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Zinc in PDB 5k77: DBR1 in Complex with 7-Mer Branched Rna

Protein crystallography data

The structure of DBR1 in Complex with 7-Mer Branched Rna, PDB code: 5k77 was solved by N.E.Clark, A.B.Taylor, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 118.01 / 2.17
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.151, 141.892, 212.511, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.3

Other elements in 5k77:

The structure of DBR1 in Complex with 7-Mer Branched Rna also contains other interesting chemical elements:

Iron (Fe) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the DBR1 in Complex with 7-Mer Branched Rna (pdb code 5k77). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the DBR1 in Complex with 7-Mer Branched Rna, PDB code: 5k77:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5k77

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Zinc binding site 1 out of 5 in the DBR1 in Complex with 7-Mer Branched Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of DBR1 in Complex with 7-Mer Branched Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:44.9
occ:1.00
O A:OH408 2.0 31.0 1.0
NE2 A:HIS232 2.2 49.5 1.0
NE2 A:HIS16 2.2 40.5 1.0
SG A:CYS14 2.6 47.1 1.0
OP1 v:G510 2.8 48.2 1.0
OD2 A:ASP45 2.9 34.0 1.0
CD2 A:HIS232 3.0 41.7 1.0
CE1 A:HIS232 3.2 45.5 1.0
CB A:CYS14 3.2 39.6 1.0
CD2 A:HIS16 3.2 45.5 1.0
CE1 A:HIS16 3.2 37.0 1.0
FE A:FE2402 3.5 34.8 1.0
P v:G510 3.9 51.3 1.0
CG A:ASP45 3.9 36.8 1.0
O A:HIS230 4.0 34.5 1.0
OP2 v:G510 4.1 54.8 1.0
CG A:HIS232 4.2 46.7 1.0
ND1 A:HIS232 4.2 44.1 1.0
CB A:ASP45 4.3 30.4 1.0
ND1 A:HIS16 4.3 40.6 1.0
CG A:HIS16 4.3 47.4 1.0
CA A:HIS230 4.4 38.5 1.0
C A:HIS230 4.5 41.3 1.0
CA A:CYS14 4.7 37.9 1.0
O A:HOH526 4.7 39.5 1.0
C5' v:G510 4.7 49.1 1.0
CE1 A:HIS180 4.7 33.5 1.0
NE2 A:HIS180 4.8 35.1 1.0
CB A:LYS249 4.8 43.2 1.0
O5' v:G510 4.8 58.2 1.0
N A:HIS230 4.9 40.7 1.0
ND1 A:HIS230 5.0 31.4 1.0

Zinc binding site 2 out of 5 in 5k77

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Zinc binding site 2 out of 5 in the DBR1 in Complex with 7-Mer Branched Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of DBR1 in Complex with 7-Mer Branched Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:44.0
occ:1.00
O B:OH407 2.0 31.4 1.0
NE2 B:HIS232 2.2 38.2 1.0
NE2 B:HIS16 2.3 38.4 1.0
SG B:CYS14 2.5 47.9 1.0
OP1 w:G510 2.6 55.6 1.0
OD2 B:ASP45 2.9 36.0 1.0
CD2 B:HIS232 3.1 42.6 1.0
CB B:CYS14 3.1 47.0 1.0
CD2 B:HIS16 3.2 36.0 1.0
CE1 B:HIS16 3.2 41.2 1.0
CE1 B:HIS232 3.2 43.2 1.0
FE B:FE2401 3.5 37.5 1.0
P w:G510 3.8 56.2 1.0
CG B:ASP45 3.9 37.9 1.0
OP2 w:G510 4.1 51.2 1.0
O B:HIS230 4.1 41.0 1.0
CG B:HIS232 4.3 43.9 1.0
CB B:ASP45 4.3 32.9 1.0
ND1 B:HIS232 4.3 39.2 1.0
ND1 B:HIS16 4.3 40.4 1.0
CG B:HIS16 4.3 39.4 1.0
C5' w:G510 4.4 66.2 1.0
CA B:HIS230 4.5 43.6 1.0
O5' w:G510 4.6 64.8 1.0
CA B:CYS14 4.6 40.0 1.0
CE1 B:HIS180 4.6 35.7 1.0
C B:HIS230 4.6 42.6 1.0
O B:HOH566 4.7 31.5 1.0
NE2 B:HIS180 4.7 33.6 1.0
N B:HIS230 4.9 36.4 1.0

Zinc binding site 3 out of 5 in 5k77

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Zinc binding site 3 out of 5 in the DBR1 in Complex with 7-Mer Branched Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of DBR1 in Complex with 7-Mer Branched Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:46.0
occ:1.00
O C:OH410 2.0 34.5 1.0
NE2 C:HIS16 2.1 38.9 1.0
NE2 C:HIS232 2.2 38.6 1.0
SG C:CYS14 2.5 41.4 1.0
OP1 x:G510 2.8 43.1 1.0
OD2 C:ASP45 2.8 38.6 1.0
CE1 C:HIS16 3.0 33.9 1.0
CD2 C:HIS232 3.1 35.1 1.0
CB C:CYS14 3.2 38.3 1.0
CD2 C:HIS16 3.2 38.0 1.0
CE1 C:HIS232 3.2 39.4 1.0
FE C:FE2402 3.6 35.1 1.0
CG C:ASP45 3.9 39.0 1.0
P x:G510 3.9 52.7 1.0
OP2 x:G510 4.1 58.1 1.0
O C:HIS230 4.2 33.4 1.0
ND1 C:HIS16 4.2 42.5 1.0
CB C:ASP45 4.2 33.2 1.0
CG C:HIS232 4.2 36.8 1.0
ND1 C:HIS232 4.3 43.0 1.0
CG C:HIS16 4.3 44.3 1.0
C5' x:G510 4.5 57.4 1.0
CA C:HIS230 4.5 35.4 1.0
CE1 C:HIS180 4.5 29.9 1.0
CA C:CYS14 4.6 36.0 1.0
NE2 C:HIS180 4.6 34.5 1.0
O5' x:G510 4.7 56.9 1.0
C C:HIS230 4.7 35.9 1.0
O C:HOH558 4.8 34.2 1.0
N C:HIS230 5.0 31.1 1.0
OD1 C:ASP45 5.0 35.0 1.0

Zinc binding site 4 out of 5 in 5k77

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Zinc binding site 4 out of 5 in the DBR1 in Complex with 7-Mer Branched Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of DBR1 in Complex with 7-Mer Branched Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:50.6
occ:1.00
O D:OH408 2.0 45.4 1.0
NE2 D:HIS16 2.2 39.5 1.0
NE2 D:HIS232 2.2 48.8 1.0
SG D:CYS14 2.4 43.9 1.0
OP1 y:G510 2.8 60.1 1.0
OD2 D:ASP45 2.8 38.1 1.0
CD2 D:HIS232 3.1 48.2 1.0
CD2 D:HIS16 3.1 36.9 1.0
CB D:CYS14 3.2 37.0 1.0
CE1 D:HIS16 3.2 42.8 1.0
CE1 D:HIS232 3.3 53.3 1.0
FE D:FE2401 3.6 39.1 1.0
CG D:ASP45 3.9 38.6 1.0
P y:G510 4.0 63.5 1.0
O D:HIS230 4.1 50.7 1.0
CB D:ASP45 4.2 30.8 1.0
OP2 y:G510 4.2 57.3 1.0
CG D:HIS232 4.3 47.6 1.0
ND1 D:HIS16 4.3 38.5 1.0
CG D:HIS16 4.3 42.4 1.0
ND1 D:HIS232 4.4 52.1 1.0
CA D:HIS230 4.4 42.5 1.0
C D:HIS230 4.5 44.4 1.0
CE1 D:HIS180 4.6 35.9 1.0
CA D:CYS14 4.6 42.7 1.0
C5' y:G510 4.6 59.6 1.0
NE2 D:HIS180 4.7 36.5 1.0
O D:HOH544 4.8 42.8 1.0
O5' y:G510 4.8 63.0 1.0
N D:HIS230 4.9 44.2 1.0
OD1 D:ASP45 5.0 45.6 1.0

Zinc binding site 5 out of 5 in 5k77

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Zinc binding site 5 out of 5 in the DBR1 in Complex with 7-Mer Branched Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of DBR1 in Complex with 7-Mer Branched Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:41.2
occ:1.00
O E:OH407 1.9 32.1 1.0
NE2 E:HIS232 2.2 38.2 1.0
NE2 E:HIS16 2.2 39.0 1.0
SG E:CYS14 2.4 42.0 1.0
OP1 z:G510 2.7 44.5 1.0
OD2 E:ASP45 2.8 35.4 1.0
CD2 E:HIS232 3.0 34.7 1.0
CB E:CYS14 3.1 33.4 1.0
CD2 E:HIS16 3.1 35.5 1.0
CE1 E:HIS16 3.2 30.8 1.0
CE1 E:HIS232 3.2 40.6 1.0
FE E:FE2401 3.5 35.5 1.0
P z:G510 3.8 53.9 1.0
CG E:ASP45 3.9 36.8 1.0
OP2 z:G510 4.0 55.0 1.0
O E:HIS230 4.0 38.8 1.0
CB E:ASP45 4.2 36.9 1.0
CG E:HIS232 4.2 42.2 1.0
ND1 E:HIS232 4.3 42.4 1.0
ND1 E:HIS16 4.3 37.7 1.0
CG E:HIS16 4.3 39.5 1.0
CA E:HIS230 4.4 35.1 1.0
C5' z:G510 4.4 50.9 1.0
CA E:CYS14 4.6 29.7 1.0
C E:HIS230 4.6 35.5 1.0
CE1 E:HIS180 4.6 26.8 1.0
O5' z:G510 4.6 54.7 1.0
NE2 E:HIS180 4.7 34.9 1.0
O E:HOH538 4.8 33.7 1.0
N E:HIS230 4.9 36.2 1.0
OD1 E:ASP45 5.0 37.6 1.0

Reference:

N.E.Clark, A.Katolik, K.M.Roberts, A.B.Taylor, S.P.Holloway, J.P.Schuermann, E.J.Montemayor, S.W.Stevens, P.F.Fitzpatrick, M.J.Damha, P.J.Hart. Metal Dependence and Branched Rna Cocrystal Structures of the Rna Lariat Debranching Enzyme DBR1. Proc. Natl. Acad. Sci. V. 113 14727 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 27930312
DOI: 10.1073/PNAS.1612729114
Page generated: Wed Dec 16 06:26:29 2020

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