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Zinc in PDB 8jwv: Untethered R0RBR

Enzymatic activity of Untethered R0RBR

All present enzymatic activity of Untethered R0RBR:
2.3.2.31;

Protein crystallography data

The structure of Untethered R0RBR, PDB code: 8jwv was solved by D.R.Lenka, A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.33 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 86.672, 132.579, 64.692, 90, 90, 90
R / Rfree (%) 21.7 / 25.4

Other elements in 8jwv:

The structure of Untethered R0RBR also contains other interesting chemical elements:

Barium (Ba) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Untethered R0RBR (pdb code 8jwv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Untethered R0RBR, PDB code: 8jwv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8jwv

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Zinc binding site 1 out of 8 in the Untethered R0RBR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Untethered R0RBR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:23.8
occ:0.70
 NE2 A:HIS215 2.1 30.4 1.0
SG A:CYS154 2.2 36.4 1.0
SG A:CYS150 2.3 32.5 1.0
SG A:CYS212 2.3 35.8 1.0
CD2 A:HIS215 3.0 31.0 1.0
CE1 A:HIS215 3.1 30.5 1.0
CB A:CYS212 3.2 30.1 1.0
CB A:CYS154 3.2 44.5 1.0
CB A:CYS150 3.2 36.6 1.0
N A:CYS154 3.8 49.8 1.0
CA A:CYS154 4.1 48.7 1.0
CG A:HIS215 4.1 33.8 1.0
ND1 A:HIS215 4.1 31.0 1.0
CD A:PRO153 4.4 52.7 1.0
CG A:GLN158 4.4 30.8 1.0
CB A:ALA214 4.5 36.6 1.0
N A:PRO153 4.6 52.8 1.0
CA A:CYS212 4.6 29.7 1.0
CA A:CYS150 4.6 37.2 1.0
CG A:PRO153 4.7 49.9 1.0
C A:PRO153 4.7 52.0 1.0
NE2 A:GLN158 4.8 35.6 1.0
C A:GLY152 4.8 56.2 1.0
O A:GLY152 5.0 59.5 1.0
N A:ALA214 5.0 34.2 1.0

Zinc binding site 2 out of 8 in 8jwv

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Zinc binding site 2 out of 8 in the Untethered R0RBR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Untethered R0RBR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:60.6
occ:1.00
 SG A:CYS196 2.3 41.9 1.0
SG A:CYS169 2.3 57.0 1.0
SG A:CYS166 2.3 51.2 1.0
SG A:CYS201 2.4 83.4 1.0
CB A:CYS166 3.1 49.0 1.0
CB A:CYS196 3.2 49.6 1.0
CB A:CYS169 3.2 58.1 1.0
CB A:CYS201 3.4 74.1 1.0
N A:CYS169 3.5 63.6 1.0
CA A:CYS169 3.9 63.2 1.0
CB A:THR168 4.4 69.8 1.0
N A:GLY203 4.4 58.2 1.0
CA A:GLY203 4.6 56.1 1.0
C A:THR168 4.6 74.3 1.0
CA A:CYS166 4.6 44.4 1.0
CG2 A:THR168 4.6 67.5 1.0
OG A:SER198 4.6 88.5 1.0
CA A:CYS196 4.6 55.4 1.0
CA A:CYS201 4.7 80.1 1.0
CA A:THR168 4.8 69.8 1.0
OG1 A:THR173 4.8 59.2 1.0
N A:THR168 4.8 59.9 1.0
O A:GLY203 4.9 52.9 1.0
C A:CYS201 4.9 72.8 1.0
C A:CYS169 4.9 67.5 1.0

Zinc binding site 3 out of 8 in 8jwv

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Zinc binding site 3 out of 8 in the Untethered R0RBR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Untethered R0RBR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:25.8
occ:1.00
 SG A:CYS260 2.3 29.8 1.0
SG A:CYS263 2.3 33.8 1.0
SG A:CYS241 2.4 31.1 1.0
SG A:CYS238 2.4 26.5 1.0
CB A:CYS241 3.2 28.0 1.0
CB A:CYS263 3.3 30.3 1.0
CB A:CYS238 3.4 29.4 1.0
CB A:CYS260 3.5 27.0 1.0
N A:CYS241 3.6 30.1 1.0
CA A:CYS241 4.0 28.1 1.0
N A:CYS260 4.0 26.1 1.0
OG1 A:THR240 4.1 32.9 1.0
N A:CYS263 4.2 28.5 1.0
CA A:CYS260 4.2 25.2 1.0
CA A:CYS263 4.3 28.1 1.0
C A:THR240 4.8 30.0 1.0
C A:CYS241 4.8 28.3 1.0
CA A:CYS238 4.8 30.0 1.0
CG1 A:ILE259 4.9 25.9 1.0
C A:CYS260 4.9 27.0 1.0
N A:THR242 4.9 29.4 1.0
O A:CYS260 4.9 28.0 1.0

Zinc binding site 4 out of 8 in 8jwv

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Zinc binding site 4 out of 8 in the Untethered R0RBR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Untethered R0RBR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:28.3
occ:1.00
 ND1 A:HIS257 1.9 29.5 1.0
SG A:CYS253 2.3 29.1 1.0
SG A:CYS289 2.3 34.8 1.0
SG A:CYS293 2.4 32.5 1.0
CE1 A:HIS257 2.8 28.7 1.0
CG A:HIS257 2.9 30.1 1.0
CB A:CYS253 3.2 25.5 1.0
CB A:CYS289 3.3 30.2 1.0
CB A:CYS293 3.3 29.3 1.0
CB A:HIS257 3.4 30.2 1.0
NE2 A:HIS257 3.9 28.8 1.0
CD2 A:HIS257 4.0 28.8 1.0
CB A:ALA291 4.2 32.1 1.0
N A:HIS257 4.2 31.7 1.0
CB A:SER255 4.4 28.2 1.0
CA A:HIS257 4.4 30.1 1.0
CA A:CYS293 4.6 34.7 1.0
CA A:CYS253 4.7 27.5 1.0
N A:CYS293 4.7 41.6 1.0
CA A:CYS289 4.7 31.2 1.0
CB A:PHE251 4.8 27.9 1.0
OG A:SER255 5.0 33.8 1.0

Zinc binding site 5 out of 8 in 8jwv

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Zinc binding site 5 out of 8 in the Untethered R0RBR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Untethered R0RBR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:51.6
occ:1.00
 SG A:CYS332 2.3 38.8 1.0
SG A:CYS360 2.3 46.8 1.0
SG A:CYS337 2.3 51.7 1.0
SG A:CYS352 2.4 64.0 1.0
CB A:CYS332 3.1 42.3 1.0
CB A:CYS337 3.3 51.8 1.0
CB A:CYS352 3.4 55.6 1.0
CB A:CYS360 3.6 49.0 1.0
N A:CYS360 3.7 67.0 1.0
CA A:CYS360 4.2 60.2 1.0
C A:GLY359 4.5 69.1 1.0
CB A:ARG334 4.5 49.1 1.0
CA A:GLY359 4.5 63.1 1.0
CA A:CYS332 4.6 43.5 1.0
CA A:CYS337 4.6 53.9 1.0
CB A:ALA339 4.6 42.2 1.0
CB A:PHE362 4.8 51.4 1.0
N A:GLY338 4.8 45.6 1.0
N A:ALA339 4.8 41.2 1.0
C A:CYS360 4.8 61.9 1.0
CA A:CYS352 4.9 51.4 1.0
C A:CYS337 5.0 53.9 1.0
N A:GLY361 5.0 63.2 1.0

Zinc binding site 6 out of 8 in 8jwv

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Zinc binding site 6 out of 8 in the Untethered R0RBR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Untethered R0RBR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:67.5
occ:1.00
 NE2 A:HIS373 1.7 72.2 1.0
SG A:CYS368 2.3 56.4 1.0
SG A:CYS365 2.3 61.6 1.0
SG A:CYS377 2.3 70.2 1.0
CE1 A:HIS373 2.6 83.3 1.0
CD2 A:HIS373 2.8 64.8 1.0
CB A:CYS368 3.1 57.6 1.0
CB A:CYS365 3.2 50.6 1.0
CB A:CYS377 3.3 67.1 1.0
ND1 A:HIS373 3.7 84.8 1.0
CA A:CYS377 3.8 67.4 1.0
CG A:HIS373 3.8 70.0 1.0
N A:CYS368 4.1 63.8 1.0
CA A:CYS368 4.1 61.1 1.0
NH1 A:ARG348 4.4 86.9 1.0
CA A:CYS365 4.5 50.7 1.0
N A:CYS377 4.5 72.9 1.0
C A:CYS368 4.7 55.0 1.0
O A:CYS365 4.8 63.8 1.0
C A:CYS365 4.9 58.4 1.0
C A:CYS377 5.0 65.8 1.0

Zinc binding site 7 out of 8 in 8jwv

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Zinc binding site 7 out of 8 in the Untethered R0RBR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Untethered R0RBR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:40.4
occ:1.00
 SG A:CYS441 2.3 31.9 1.0
SG A:CYS436 2.3 44.8 1.0
SG A:CYS421 2.3 55.1 1.0
SG A:CYS418 2.4 38.3 1.0
CB A:CYS441 3.1 38.3 1.0
CB A:CYS436 3.2 38.4 1.0
CB A:CYS418 3.2 38.9 1.0
CB A:CYS421 3.4 45.5 1.0
N A:CYS421 3.8 52.5 1.0
CA A:CYS421 4.2 49.3 1.0
CA A:CYS441 4.5 39.5 1.0
CB A:ARG420 4.5 49.4 1.0
CA A:CYS436 4.6 36.1 1.0
CB A:GLN438 4.7 50.1 1.0
CA A:CYS418 4.7 39.6 1.0
CB A:LEU443 4.7 37.4 1.0
N A:ARG442 4.7 39.2 1.0
N A:LEU443 4.7 36.6 1.0
CG A:GLN438 4.8 59.5 1.0
C A:ARG420 4.8 53.1 1.0
C A:CYS441 4.9 37.8 1.0
N A:HIS422 4.9 48.3 1.0
N A:ARG420 4.9 52.6 1.0
CA A:ARG420 5.0 52.3 1.0

Zinc binding site 8 out of 8 in 8jwv

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Zinc binding site 8 out of 8 in the Untethered R0RBR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Untethered R0RBR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:25.9
occ:1.00
 NE2 A:HIS461 2.1 24.6 1.0
SG A:CYS449 2.3 34.9 1.0
SG A:CYS457 2.3 27.0 1.0
SG A:CYS446 2.3 24.2 1.0
CE1 A:HIS461 2.9 26.6 1.0
CD2 A:HIS461 3.1 24.4 1.0
CB A:CYS449 3.2 31.8 1.0
CB A:CYS457 3.3 25.2 1.0
CB A:CYS446 3.3 25.9 1.0
N A:CYS449 3.9 31.2 1.0
CA A:CYS457 4.0 27.6 1.0
ND1 A:HIS461 4.1 28.0 1.0
CA A:CYS449 4.2 33.6 1.0
CG A:HIS461 4.2 27.1 1.0
CB A:ASN448 4.5 29.6 1.0
CA A:CYS446 4.7 26.6 1.0
ND2 A:ASN448 4.7 30.1 1.0
CZ3 A:TRP453 4.9 23.7 1.0
N A:CYS457 4.9 26.9 1.0
C A:ASN448 4.9 33.4 1.0

Reference:

D.R.Lenka, A.Kumar. A New Feedforward Mechanism of Parkin Activation. To Be Published.
Page generated: Thu Oct 31 08:28:31 2024

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