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Zinc in PDB 6owu: The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+

Protein crystallography data

The structure of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+, PDB code: 6owu was solved by Z.Li, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.09 / 1.84
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.093, 63.039, 78.636, 94.86, 103.13, 117.44
R / Rfree (%) 19.9 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ (pdb code 6owu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+, PDB code: 6owu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6owu

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Zinc binding site 1 out of 9 in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:85.7
occ:1.00
 O A:HOH301 2.0 29.7 1.0
O A:HOH383 2.0 40.6 1.0
O A:ASN171 2.0 18.6 0.6
C A:ASN171 3.0 26.7 0.6
O A:PHE153 3.3 24.6 1.0
C A:ASN171 3.3 26.6 0.4
N A:PHE153 3.6 21.3 1.0
CA A:ASN171 3.7 28.9 0.6
CA A:ASN171 3.7 28.9 0.4
CA A:CYS1 3.9 22.7 1.0
CA A:GLY152 3.9 21.8 1.0
O A:HOH354 4.1 42.1 1.0
N A:CYS1 4.1 22.3 1.0
OH A:TYR161 4.1 27.1 1.0
CE1 A:HIS65 4.2 20.0 1.0
C A:PHE153 4.3 31.3 1.0
O A:HIS170 4.3 20.6 1.0
C A:GLY152 4.3 23.6 1.0
ND1 A:HIS65 4.4 21.0 1.0
O A:ASN171 4.4 23.9 0.4
CB A:ASN171 4.6 30.5 0.4
CB A:ASN171 4.6 30.6 0.6
CA A:PHE153 4.6 23.1 1.0
OD1 A:ASN171 4.7 33.8 0.6
CB A:CYS1 4.8 22.2 1.0
N A:ASN171 4.8 27.0 0.4
N A:ASN171 4.8 26.5 0.6
C A:CYS1 4.8 21.0 1.0
SG A:CYS1 4.9 30.5 1.0
CD1 A:PHE153 4.9 25.6 1.0
O A:SER151 5.0 19.7 1.0

Zinc binding site 2 out of 9 in 6owu

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Zinc binding site 2 out of 9 in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:79.3
occ:1.00
 O B:HOH301 2.0 27.4 1.0
O B:HOH371 2.0 31.9 1.0
O B:ASN171 2.0 23.9 0.5
C B:ASN171 3.1 25.3 0.5
O B:PHE153 3.3 26.0 1.0
C B:ASN171 3.5 24.8 0.5
N B:PHE153 3.6 21.1 1.0
CA B:ASN171 3.7 27.5 0.5
CA B:ASN171 3.8 27.3 0.5
CA B:GLY152 3.9 20.9 1.0
CA B:CYS1 4.0 22.0 1.0
OH B:TYR161 4.1 28.5 1.0
CE1 B:HIS65 4.2 24.1 1.0
N B:CYS1 4.2 27.4 1.0
ND2 B:ASN171 4.3 30.7 0.5
C B:PHE153 4.3 28.3 1.0
C B:GLY152 4.3 28.9 1.0
ZN B:ZN202 4.4 82.5 1.0
O B:HIS170 4.4 23.7 1.0
ND1 B:HIS65 4.5 20.2 1.0
O B:ASN171 4.6 26.5 0.5
CB B:ASN171 4.6 31.6 0.5
CB B:ASN171 4.6 31.3 0.5
CA B:PHE153 4.6 24.1 1.0
CD1 B:PHE153 4.7 27.7 1.0
CB B:CYS1 4.8 26.4 1.0
C B:CYS1 4.9 24.4 1.0
CE1 B:PHE153 4.9 24.7 1.0
N B:ASN171 4.9 27.0 0.5
N B:ASN171 4.9 27.4 0.5
O B:SER151 5.0 18.5 1.0
CZ B:TYR161 5.0 24.2 1.0
CG B:ASN171 5.0 30.9 0.5

Zinc binding site 3 out of 9 in 6owu

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Zinc binding site 3 out of 9 in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:82.5
occ:1.00
 N B:CYS1 2.0 27.4 1.0
SG B:CYS1 2.0 34.4 1.0
CA B:CYS1 2.8 22.0 1.0
CB B:CYS1 2.9 26.4 1.0
OG1 B:THR62 3.8 20.1 1.0
O B:ASN171 4.1 23.9 0.5
C B:CYS1 4.2 24.4 1.0
ND1 B:HIS65 4.2 20.2 1.0
OD1 B:ASN64 4.3 20.6 1.0
ZN B:ZN201 4.4 79.3 1.0
O B:CYS1 4.6 18.8 1.0
ND2 B:ASN64 4.6 27.6 1.0
CG B:ASN64 4.8 22.6 1.0
CA B:HIS65 4.8 18.6 1.0
CB B:HIS65 4.9 18.1 1.0
CB B:THR62 5.0 19.4 1.0

Zinc binding site 4 out of 9 in 6owu

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Zinc binding site 4 out of 9 in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:67.0
occ:1.00
 O C:HOH301 2.0 31.5 1.0
O C:HOH355 2.0 32.4 1.0
O C:ASN171 2.0 21.4 0.4
C C:ASN171 3.1 25.9 0.4
O C:PHE153 3.2 26.2 1.0
N C:PHE153 3.5 21.3 1.0
C C:ASN171 3.7 24.1 0.6
CA C:ASN171 3.8 30.5 0.4
OH C:TYR161 3.9 25.0 1.0
CA C:GLY152 3.9 21.3 1.0
CA C:ASN171 3.9 30.8 0.6
CA C:CYS1 4.1 19.2 1.0
C C:PHE153 4.2 25.8 1.0
C C:GLY152 4.2 22.4 1.0
O C:HIS170 4.3 21.8 1.0
CE1 C:HIS65 4.4 19.3 1.0
CD1 C:PHE153 4.4 20.9 1.0
N C:CYS1 4.4 23.1 1.0
CA C:PHE153 4.5 23.0 1.0
OD1 C:ASN171 4.5 35.3 0.6
CE1 C:PHE153 4.6 23.2 1.0
ND1 C:HIS65 4.6 21.7 1.0
CB C:ASN171 4.7 31.5 0.4
CG C:PHE153 4.8 23.5 1.0
CZ C:TYR161 4.8 25.1 1.0
O C:ASN171 4.8 22.1 0.6
CB C:ASN171 4.8 31.5 0.6
N C:ASN171 4.9 29.7 0.4
CE1 C:TYR161 4.9 28.8 1.0
N C:ASN171 4.9 29.7 0.6
O C:SER151 4.9 19.7 1.0
CB C:CYS1 4.9 23.4 1.0

Zinc binding site 5 out of 9 in 6owu

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Zinc binding site 5 out of 9 in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:69.0
occ:1.00
 O D:HOH302 2.0 26.9 1.0
O D:HOH376 2.0 30.1 1.0
O D:ASN171 2.0 21.2 0.4
C D:ASN171 3.0 25.7 0.4
O D:PHE153 3.2 21.2 1.0
CA D:ASN171 3.5 24.2 0.4
N D:PHE153 3.5 22.4 1.0
C D:ASN171 3.5 25.3 0.6
CA D:ASN171 3.5 24.1 0.6
CA D:GLY152 3.9 20.5 1.0
OH D:TYR161 4.0 29.4 1.0
CA D:CYS1 4.1 20.1 1.0
CB D:ASN171 4.1 25.4 0.6
CB D:ASN171 4.1 25.4 0.4
ZN D:ZN202 4.2 70.7 1.0
C D:PHE153 4.2 26.5 1.0
C D:GLY152 4.2 23.9 1.0
N D:CYS1 4.3 26.1 1.0
CE1 D:HIS65 4.3 20.2 1.0
O D:HIS170 4.4 19.0 1.0
CA D:PHE153 4.5 23.8 1.0
ND1 D:HIS65 4.5 21.7 1.0
CD1 D:PHE153 4.5 26.8 1.0
O D:ASN171 4.7 19.7 0.6
CE1 D:PHE153 4.7 29.3 1.0
N D:ASN171 4.7 24.5 0.4
N D:ASN171 4.7 24.5 0.6
CG D:PHE153 4.8 26.8 1.0
O D:SER151 4.9 20.7 1.0
CB D:CYS1 4.9 25.8 1.0
CZ D:TYR161 4.9 25.5 1.0
C D:CYS1 5.0 18.7 1.0

Zinc binding site 6 out of 9 in 6owu

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Zinc binding site 6 out of 9 in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:70.7
occ:1.00
 N D:CYS1 2.0 26.1 1.0
SG D:CYS1 2.1 27.9 1.0
CA D:CYS1 2.7 20.1 1.0
CB D:CYS1 2.9 25.8 1.0
OG1 D:THR62 3.9 18.0 1.0
O D:ASN171 4.0 21.2 0.4
C D:CYS1 4.1 18.7 1.0
ZN D:ZN201 4.2 69.0 1.0
ND1 D:HIS65 4.2 21.7 1.0
O D:HOH319 4.3 29.9 1.0
OD1 D:ASN64 4.5 22.4 1.0
O D:HOH389 4.5 44.8 1.0
O D:CYS1 4.6 16.7 1.0
ND2 D:ASN64 4.7 29.6 1.0
CA D:GLY152 4.7 20.5 1.0
CA D:HIS65 4.8 18.8 1.0
CB D:HIS65 4.8 17.5 1.0
CG D:ASN64 4.9 25.1 1.0
CG D:HIS65 5.0 20.6 1.0

Zinc binding site 7 out of 9 in 6owu

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Zinc binding site 7 out of 9 in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:75.3
occ:1.00
 O E:HOH301 2.0 29.1 1.0
O E:HOH361 2.0 30.4 1.0
O E:ASN171 2.0 27.7 0.4
C E:ASN171 3.2 26.5 0.4
O E:PHE153 3.5 26.0 1.0
N E:PHE153 3.5 21.8 1.0
C E:ASN171 3.6 26.2 0.6
CA E:GLY152 3.7 21.4 1.0
CA E:CYS1 3.8 17.0 1.0
OH E:TYR161 3.9 34.5 1.0
CA E:ASN171 4.0 29.2 0.6
CA E:ASN171 4.0 29.2 0.4
CE1 E:HIS65 4.1 23.0 1.0
N E:CYS1 4.2 21.4 1.0
C E:GLY152 4.2 26.4 1.0
ND1 E:HIS65 4.3 20.8 1.0
C E:PHE153 4.4 28.0 1.0
O E:HIS170 4.5 24.5 1.0
CA E:PHE153 4.6 24.7 1.0
O E:ASN171 4.6 26.8 0.6
CB E:CYS1 4.7 22.2 1.0
C E:CYS1 4.7 19.0 1.0
O E:SER151 4.7 18.9 1.0
CD1 E:PHE153 4.8 22.8 1.0
N E:LEU2 4.8 17.9 1.0
CG E:LEU2 4.8 19.5 1.0
CB E:ASN171 4.9 29.9 0.6
SG E:CYS1 4.9 32.2 1.0
CE1 E:PHE153 4.9 29.1 1.0
CZ E:TYR161 4.9 27.6 1.0
CG E:PHE153 4.9 23.6 1.0
N E:GLY152 5.0 23.9 1.0
CB E:ASN171 5.0 30.7 0.4

Zinc binding site 8 out of 9 in 6owu

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Zinc binding site 8 out of 9 in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:65.0
occ:1.00
 O F:HOH302 2.0 27.8 1.0
O F:HOH364 2.0 31.4 1.0
O F:ASN171 2.0 26.2 0.4
O F:PHE153 3.0 21.9 1.0
C F:ASN171 3.1 25.1 0.4
N F:PHE153 3.3 25.7 1.0
C F:ASN171 3.4 24.9 0.6
CA F:ASN171 3.5 26.1 0.4
CA F:ASN171 3.5 26.1 0.6
CA F:GLY152 3.8 20.1 1.0
ZN F:ZN202 3.9 87.0 1.0
CB F:ASN171 4.0 25.3 0.4
C F:PHE153 4.0 26.4 1.0
CB F:ASN171 4.0 25.2 0.6
CA F:CYS1 4.1 21.5 1.0
C F:GLY152 4.1 25.4 1.0
OH F:TYR161 4.2 27.9 1.0
CA F:PHE153 4.3 29.6 1.0
N F:CYS1 4.4 24.1 1.0
CE1 F:HIS65 4.4 21.3 1.0
O F:ASN171 4.5 21.2 0.6
CD1 F:PHE153 4.6 27.6 1.0
O F:HIS170 4.6 22.3 1.0
ND1 F:HIS65 4.7 21.7 1.0
CG F:PHE153 4.7 24.2 1.0
O F:SER151 4.8 20.4 1.0
CE1 F:PHE153 4.8 25.7 1.0
N F:ASN171 4.8 24.5 0.4
CB F:CYS1 4.8 23.1 1.0
N F:ASN171 4.8 24.5 0.6
ND2 F:ASN171 4.9 28.2 0.6

Zinc binding site 9 out of 9 in 6owu

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Zinc binding site 9 out of 9 in the The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The PRP8 Intein of Cryptococcus Neoformans in Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:87.0
occ:1.00
 N F:CYS1 2.0 24.1 1.0
SG F:CYS1 2.0 29.2 1.0
CA F:CYS1 2.6 21.5 1.0
CB F:CYS1 2.8 23.1 1.0
O F:ASN171 3.8 26.2 0.4
ZN F:ZN201 3.9 65.0 1.0
O F:HOH305 4.1 24.9 1.0
C F:CYS1 4.1 17.9 1.0
ND1 F:HIS65 4.2 21.7 1.0
OG1 F:THR62 4.2 17.9 1.0
CA F:GLY152 4.6 20.1 1.0
O F:CYS1 4.6 16.5 1.0
OD1 F:ASN64 4.8 23.2 1.0
C F:ASN171 4.8 25.1 0.4
ND2 F:ASN64 4.9 26.4 1.0
C F:ASN171 4.9 24.9 0.6

Reference:

C.M.Green, Z.Li, A.D.Smith, O.Novikova, V.R.Bacot-Davis, F.Gao, S.Hu, N.K.Banavali, D.J.Thiele, H.Li, M.Belfort. Spliceosomal PRP8 Intein at the Crossroads of Protein and Rna Splicing. Plos Biol. V. 17 00104 2019.
ISSN: ESSN 1545-7885
PubMed: 31600193
DOI: 10.1371/JOURNAL.PBIO.3000104
Page generated: Tue Oct 29 04:37:52 2024

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