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Zinc in PDB 1vgx: Crystal Structure of A Autoinducer-2 Synthesis Protein

Protein crystallography data

The structure of Crystal Structure of A Autoinducer-2 Synthesis Protein, PDB code: 1vgx was solved by Structural Genomix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.82 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.220, 42.860, 49.354, 103.19, 90.55, 114.32
R / Rfree (%) 17.1 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Autoinducer-2 Synthesis Protein (pdb code 1vgx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Autoinducer-2 Synthesis Protein, PDB code: 1vgx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1vgx

Go back to Zinc Binding Sites List in 1vgx
Zinc binding site 1 out of 2 in the Crystal Structure of A Autoinducer-2 Synthesis Protein


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 Autoinducer-2 Synthesis Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn167

b:10.7
occ:1.00
NE2 A:HIS57 2.0 10.0 1.0
NE2 A:HIS61 2.0 9.7 1.0
O B:HOH190 2.2 6.9 1.0
SG A:CYS125 2.3 7.3 1.0
CE1 A:HIS61 2.9 11.0 1.0
CE1 A:HIS57 2.9 9.0 1.0
CD2 A:HIS57 3.1 9.6 1.0
CD2 A:HIS61 3.2 9.0 1.0
CB A:CYS125 3.3 6.0 1.0
NE2 A:HIS131 3.9 8.1 1.0
CA A:CYS125 3.9 8.6 1.0
O A:HOH180 3.9 23.2 1.0
ND1 A:HIS61 4.1 10.0 1.0
ND1 A:HIS57 4.1 7.8 1.0
CG A:HIS57 4.2 6.9 1.0
CE1 A:HIS131 4.2 7.6 1.0
CG A:HIS61 4.2 10.7 1.0
CB B:CSD82 4.2 9.3 1.0
N A:GLY126 4.3 9.6 1.0
OE1 A:GLU60 4.4 16.3 1.0
C A:CYS125 4.5 9.8 1.0
N B:CSD82 4.8 7.6 1.0
CA B:CSD82 4.9 8.5 1.0
N A:ASN127 4.9 10.6 1.0
OD2 B:CSD82 4.9 15.4 1.0

Zinc binding site 2 out of 2 in 1vgx

Go back to Zinc Binding Sites List in 1vgx
Zinc binding site 2 out of 2 in the Crystal Structure of A Autoinducer-2 Synthesis Protein


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 Autoinducer-2 Synthesis Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn167

b:11.8
occ:1.00
NE2 B:HIS61 2.0 6.8 1.0
NE2 B:HIS57 2.2 9.2 1.0
O B:HOH184 2.2 8.3 1.0
SG B:CYS125 2.3 8.2 1.0
CE1 B:HIS61 2.9 8.6 1.0
CE1 B:HIS57 3.1 10.4 1.0
CD2 B:HIS61 3.1 6.5 1.0
CD2 B:HIS57 3.2 8.2 1.0
CB B:CYS125 3.4 9.2 1.0
NE2 B:HIS131 3.8 8.8 1.0
O B:HOH214 3.9 19.0 1.0
CA B:CYS125 4.0 12.2 1.0
ND1 B:HIS61 4.1 9.1 1.0
CE1 B:HIS131 4.2 10.1 1.0
CG B:HIS61 4.2 9.2 1.0
CB A:CSD82 4.2 8.3 1.0
ND1 B:HIS57 4.2 9.2 1.0
CG B:HIS57 4.3 6.0 1.0
N B:GLY126 4.3 10.8 1.0
OE1 B:GLU60 4.4 15.2 1.0
C B:CYS125 4.6 12.1 1.0
N A:CSD82 4.8 7.2 1.0
CA A:CSD82 4.8 6.6 1.0
N B:ASN127 4.9 10.9 1.0
OD2 A:CSD82 5.0 17.7 1.0
SG A:CSD82 5.0 11.4 1.0

Reference:

J.Badger, J.M.Sauder, J.M.Adams, S.Antonysamy, K.Bain, M.G.Bergseid, S.G.Buchanan, M.D.Buchanan, Y.Batiyenko, J.A.Christopher, S.Emtage, A.Eroshkina, I.Feil, E.B.Furlong, K.S.Gajiwala, X.Gao, D.He, J.Hendle, A.Huber, K.Hoda, P.Kearins, C.Kissinger, B.Laubert, H.A.Lewis, J.Lin, K.Loomis, D.Lorimer, G.Louie, M.Maletic, C.D.Marsh, I.Miller, J.Molinari, H.J.Muller-Dieckmann, J.M.Newman, B.W.Noland, B.Pagarigan, F.Park, T.S.Peat, K.W.Post, S.Radojicic, A.Ramos, R.Romero, M.E.Rutter, W.E.Sanderson, K.D.Schwinn, J.Tresser, J.Winhoven, T.A.Wright, L.Wu, J.Xu, T.J.Harris. Structural Analysis of A Set of Proteins Resulting From A Bacterial Genomics Project Proteins V. 60 787 2005.
ISSN: ISSN 0887-3585
PubMed: 16021622
DOI: 10.1002/PROT.20541
Page generated: Fri Sep 25 23:54:31 2020
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