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Zinc in PDB 3nyb: Structure and Function of the Polymerase Core of Tramp, A Rna Surveillance Complex

Protein crystallography data

The structure of Structure and Function of the Polymerase Core of Tramp, A Rna Surveillance Complex, PDB code: 3nyb was solved by K.M.Reinisch, S.Hamill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.66 / 2.70
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.720, 92.720, 103.630, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure and Function of the Polymerase Core of Tramp, A Rna Surveillance Complex (pdb code 3nyb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure and Function of the Polymerase Core of Tramp, A Rna Surveillance Complex, PDB code: 3nyb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3nyb

Go back to Zinc Binding Sites List in 3nyb
Zinc binding site 1 out of 2 in the Structure and Function of the Polymerase Core of Tramp, A Rna Surveillance Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure and Function of the Polymerase Core of Tramp, A Rna Surveillance Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2147

b:0.8
occ:1.00
NE2 B:HIS131 2.2 92.8 1.0
CB B:CYS126 2.4 95.4 1.0
SG B:CYS123 2.7 0.3 1.0
CB B:CYS123 2.7 0.7 1.0
CD2 B:HIS131 2.7 91.7 1.0
SG B:CYS136 2.9 79.2 1.0
CB B:CYS136 3.1 45.0 1.0
SG B:CYS126 3.3 0.7 1.0
CE1 B:HIS131 3.4 95.0 1.0
CA B:CYS136 3.5 60.5 1.0
CA B:CYS126 3.7 0.0 1.0
N B:CYS126 3.8 0.5 1.0
CG B:HIS131 4.0 96.3 1.0
CD B:PRO137 4.1 74.2 1.0
CA B:CYS123 4.2 0.1 1.0
ND1 B:HIS131 4.3 93.6 1.0
O B:SER132 4.4 98.5 1.0
N B:CYS136 4.5 65.9 1.0
C B:CYS136 4.6 71.0 1.0
C B:CYS126 4.6 0.9 1.0
N B:PRO137 4.7 71.2 1.0
N B:CYS123 4.8 0.3 1.0
CB B:SER128 4.9 0.8 1.0
N B:LYS127 5.0 0.3 1.0

Zinc binding site 2 out of 2 in 3nyb

Go back to Zinc Binding Sites List in 3nyb
Zinc binding site 2 out of 2 in the Structure and Function of the Polymerase Core of Tramp, A Rna Surveillance Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure and Function of the Polymerase Core of Tramp, A Rna Surveillance Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2148

b:82.4
occ:1.00
SG B:CYS167 2.4 75.2 1.0
SG B:CYS177 2.4 72.6 1.0
NE2 B:HIS172 2.4 84.4 1.0
SG B:CYS164 2.6 69.3 1.0
CB B:CYS177 3.2 93.0 1.0
CE1 B:HIS172 3.2 85.8 1.0
CB B:CYS167 3.3 53.5 1.0
CB B:CYS164 3.4 60.8 1.0
CD2 B:HIS172 3.5 78.3 1.0
N B:CYS167 3.6 63.9 1.0
O B:CYS167 3.9 90.7 1.0
CA B:CYS167 3.9 62.1 1.0
CA B:CYS177 4.3 98.3 1.0
C B:CYS167 4.3 78.5 1.0
ND1 B:HIS172 4.4 82.3 1.0
CB B:ASN166 4.5 63.1 1.0
CG B:HIS172 4.6 78.4 1.0
C B:ASN166 4.6 62.4 1.0
CG B:GLU179 4.7 0.1 1.0
N B:LYS178 4.8 0.5 1.0
CA B:CYS164 4.8 55.4 1.0
OD1 B:ASN166 4.8 89.5 1.0
CA B:ASN166 5.0 62.9 1.0

Reference:

S.Hamill, S.L.Wolin, K.M.Reinisch. Structure and Function of the Polymerase Core of Tramp, A Rna Surveillance Complex. Proc.Natl.Acad.Sci.Usa V. 107 15045 2010.
ISSN: ISSN 0027-8424
PubMed: 20696927
DOI: 10.1073/PNAS.1003505107
Page generated: Wed Dec 16 04:39:27 2020

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