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Zinc in PDB 2djw: Crystal Structure of TTHA0845 From Thermus Thermophilus HB8

Protein crystallography data

The structure of Crystal Structure of TTHA0845 From Thermus Thermophilus HB8, PDB code: 2djw was solved by N.Okazaki, N.Nakano, A.Shinkai, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 95.883, 95.883, 119.010, 90.00, 90.00, 120.00
R / Rfree (%) 25 / 29.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TTHA0845 From Thermus Thermophilus HB8 (pdb code 2djw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of TTHA0845 From Thermus Thermophilus HB8, PDB code: 2djw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2djw

Go back to Zinc Binding Sites List in 2djw
Zinc binding site 1 out of 4 in the Crystal Structure of TTHA0845 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of TTHA0845 From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2003

b:47.4
occ:1.00
OE2 B:GLU50 1.4 29.4 1.0
OD2 B:ASP54 1.9 38.4 1.0
CD B:GLU50 2.6 35.5 1.0
CG B:ASP54 2.9 40.9 1.0
OD1 B:ASP54 3.2 44.7 1.0
OE1 B:GLU50 3.4 42.4 1.0
CG B:GLU50 3.6 36.4 1.0
O B:GLU50 4.2 38.0 1.0
OD2 B:ASP53 4.2 42.8 1.0
CB B:ASP54 4.2 39.4 1.0
N B:ASP54 4.4 39.4 1.0
CB B:ASP53 4.4 39.8 1.0
CA B:GLU51 4.6 37.7 1.0
C B:GLU50 4.6 38.0 1.0
CA B:ASP54 4.8 39.7 1.0
CG B:ASP53 4.8 41.4 1.0
N B:GLU51 4.9 37.1 1.0
O B:HOH2015 4.9 55.8 1.0
CB B:GLU50 5.0 38.9 1.0

Zinc binding site 2 out of 4 in 2djw

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Zinc binding site 2 out of 4 in the Crystal Structure of TTHA0845 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of TTHA0845 From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn2002

b:46.2
occ:1.00
OE1 E:GLU50 1.9 40.0 1.0
OD2 E:ASP54 1.9 42.6 1.0
CD E:GLU50 2.6 40.7 1.0
OE2 E:GLU50 2.6 42.6 1.0
CG E:ASP54 2.7 42.3 1.0
OD1 E:ASP54 2.8 47.0 1.0
CG E:GLU50 4.1 41.5 1.0
CB E:ASP54 4.1 40.4 1.0
OD2 E:ASP53 4.2 40.7 1.0
O E:GLU50 4.2 40.0 1.0
N E:ASP54 4.3 39.7 1.0
CB E:ASP53 4.3 38.6 1.0
CA E:GLU51 4.5 39.5 1.0
C E:GLU50 4.6 40.0 1.0
CA E:ASP54 4.7 40.5 1.0
N E:GLU51 4.8 39.7 1.0
CG E:ASP53 4.8 39.5 1.0

Zinc binding site 3 out of 4 in 2djw

Go back to Zinc Binding Sites List in 2djw
Zinc binding site 3 out of 4 in the Crystal Structure of TTHA0845 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of TTHA0845 From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2004

b:50.3
occ:1.00
OE1 G:GLU50 1.5 42.0 1.0
OD1 G:ASP54 1.9 42.6 1.0
CG G:ASP54 2.6 43.4 1.0
CD G:GLU50 2.6 44.0 1.0
OD2 G:ASP54 2.7 46.3 1.0
OE2 G:GLU50 3.2 47.9 1.0
CG G:GLU50 3.8 44.2 1.0
CB G:ASP54 4.0 41.1 1.0
OD2 G:ASP53 4.1 41.1 1.0
CB G:ASP53 4.2 39.9 1.0
N G:ASP54 4.2 40.9 1.0
O G:GLU50 4.2 42.6 1.0
CA G:GLU51 4.6 42.3 1.0
C G:GLU50 4.6 42.3 1.0
CG G:ASP53 4.6 41.1 1.0
CA G:ASP54 4.7 41.5 1.0
N G:GLU51 4.9 42.0 1.0

Zinc binding site 4 out of 4 in 2djw

Go back to Zinc Binding Sites List in 2djw
Zinc binding site 4 out of 4 in the Crystal Structure of TTHA0845 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of TTHA0845 From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2001

b:48.5
occ:1.00
OE2 J:GLU50 1.5 28.7 1.0
OD1 J:ASP54 1.9 38.5 1.0
CD J:GLU50 2.7 35.0 1.0
CG J:ASP54 2.7 40.5 1.0
OD2 J:ASP54 3.0 44.0 1.0
OE1 J:GLU50 3.5 42.2 1.0
CG J:GLU50 3.7 36.2 1.0
CB J:ASP54 4.1 38.2 1.0
O J:GLU50 4.2 37.1 1.0
OD2 J:ASP53 4.2 41.9 1.0
N J:ASP54 4.3 38.4 1.0
CB J:ASP53 4.4 39.4 1.0
C J:GLU50 4.6 37.8 1.0
O J:HOH2010 4.6 58.6 1.0
CA J:GLU51 4.7 38.1 1.0
CA J:ASP54 4.7 38.7 1.0
CG J:ASP53 4.8 41.3 1.0
N J:GLU51 4.9 37.4 1.0

Reference:

N.Nakano, N.Okazaki, S.Satoh, K.Takio, S.Kuramitsu, A.Shinkai, S.Yokoyama. Structure of the Stand-Alone Ram-Domain Protein From Thermus Thermophilus HB8 Acta Crystallogr.,Sect.F V. 62 855 2006.
ISSN: ESSN 1744-3091
PubMed: 16946463
DOI: 10.1107/S1744309106031150
Page generated: Wed Dec 16 03:21:30 2020

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