0.2 1.0
N J:CYS309 4.4 0.7 1.0
N J:CYS322 4.5 88.9 1.0
N J:LYS307 4.5 0.3 1.0
CA J:LYS307 4.5 0.6 1.0
CA J:CYS322 4.6 91.0 1.0
N J:ASP308 4.7 0.8 1.0
C J:ASP308 4.7 0.0 1.0
CB J:ALA305 4.7 95.0 1.0
CA J:CYS319 4.7 87.2 1.0
C J:LYS307 4.7 0.3 1.0
C J:CYS303 4.8 96.0 1.0
O J:ASP308 4.8 0.8 1.0
N J:ALA305 4.9 0.8 1.0

Zinc binding site 2 out of 8 in 6lc1

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Zinc binding site 2 out of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn402

b:87.6
occ:1.00
SG J:CYS287 2.4 78.1 1.0
SG J:CYS267 2.4 79.8 1.0
SG J:CYS270 2.5 94.4 1.0
SG J:CYS284 2.6 90.5 1.0
CB J:CYS284 2.9 82.5 1.0
CB J:CYS270 3.3 91.5 1.0
CB J:CYS287 3.4 79.7 1.0
CB J:CYS267 3.7 82.2 1.0
N J:CYS270 3.7 91.9 1.0
NH1 J:ARG316 4.0 89.9 1.0
N J:CYS284 4.0 85.0 1.0
CA J:CYS284 4.0 84.6 1.0
CA J:CYS270 4.1 89.5 1.0
N J:CYS287 4.1 74.7 1.0
CA J:CYS287 4.4 74.5 1.0
CB J:VAL269 4.4 83.7 1.0
N J:GLY271 4.7 82.0 1.0
C J:CYS270 4.8 85.5 1.0
NH2 J:ARG323 4.8 75.3 1.0
C J:VAL269 4.8 86.0 1.0
CD J:ARG316 4.9 84.0 1.0
CB J:ASP272 4.9 93.0 1.0
N J:ASP272 5.0 86.3 1.0

Zinc binding site 3 out of 8 in 6lc1

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Zinc binding site 3 out of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:81.1
occ:1.00
SG A:CYS270 2.4 0.5 1.0
SG A:CYS267 2.4 88.4 1.0
SG A:CYS287 2.6 79.3 1.0
CB A:CYS284 2.7 91.2 1.0
CB A:CYS270 3.2 0.2 1.0
N A:CYS270 3.6 99.8 1.0
CB A:CYS267 3.6 92.7 1.0
CB A:CYS287 3.6 79.0 1.0
N A:CYS284 3.8 81.5 1.0
CA A:CYS284 3.9 84.3 1.0
SG A:CYS284 3.9 0.3 1.0
CA A:CYS270 4.0 98.3 1.0
N A:CYS287 4.1 76.0 1.0
NH1 A:ARG316 4.1 80.5 1.0
CB A:VAL269 4.3 91.4 1.0
NH2 A:ARG323 4.4 82.2 1.0
CA A:CYS287 4.5 76.4 1.0
CB A:ASP272 4.5 0.5 1.0
C A:VAL269 4.7 94.3 1.0
C A:CYS284 4.7 82.5 1.0
CA A:VAL269 4.9 91.1 1.0
CG1 A:VAL269 4.9 90.9 1.0
N A:ASP272 4.9 0.2 1.0
N A:GLY271 5.0 97.2 1.0
N A:VAL269 5.0 90.0 1.0

Zinc binding site 4 out of 8 in 6lc1

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Zinc binding site 4 out of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:0.8
occ:1.00
SG A:CYS322 2.5 83.3 1.0
SG A:CYS303 2.5 0.8 1.0
SG A:CYS319 2.6 94.0 1.0
SG A:CYS309 2.7 0.3 1.0
CB A:CYS309 2.9 0.8 1.0
CB A:CYS319 3.1 99.7 1.0
N A:CYS309 3.5 0.6 1.0
CB A:CYS303 3.6 95.0 1.0
CB A:CYS322 3.6 90.3 1.0
CA A:CYS309 3.8 0.9 1.0
CA A:CYS303 4.4 96.7 1.0
N A:ASP308 4.5 99.9 1.0
N A:CYS322 4.6 87.7 1.0
CA A:CYS319 4.7 0.2 1.0
CB A:ALA305 4.7 0.2 1.0
C A:ASP308 4.7 0.8 1.0
CA A:CYS322 4.7 90.9 1.0
C A:LYS307 4.7 0.7 1.0
CA A:LYS307 4.9 0.4 1.0
N A:LYS307 4.9 0.1 1.0
N A:LEU304 4.9 0.3 1.0
C A:CYS303 4.9 0.4 1.0
N A:ALA305 4.9 0.0 1.0
C A:CYS309 4.9 0.9 1.0

Zinc binding site 5 out of 8 in 6lc1

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Zinc binding site 5 out of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:83.2
occ:1.00
SG D:CYS267 2.4 91.2 1.0
SG D:CYS287 2.4 89.6 1.0
SG D:CYS270 2.4 91.0 1.0
CB D:CYS270 2.5 89.7 1.0
SG D:CYS284 2.5 76.7 1.0
N D:CYS270 3.0 91.3 1.0
CA D:CYS270 3.3 89.2 1.0
CB D:CYS284 3.4 82.1 1.0
CB D:CYS267 3.6 91.5 1.0
N D:CYS284 3.9 83.7 1.0
CB D:CYS287 4.0 85.4 1.0
C D:VAL269 4.1 95.6 1.0
N D:GLY271 4.1 89.6 1.0
CA D:CYS284 4.2 83.0 1.0
C D:CYS270 4.2 85.1 1.0
NH1 D:ARG316 4.3 94.0 1.0
CB D:VAL269 4.3 85.4 1.0
N D:CYS287 4.5 79.9 1.0
CA D:VAL269 4.5 91.1 1.0
N D:VAL269 4.6 92.1 1.0
N D:ASP272 4.7 91.2 1.0
CB D:ASP272 4.7 96.0 1.0
CG1 D:VAL269 4.8 78.8 1.0
CA D:CYS287 4.9 79.0 1.0
C D:CYS284 4.9 84.6 1.0
CA D:CYS267 4.9 90.9 1.0
O D:CYS284 5.0 86.2 1.0

Zinc binding site 6 out of 8 in 6lc1

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Zinc binding site 6 out of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:98.7
occ:1.00
SG D:CYS303 2.3 89.8 1.0
SG D:CYS309 2.3 0.5 1.0
SG D:CYS319 2.3 94.4 1.0
SG D:CYS322 2.5 83.2 1.0
CB D:CYS303 3.1 87.4 1.0
CB D:CYS319 3.3 91.9 1.0
CB D:CYS322 3.4 82.7 1.0
CB D:CYS309 3.5 0.3 1.0
CA D:CYS303 4.0 86.8 1.0
N D:CYS309 4.2 0.6 1.0
N D:CYS322 4.2 81.5 1.0
CA D:CYS322 4.4 81.9 1.0
CA D:CYS309 4.5 0.2 1.0
CA D:LYS307 4.5 0.8 1.0
C D:CYS303 4.6 93.5 1.0
CA D:CYS319 4.7 85.1 1.0
N D:LYS307 4.7 0.8 1.0
N D:ASP308 4.7 0.5 1.0
N D:LEU304 4.9 96.0 1.0
N D:ALA305 4.9 0.4 1.0
CB D:ALA305 4.9 96.7 1.0
C D:LYS307 5.0 0.1 1.0

Zinc binding site 7 out of 8 in 6lc1

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Zinc binding site 7 out of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:77.1
occ:1.00
SG G:CYS267 2.3 86.5 1.0
SG G:CYS270 2.3 0.7 1.0
SG G:CYS287 2.7 83.2 1.0
SG G:CYS284 2.7 92.0 1.0
CB G:CYS270 3.2 0.6 1.0
CB G:CYS284 3.2 90.2 1.0
CB G:CYS267 3.4 89.5 1.0
N G:CYS270 3.6 96.4 1.0
CB G:CYS287 3.7 80.5 1.0
N G:CYS284 4.0 81.9 1.0
CA G:CYS270 4.0 0.3 1.0
CA G:CYS284 4.2 87.3 1.0
NH1 G:ARG316 4.3 98.8 1.0
N G:CYS287 4.3 76.7 1.0
CB G:VAL269 4.5 86.3 1.0
CB G:ASP272 4.5 0.5 1.0
C G:VAL269 4.6 96.5 1.0
CA G:CYS287 4.6 77.3 1.0
CA G:CYS267 4.8 88.3 1.0
N G:VAL269 4.9 93.5 1.0
C G:CYS284 4.9 89.9 1.0
CA G:VAL269 4.9 90.9 1.0
N G:ASP272 4.9 0.2 1.0
N G:GLY271 5.0 0.1 1.0

Zinc binding site 8 out of 8 in 6lc1

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Zinc binding site 8 out of 8 in the Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn402

b:0.6
occ:1.00
SG G:CYS319 2.4 99.4 1.0
SG G:CYS303 2.4 0.8 1.0
SG G:CYS322 2.4 100.0 1.0
SG G:CYS309 2.5 0.9 1.0
CB G:CYS309 3.1 0.1 1.0
CB G:CYS303 3.2 0.3 1.0
CB G:CYS319 3.2 0.1 1.0
CB G:CYS322 3.4 97.5 1.0
N G:CYS309 3.8 0.2 1.0
CA G:CYS309 4.0 0.8 1.0
CA G:CYS303 4.0 0.7 1.0
N G:CYS322 4.2 89.6 1.0
C G:ASP308 4.3 0.5 1.0
CA G:CYS322 4.3 93.5 1.0
N G:ASP308 4.4 0.6 1.0
CA G:CYS319 4.6 0.4 1.0
C G:LYS307 4.7 0.1 1.0
C G:CYS303 4.7 0.2 1.0
CA G:ASP308 4.8 0.2 1.0
O G:ASP308 4.8 0.3 1.0
CB G:ALA305 4.8 0.6 1.0
CD2 G:PHE321 4.8 95.0 1.0
CA G:LYS307 4.9 0.9 1.0
N G:LYS307 5.0 0.8 1.0
N G:ALA305 5.0 0.7 1.0

Reference:

L.Jiang, H.Wei, N.Yan, S.Dai, J.Li, L.Qu, X.Chen, M.Guo, Z.Chen, Y.Chen. Structural Basis of NR4A1 Bound to the Human Pituitary Proopiomelanocortin Gene Promoter. Biochem.Biophys.Res.Commun. 2019.
ISSN: ESSN 1090-2104
PubMed: 31822342
DOI: 10.1016/J.BBRC.2019.11.192
Page generated: Wed Dec 16 12:14:14 2020

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