Zinc in PDB 7wnh: Crystal Structure of NURR1 Binding to Nbre

Protein crystallography data

The structure of Crystal Structure of NURR1 Binding to Nbre, PDB code: 7wnh was solved by M.Zhao, T.Xu, N.Wang, Y.Guo, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.39 / 3.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 124.002, 124.002, 119.518, 90, 90, 120
R / Rfree (%) 22.3 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of NURR1 Binding to Nbre (pdb code 7wnh). 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 NURR1 Binding to Nbre, PDB code: 7wnh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7wnh

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Zinc binding site 1 out of 8 in the Crystal Structure of NURR1 Binding to Nbre


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 NURR1 Binding to Nbre within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:81.5
occ:1.00
 SG A:CYS266 2.1 103.5 1.0
SG A:CYS263 2.3 84.6 1.0
SG A:CYS283 2.3 68.2 1.0
SG A:CYS280 2.4 70.1 1.0
CB A:CYS266 3.1 80.2 1.0
CB A:CYS283 3.1 64.7 1.0
N A:CYS266 3.3 87.7 1.0
CB A:CYS280 3.6 74.9 1.0
CB A:CYS263 3.7 86.3 1.0
CA A:CYS266 3.7 82.0 1.0
CB A:VAL265 3.9 74.1 1.0
N A:CYS280 3.9 75.5 1.0
N A:CYS283 4.3 58.1 1.0
CA A:CYS283 4.3 61.6 1.0
CA A:CYS280 4.4 72.8 1.0
C A:VAL265 4.4 91.6 1.0
NH1 A:ARG312 4.4 77.6 1.0
CG1 A:VAL265 4.4 65.8 1.0
C A:CYS266 4.5 94.3 1.0
CA A:VAL265 4.5 79.0 1.0
N A:GLY267 4.6 99.8 1.0
N A:VAL265 4.7 70.9 1.0
CB A:ASP268 4.8 100.0 1.0
CG2 A:VAL265 4.9 77.2 1.0
O A:CYS280 4.9 72.1 1.0
NH2 A:ARG319 4.9 86.5 1.0
N A:ASP268 4.9 101.8 1.0
CA A:CYS263 5.0 87.0 1.0
C A:THR279 5.0 74.5 1.0

Zinc binding site 2 out of 8 in 7wnh

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Zinc binding site 2 out of 8 in the Crystal Structure of NURR1 Binding to Nbre


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 NURR1 Binding to Nbre within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:105.0
occ:1.00
 SG A:CYS315 2.1 93.4 1.0
SG A:CYS299 2.5 109.4 1.0
SG A:CYS305 2.5 97.0 1.0
SG A:CYS318 2.6 113.8 1.0
CB A:CYS315 3.2 105.3 1.0
CB A:CYS305 3.4 97.5 1.0
CB A:CYS318 3.6 110.4 1.0
CB A:CYS299 3.8 121.3 1.0
N A:CYS305 4.0 117.9 1.0
CA A:CYS299 4.2 112.7 1.0
CA A:CYS305 4.3 106.7 1.0
CA A:LYS303 4.5 123.5 1.0
N A:ASN304 4.5 124.3 1.0
N A:CYS318 4.6 92.0 1.0
CA A:CYS318 4.6 96.9 1.0
CA A:CYS315 4.6 99.3 1.0
N A:LEU300 4.6 110.4 1.0
CB A:ALA301 4.7 80.3 1.0
N A:LYS303 4.7 137.4 1.0
C A:CYS299 4.9 108.7 1.0
C A:LYS303 4.9 118.8 1.0
CD1 A:TYR317 5.0 85.8 1.0

Zinc binding site 3 out of 8 in 7wnh

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Zinc binding site 3 out of 8 in the Crystal Structure of NURR1 Binding to Nbre


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 NURR1 Binding to Nbre within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:92.3
occ:1.00
 SG B:CYS266 2.0 80.8 1.0
SG B:CYS280 2.3 86.6 1.0
SG B:CYS283 2.4 77.2 1.0
SG B:CYS263 2.4 84.4 1.0
CB B:CYS266 3.1 87.2 1.0
CB B:CYS283 3.3 73.1 1.0
CB B:CYS280 3.5 83.9 1.0
N B:CYS266 3.5 93.9 1.0
CB B:CYS263 3.7 84.8 1.0
CA B:CYS266 3.8 85.4 1.0
N B:CYS280 3.9 76.6 1.0
CB B:VAL265 4.1 80.0 1.0
NH1 B:ARG312 4.2 76.5 1.0
N B:CYS283 4.2 85.4 1.0
CA B:CYS280 4.3 77.4 1.0
CA B:CYS283 4.4 77.2 1.0
C B:CYS266 4.6 80.3 1.0
C B:VAL265 4.6 89.1 1.0
CG1 B:VAL265 4.6 79.2 1.0
CB B:ASP268 4.7 91.7 1.0
N B:GLY267 4.7 82.1 1.0
CA B:VAL265 4.8 77.7 1.0
N B:ASP268 4.9 95.6 1.0
O B:CYS280 4.9 70.1 1.0
NH2 B:ARG319 4.9 95.5 1.0
N B:VAL265 4.9 74.1 1.0
C B:CYS280 4.9 75.4 1.0
C B:THR279 5.0 74.7 1.0

Zinc binding site 4 out of 8 in 7wnh

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Zinc binding site 4 out of 8 in the Crystal Structure of NURR1 Binding to Nbre


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 NURR1 Binding to Nbre within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:91.5
occ:1.00
 SG B:CYS305 2.2 95.5 1.0
SG B:CYS315 2.4 102.2 1.0
SG B:CYS299 2.5 90.3 1.0
SG B:CYS318 2.6 112.2 1.0
CB B:CYS305 3.1 96.2 1.0
CB B:CYS315 3.4 110.0 1.0
N B:CYS305 3.7 83.6 1.0
CB B:CYS318 3.7 105.7 1.0
CB B:CYS299 3.9 102.7 1.0
CA B:CYS305 3.9 93.5 1.0
N B:ASN304 4.3 100.8 1.0
CA B:CYS299 4.3 109.2 1.0
CA B:LYS303 4.4 100.3 1.0
N B:LEU300 4.6 121.2 1.0
CB B:ALA301 4.6 114.0 1.0
N B:LYS303 4.6 111.4 1.0
C B:LYS303 4.8 103.4 1.0
CA B:CYS318 4.8 93.7 1.0
C B:ASN304 4.8 82.9 1.0
N B:CYS318 4.8 89.4 1.0
CA B:CYS315 4.8 119.2 1.0
C B:CYS299 4.9 124.1 1.0

Zinc binding site 5 out of 8 in 7wnh

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Zinc binding site 5 out of 8 in the Crystal Structure of NURR1 Binding to Nbre


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 NURR1 Binding to Nbre within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:124.2
occ:1.00
 SG C:CYS263 2.2 180.0 1.0
SG C:CYS283 2.2 90.6 1.0
SG C:CYS266 2.4 88.5 1.0
SG C:CYS280 2.7 83.8 1.0
CB C:CYS283 3.0 91.7 1.0
CB C:CYS266 3.2 96.4 1.0
N C:CYS266 3.2 102.4 1.0
CB C:VAL265 3.6 119.8 1.0
CB C:CYS263 3.7 184.4 1.0
CA C:CYS266 3.8 100.1 1.0
CB C:CYS280 3.8 98.9 1.0
N C:CYS280 3.9 102.9 1.0
CG1 C:VAL265 4.1 118.0 1.0
C C:VAL265 4.2 122.4 1.0
CA C:CYS283 4.3 88.5 1.0
CA C:VAL265 4.3 131.9 1.0
N C:CYS283 4.3 87.4 1.0
CA C:CYS280 4.4 92.5 1.0
N C:VAL265 4.5 136.1 1.0
CG2 C:VAL265 4.5 113.8 1.0
C C:CYS266 4.6 116.7 1.0
NH1 C:ARG312 4.7 114.1 1.0
N C:GLY267 4.7 121.6 1.0
CA C:THR279 4.9 126.7 1.0
C C:THR279 4.9 120.2 1.0
O C:CYS280 4.9 73.2 1.0
CA C:CYS263 5.0 176.4 1.0
CB C:THR279 5.0 133.0 1.0

Zinc binding site 6 out of 8 in 7wnh

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Zinc binding site 6 out of 8 in the Crystal Structure of NURR1 Binding to Nbre


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 NURR1 Binding to Nbre within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:182.0
occ:1.00
 SG C:CYS318 2.0 209.2 1.0
SG C:CYS299 2.5 130.8 1.0
SG C:CYS315 2.6 126.2 1.0
SG C:CYS305 2.7 140.0 1.0
CB C:CYS305 3.2 148.9 1.0
CB C:CYS318 3.3 182.8 1.0
N C:CYS305 3.4 134.2 1.0
CB C:CYS315 3.7 129.7 1.0
CA C:CYS305 3.9 147.2 1.0
N C:ASN304 3.9 140.5 1.0
CB C:CYS299 4.0 126.6 1.0
CA C:LYS303 4.0 171.6 1.0
C C:LYS303 4.3 161.2 1.0
CA C:CYS318 4.4 164.4 1.0
N C:LYS303 4.4 163.9 1.0
C C:ASN304 4.5 139.4 1.0
CA C:CYS299 4.5 132.4 1.0
N C:CYS318 4.5 162.2 1.0
CA C:ASN304 4.8 135.9 1.0
CD1 C:TYR317 4.8 131.7 1.0
CB C:ALA301 4.9 142.9 1.0

Zinc binding site 7 out of 8 in 7wnh

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Zinc binding site 7 out of 8 in the Crystal Structure of NURR1 Binding to Nbre


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 NURR1 Binding to Nbre within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:112.3
occ:1.00
 SG D:CYS263 2.1 113.0 1.0
SG D:CYS266 2.1 115.5 1.0
SG D:CYS280 2.5 64.5 1.0
SG D:CYS283 2.5 113.1 1.0
CB D:CYS266 3.2 118.9 1.0
CB D:CYS283 3.3 109.6 1.0
N D:CYS266 3.4 115.7 1.0
CB D:CYS263 3.5 117.7 1.0
CB D:CYS280 3.5 75.0 1.0
N D:CYS280 3.8 73.9 1.0
CA D:CYS266 3.8 115.6 1.0
CB D:VAL265 4.0 166.0 1.0
CA D:CYS280 4.2 69.4 1.0
NH1 D:ARG312 4.4 98.7 1.0
N D:CYS283 4.4 88.7 1.0
C D:VAL265 4.4 135.0 1.0
C D:CYS266 4.5 123.8 1.0
CA D:CYS283 4.5 101.6 1.0
N D:GLY267 4.5 117.3 1.0
CG1 D:VAL265 4.6 151.6 1.0
CA D:VAL265 4.6 147.7 1.0
CB D:ASP268 4.7 108.0 1.0
N D:VAL265 4.7 132.5 1.0
CA D:CYS263 4.8 122.8 1.0
N D:ASP268 4.8 122.2 1.0
C D:THR279 4.8 71.4 1.0
O D:CYS280 4.9 76.8 1.0
CA D:THR279 4.9 73.8 1.0
CG2 D:VAL265 4.9 178.4 1.0
C D:CYS280 5.0 73.0 1.0

Zinc binding site 8 out of 8 in 7wnh

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Zinc binding site 8 out of 8 in the Crystal Structure of NURR1 Binding to Nbre


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 NURR1 Binding to Nbre within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:188.2
occ:1.00
 SG D:CYS318 2.2 143.6 1.0
SG D:CYS305 2.5 118.6 1.0
SG D:CYS299 2.7 124.0 1.0
SG D:CYS315 2.7 128.0 1.0
CB D:CYS305 3.0 137.1 1.0
N D:CYS305 3.2 133.6 1.0
CB D:CYS318 3.4 141.8 1.0
CB D:CYS315 3.6 129.9 1.0
CA D:CYS305 3.6 141.0 1.0
N D:ASN304 3.8 164.5 1.0
CA D:LYS303 4.1 162.4 1.0
CB D:CYS299 4.1 125.8 1.0
C D:LYS303 4.3 158.0 1.0
C D:ASN304 4.3 151.9 1.0
N D:LYS303 4.4 170.6 1.0
CA D:CYS318 4.5 136.8 1.0
CA D:ASN304 4.7 159.4 1.0
CA D:CYS299 4.7 129.8 1.0
N D:CYS318 4.7 145.2 1.0
CB D:ALA301 4.8 131.6 1.0
C D:CYS305 4.9 162.5 1.0
N D:LEU300 5.0 145.4 1.0

Reference:

M.Zhao, T.Xu, N.Wang, Y.Guo, J.Liu. Crystal Structure of NURR1 Binding to Nbre To Be Published.
Page generated: Wed Oct 30 14:27:36 2024

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