Zinc in PDB 1vk9: Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution

The structure of Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution, PDB code: 1vk9 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.50 / 2.70
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.891, 132.891, 66.379, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 25.1

The binding sites of Zinc atom in the Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution (pdb code 1vk9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution, PDB code: 1vk9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution


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 A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn140 b:51.8 occ:0.50 OE1 A:GLU90 2.2 27.4 1.0 OE2 A:GLU90 2.5 28.1 1.0 CD A:GLU90 2.7 22.2 1.0 O A:ASP123 3.5 39.5 1.0 CG A:GLU90 4.2 22.2 1.0 CB A:ASP123 4.2 33.0 1.0 CD1 A:LEU87 4.3 19.4 1.0 CE1 A:TYR91 4.4 29.9 1.0 C A:ASP123 4.4 32.5 1.0 CG A:ASP123 4.5 37.6 1.0 OH A:TYR91 4.6 26.0 1.0 CA A:ASP123 4.6 33.2 1.0 OD1 A:ASP123 4.7 47.1 1.0 CB A:GLU90 4.9 23.2 1.0 OD2 A:ASP123 4.9 44.5 1.0 CZ A:TYR91 5.0 22.0 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution


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 A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn141 b:56.6 occ:1.00 OD2 A:ASP-8 2.0 35.2 1.0 OD1 A:ASP-8 2.7 21.6 1.0 CG A:ASP-8 2.8 26.2 1.0 CB A:ASP-8 4.3 18.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution


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 A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn142 b:62.1 occ:1.00 OE1 A:GLU50 1.8 20.4 1.0 ND1 A:HIS-4 2.0 37.3 1.0 NE2 A:HIS-2 2.0 36.7 1.0 CG A:HIS-4 2.9 22.5 1.0 CD A:GLU50 2.9 43.5 1.0 CE1 A:HIS-2 3.0 30.9 1.0 CE1 A:HIS-4 3.0 28.6 1.0 CD2 A:HIS-2 3.1 27.8 1.0 CB A:HIS-4 3.2 25.3 1.0 CB A:GLU50 3.6 27.0 1.0 CG A:GLU50 3.8 32.3 1.0 OE2 A:GLU50 3.9 50.1 1.0 CD2 A:HIS-4 4.1 24.1 1.0 NE2 A:HIS-4 4.1 19.0 1.0 ND1 A:HIS-2 4.1 35.9 1.0 CG A:HIS-2 4.2 30.2 1.0 CA A:HIS-4 4.7 27.3 1.0 CA A:GLU50 5.0 28.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution


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 A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn143 b:72.2 occ:1.00 OD2 A:ASP98 1.8 32.1 1.0 NE2 A:HIS76 2.1 43.0 1.0 O A:HOH203 2.2 32.5 1.0 O A:HOH205 2.7 45.0 1.0 CG A:ASP98 2.7 29.6 1.0 OD1 A:ASP98 2.9 28.9 1.0 CE1 A:HIS76 3.0 36.9 1.0 CD2 A:HIS76 3.1 35.5 1.0 CD2 A:LEU10 4.0 27.4 1.0 ND1 A:HIS76 4.2 31.7 1.0 CG A:HIS76 4.2 30.3 1.0 CB A:ASP98 4.2 24.1 1.0 CA A:LYS78 4.6 33.3 1.0 CB A:LYS78 4.8 34.4 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn144 b:59.4 occ:1.00 OD1 A:ASP124 1.9 32.8 1.0 O A:HOH207 2.6 54.1 1.0 CG A:ASP124 2.9 31.5 1.0 OD2 A:ASP124 3.2 44.0 1.0 CD A:PRO125 4.1 29.0 1.0 CB A:ASP124 4.3 26.4 1.0 OH A:TYR91 4.3 26.0 1.0 CB A:GLU126 4.3 35.0 1.0 N A:GLU126 4.4 33.2 1.0 N A:PRO125 4.6 31.6 1.0 CA A:ASP124 4.8 28.1 1.0 CG A:PRO125 4.9 26.6 1.0 C A:ASP124 4.9 30.8 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A DUF1893 Family Protein (TM1506) From Thermotoga Maritima at 2.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn145 b:0.9 occ:0.50 ND1 A:HIS-5 2.4 67.8 1.0 CE1 A:HIS-5 3.3 63.6 1.0 CG A:HIS-5 3.4 56.5 1.0 CB A:HIS-5 3.7 33.6 1.0 CA A:HIS-5 4.1 31.4 1.0 NE2 A:HIS-5 4.4 70.4 1.0 CD2 A:HIS-5 4.4 65.7 1.0 O A:ILE-6 4.6 23.9 1.0 N A:HIS-5 4.9 27.5 1.0

Q.Xu, P.Kozbial, D.Mcmullan, S.S.Krishna, S.M.Brittain, S.B.Ficarro, M.Didonato, M.D.Miller, P.Abdubek, H.L.Axelrod, H.J.Chiu, T.Clayton, L.Duan, M.A.Elsliger, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, H.E.Klock, A.T.Morse, E.Nigoghossian, J.Paulsen, R.Reyes, C.L.Rife, H.Van Den Bedem, A.White, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Crystal Structure of An Adp-Ribosylated Protein with A Cytidine Deaminase-Like Fold, But Unknown Function (TM1506), From Thermotoga Maritima at 2.70 A Resolution. Proteins V. 71 1546 2008.
ISSN: ISSN 0887-3585
PubMed: 18275082
DOI: 10.1002/PROT.21992