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Zinc in PDB 3pih: T. Maritima Uvra in Complex with Fluorescein-Modified Dna

Protein crystallography data

The structure of T. Maritima Uvra in Complex with Fluorescein-Modified Dna, PDB code: 3pih was solved by M.Jaciuk, E.Nowak, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.08 / 2.90
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 107.510, 107.510, 108.256, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the T. Maritima Uvra in Complex with Fluorescein-Modified Dna (pdb code 3pih). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the T. Maritima Uvra in Complex with Fluorescein-Modified Dna, PDB code: 3pih:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3pih

Go back to Zinc Binding Sites List in 3pih
Zinc binding site 1 out of 3 in the T. Maritima Uvra in Complex with Fluorescein-Modified Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of T. Maritima Uvra in Complex with Fluorescein-Modified Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn917

b:68.4
occ:1.00
SG A:CYS719 2.2 74.3 1.0
SG A:CYS716 2.4 78.4 1.0
SG A:CYS742 2.4 65.8 1.0
SG A:CYS739 2.5 80.6 1.0
CB A:CYS716 2.9 70.8 1.0
CB A:CYS742 3.1 65.7 1.0
CB A:CYS739 3.2 64.2 1.0
CB A:CYS719 3.4 73.1 1.0
N A:CYS719 3.7 77.7 1.0
N A:CYS742 3.8 71.6 1.0
CA A:CYS742 4.1 73.5 1.0
CA A:CYS719 4.2 71.3 1.0
CA A:CYS716 4.2 67.2 1.0
CB A:ALA718 4.2 64.0 1.0
O A:CYS716 4.2 70.7 1.0
C A:CYS716 4.4 71.8 1.0
CA A:ARG746 4.5 66.7 1.0
CB A:VAL741 4.5 63.0 1.0
CA A:CYS739 4.6 77.4 1.0
CA A:GLY723 4.7 64.1 1.0
C A:ALA718 4.7 75.4 1.0
N A:GLY723 4.8 56.6 1.0
N A:ALA718 4.8 74.5 1.0
CA A:ALA718 4.8 60.7 1.0
C A:VAL741 4.9 69.6 1.0
N A:ARG746 4.9 69.1 1.0
C A:CYS719 4.9 71.3 1.0

Zinc binding site 2 out of 3 in 3pih

Go back to Zinc Binding Sites List in 3pih
Zinc binding site 2 out of 3 in the T. Maritima Uvra in Complex with Fluorescein-Modified Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of T. Maritima Uvra in Complex with Fluorescein-Modified Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn918

b:70.4
occ:1.00
SG A:CYS384 2.4 67.0 1.0
SG A:CYS387 2.5 61.7 1.0
SG A:CYS279 2.6 61.3 1.0
SG A:CYS276 2.6 70.6 1.0
CB A:CYS279 3.0 66.2 1.0
CB A:CYS276 3.1 64.0 1.0
CB A:CYS387 3.1 56.6 1.0
CB A:CYS384 3.2 77.6 1.0
N A:CYS387 3.7 66.7 1.0
CA A:CYS387 4.0 55.4 1.0
N A:CYS279 4.1 70.2 1.0
CA A:CYS279 4.1 66.2 1.0
OD1 A:ASN278 4.1 76.2 1.0
CA A:CYS276 4.5 60.5 1.0
C A:ASN278 4.6 76.1 1.0
CA A:CYS384 4.6 75.6 1.0
CB A:VAL386 4.8 67.6 1.0
C A:CYS276 4.8 67.3 1.0
C A:CYS279 4.9 70.3 1.0
C A:VAL386 4.9 70.4 1.0
O A:ASN278 4.9 82.8 1.0
O A:CYS276 4.9 66.6 1.0
C A:CYS387 4.9 57.2 1.0
CG A:ASN278 4.9 65.1 1.0
O A:ARG391 5.0 56.6 1.0

Zinc binding site 3 out of 3 in 3pih

Go back to Zinc Binding Sites List in 3pih
Zinc binding site 3 out of 3 in the T. Maritima Uvra in Complex with Fluorescein-Modified Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of T. Maritima Uvra in Complex with Fluorescein-Modified Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn919

b:80.2
occ:0.70
SG A:CYS123 2.3 81.8 1.0
SG A:CYS255 2.4 0.5 1.0
SG A:CYS120 2.6 96.1 1.0
CB A:CYS123 2.8 89.9 1.0
SG A:CYS252 2.9 77.5 1.0
CB A:CYS120 3.5 94.8 1.0
CB A:CYS255 3.7 1.0 1.0
N A:CYS123 3.9 0.3 1.0
CG A:GLU122 3.9 0.4 1.0
CA A:CYS123 3.9 97.2 1.0
CB A:CYS252 4.0 86.7 1.0
OE1 A:GLU122 4.1 0.2 1.0
CB A:VAL254 4.5 86.5 1.0
CD A:GLU122 4.5 0.6 1.0
N A:CYS255 4.6 96.8 1.0
C A:VAL254 4.7 88.5 1.0
CA A:CYS255 4.8 95.9 1.0
C A:CYS123 4.8 99.9 1.0
CA A:CYS120 5.0 88.4 1.0

Reference:

M.Jaciuk, E.Nowak, K.Skowronek, A.Tanska, M.Nowotny. Structure of Uvra Nucleotide Excision Repair Protein in Complex with Modified Dna. Nat.Struct.Mol.Biol. V. 18 191 2011.
ISSN: ISSN 1545-9993
PubMed: 21240268
DOI: 10.1038/NSMB.1973
Page generated: Wed Dec 16 04:43:09 2020

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