Atomistry » Zinc » PDB 5k16-5kar » 5k73
Atomistry »
  Zinc »
    PDB 5k16-5kar »
      5k73 »

Zinc in PDB 5k73: As-Isolated DBR1 with Fe(II) and Zn(II)

Protein crystallography data

The structure of As-Isolated DBR1 with Fe(II) and Zn(II), PDB code: 5k73 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) 69.22 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.161, 141.705, 213.777, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.3

Other elements in 5k73:

The structure of As-Isolated DBR1 with Fe(II) and Zn(II) also contains other interesting chemical elements:

Iron (Fe) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the As-Isolated DBR1 with Fe(II) and Zn(II) (pdb code 5k73). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the As-Isolated DBR1 with Fe(II) and Zn(II), PDB code: 5k73:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5k73

Go back to Zinc Binding Sites List in 5k73
Zinc binding site 1 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:49.5
occ:1.00
O A:OH406 2.1 53.0 1.0
NE2 A:HIS16 2.3 53.6 1.0
NE2 A:HIS232 2.3 53.1 1.0
SG A:CYS14 2.4 40.0 1.0
OD2 A:ASP45 2.6 39.6 1.0
CB A:CYS14 3.1 40.7 1.0
CD2 A:HIS232 3.1 49.9 1.0
CE1 A:HIS16 3.1 49.9 1.0
CD2 A:HIS16 3.3 51.6 1.0
FE A:FE2401 3.3 47.4 1.0
CE1 A:HIS232 3.4 58.0 1.0
CG A:ASP45 3.8 39.2 1.0
O A:HIS230 3.8 38.1 1.0
O A:HOH501 3.9 44.3 1.0
CA A:HIS230 4.2 39.7 1.0
ND1 A:HIS16 4.3 57.9 1.0
CG A:HIS232 4.3 48.7 1.0
CB A:ASP45 4.3 40.8 1.0
C A:HIS230 4.4 45.1 1.0
CG A:HIS16 4.4 55.5 1.0
ND1 A:HIS232 4.5 49.9 1.0
CA A:CYS14 4.5 38.2 1.0
NE2 A:HIS180 4.6 36.0 1.0
O A:HOH542 4.6 40.0 1.0
N A:HIS230 4.6 41.3 1.0
CE1 A:HIS180 4.6 34.2 1.0
OD1 A:ASP45 4.8 36.8 1.0
CB A:LYS249 4.9 42.1 1.0

Zinc binding site 2 out of 5 in 5k73

Go back to Zinc Binding Sites List in 5k73
Zinc binding site 2 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:49.2
occ:1.00
NE2 B:HIS232 2.2 44.5 1.0
O B:OH406 2.2 57.2 1.0
NE2 B:HIS16 2.3 39.1 1.0
SG B:CYS14 2.4 41.0 1.0
OD2 B:ASP45 2.6 33.3 1.0
CB B:CYS14 3.0 38.8 1.0
CD2 B:HIS232 3.0 46.7 1.0
CD2 B:HIS16 3.2 41.5 1.0
CE1 B:HIS16 3.3 45.0 1.0
CE1 B:HIS232 3.3 54.0 1.0
FE B:FE2401 3.4 47.0 1.0
CG B:ASP45 3.8 37.4 1.0
O B:HOH501 3.9 43.7 1.0
O B:HIS230 4.0 37.0 1.0
CA B:HIS230 4.2 30.7 1.0
CG B:HIS232 4.2 46.0 1.0
ND1 B:HIS232 4.3 47.2 1.0
CB B:ASP45 4.3 40.4 1.0
ND1 B:HIS16 4.3 47.8 1.0
CG B:HIS16 4.4 40.9 1.0
C B:HIS230 4.4 41.0 1.0
CA B:CYS14 4.5 40.1 1.0
O B:HOH559 4.5 34.9 1.0
NE2 B:HIS180 4.6 37.4 1.0
N B:HIS230 4.7 34.3 1.0
CE1 B:HIS180 4.7 42.8 1.0
CB B:LYS249 4.8 50.1 1.0
OD1 B:ASP45 4.8 40.3 1.0

Zinc binding site 3 out of 5 in 5k73

Go back to Zinc Binding Sites List in 5k73
Zinc binding site 3 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:53.1
occ:1.00
O C:OH406 2.1 74.8 1.0
NE2 C:HIS232 2.2 54.6 1.0
NE2 C:HIS16 2.3 49.0 1.0
SG C:CYS14 2.5 47.0 1.0
OD2 C:ASP45 2.7 50.8 1.0
CD2 C:HIS232 3.0 48.7 1.0
CB C:CYS14 3.1 45.0 1.0
CE1 C:HIS16 3.1 43.5 1.0
FE C:FE2402 3.3 49.1 1.0
CD2 C:HIS16 3.3 50.4 1.0
CE1 C:HIS232 3.3 53.1 1.0
CG C:ASP45 3.8 43.2 1.0
O C:HIS230 3.9 45.4 1.0
O C:HOH501 4.0 49.6 1.0
CG C:HIS232 4.2 51.7 1.0
CA C:HIS230 4.2 45.4 1.0
ND1 C:HIS16 4.2 49.5 1.0
CB C:ASP45 4.3 44.8 1.0
ND1 C:HIS232 4.4 55.1 1.0
CG C:HIS16 4.4 50.6 1.0
C C:HIS230 4.4 43.7 1.0
O C:HOH558 4.5 40.2 1.0
CA C:CYS14 4.5 43.6 1.0
NE2 C:HIS180 4.6 49.7 1.0
CE1 C:HIS180 4.7 48.8 1.0
N C:HIS230 4.7 48.0 1.0
CB C:LYS249 4.8 56.3 1.0
OD1 C:ASP45 4.9 36.9 1.0
ND1 C:HIS230 5.0 43.6 1.0

Zinc binding site 4 out of 5 in 5k73

Go back to Zinc Binding Sites List in 5k73
Zinc binding site 4 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:59.0
occ:1.00
O D:OH407 2.1 47.6 1.0
SG D:CYS14 2.3 53.8 1.0
NE2 D:HIS16 2.4 58.4 1.0
NE2 D:HIS232 2.5 70.6 1.0
OD2 D:ASP45 2.7 49.2 1.0
CB D:CYS14 2.9 54.0 1.0
CD2 D:HIS232 3.1 73.9 1.0
CD2 D:HIS16 3.3 64.0 1.0
CE1 D:HIS16 3.4 61.7 1.0
FE D:FE2401 3.4 59.1 1.0
CE1 D:HIS232 3.7 71.2 1.0
CG D:ASP45 3.8 42.2 1.0
O D:HIS230 4.2 65.0 1.0
CB D:ASP45 4.3 42.8 1.0
CA D:HIS230 4.3 53.3 1.0
O D:HOH501 4.3 49.5 1.0
CA D:CYS14 4.4 50.2 1.0
CG D:HIS232 4.4 73.6 1.0
O D:HOH569 4.4 52.9 1.0
ND1 D:HIS16 4.4 66.7 1.0
CG D:HIS16 4.4 62.1 1.0
C D:HIS230 4.5 57.8 1.0
ND1 D:HIS232 4.7 72.0 1.0
CE1 D:HIS180 4.7 52.5 1.0
N D:HIS230 4.7 46.0 1.0
NE2 D:HIS180 4.7 49.0 1.0
CB D:LYS249 4.8 60.0 1.0
OD1 D:ASP45 4.9 44.6 1.0

Zinc binding site 5 out of 5 in 5k73

Go back to Zinc Binding Sites List in 5k73
Zinc binding site 5 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:45.5
occ:1.00
O E:OH404 2.1 50.0 1.0
NE2 E:HIS232 2.3 44.2 1.0
NE2 E:HIS16 2.3 46.1 1.0
SG E:CYS14 2.3 41.7 1.0
OD2 E:ASP45 2.7 32.4 1.0
CB E:CYS14 2.9 35.9 1.0
CD2 E:HIS232 3.0 39.2 1.0
CE1 E:HIS16 3.2 46.2 1.0
CD2 E:HIS16 3.2 46.6 1.0
FE E:FE2401 3.3 43.1 1.0
CE1 E:HIS232 3.4 50.2 1.0
CG E:ASP45 3.8 39.0 1.0
O E:HIS230 3.9 44.2 1.0
O E:HOH501 4.0 40.8 1.0
CA E:HIS230 4.3 38.8 1.0
CG E:HIS232 4.3 44.6 1.0
ND1 E:HIS16 4.3 46.5 1.0
CB E:ASP45 4.3 38.0 1.0
CG E:HIS16 4.3 45.0 1.0
CA E:CYS14 4.4 38.3 1.0
ND1 E:HIS232 4.4 50.6 1.0
O E:HOH548 4.5 39.8 1.0
C E:HIS230 4.5 41.5 1.0
CE1 E:HIS180 4.7 34.7 1.0
NE2 E:HIS180 4.7 33.3 1.0
CB E:LYS249 4.7 46.4 1.0
N E:HIS230 4.7 45.1 1.0
OD1 E:ASP45 4.9 34.0 1.0

Reference:

N.E.Clark, A.Katolik, K.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. The Rna Lariat Debranching Enzyme DBR1: Metal Dependence and Branched Rna Co-Crystal Structures Proc.Natl.Acad.Sci.Usa 2016.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1612729114
Page generated: Wed Dec 16 06:26:25 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy