Atomistry » Zinc » PDB 2x8z-2xjl » 2xev
Atomistry »
  Zinc »
    PDB 2x8z-2xjl »
      2xev »

Zinc in PDB 2xev: Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf

Protein crystallography data

The structure of Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf, PDB code: 2xev was solved by A.M.Krachler, A.Sharma, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.75 / 1.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.360, 37.120, 90.610, 90.00, 117.14, 90.00
R / Rfree (%) 20.407 / 22.813

Other elements in 2xev:

The structure of Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf (pdb code 2xev). 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 the Tpr Domain of Xanthomonas Campestris Ybgf, PDB code: 2xev:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2xev

Go back to Zinc Binding Sites List in 2xev
Zinc binding site 1 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1123

b:16.5
occ:0.80
OE1 A:GLU88 1.9 19.6 1.0
OE2 A:GLU58 1.9 21.4 1.0
OE1 A:GLU93 2.2 29.6 1.0
CD A:GLU58 2.8 18.7 1.0
CD A:GLU88 2.9 21.9 1.0
OE1 A:GLU58 3.2 19.6 1.0
OE2 A:GLU88 3.3 20.6 1.0
CD A:GLU93 3.4 35.9 1.0
O A:HOH2033 3.9 22.8 1.0
CG A:GLN85 3.9 21.3 1.0
OE2 A:GLU93 4.0 38.8 1.0
CG A:GLU58 4.2 16.3 1.0
CG A:GLU88 4.3 22.8 1.0
CG A:LYS90 4.3 30.9 1.0
NE2 A:GLN85 4.4 26.6 1.0
NH2 A:ARG62 4.6 32.0 1.0
CB A:GLN85 4.6 19.2 1.0
CG A:GLU93 4.6 32.6 1.0
CD A:GLN85 4.7 25.1 1.0
CB A:GLU88 4.7 23.5 1.0
CA A:GLN85 4.7 19.0 1.0
CB A:LYS90 4.8 29.3 1.0
CB A:GLU58 4.9 13.5 1.0

Zinc binding site 2 out of 6 in 2xev

Go back to Zinc Binding Sites List in 2xev
Zinc binding site 2 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1125

b:17.6
occ:0.50
O B:HOH2036 2.8 35.0 1.0
OE1 A:GLN22 3.2 25.5 1.0
C B:ASN53 3.2 11.7 1.0
CA B:ASN53 3.3 12.1 1.0
N B:GLN55 3.3 11.9 1.0
N B:LEU56 3.3 11.4 1.0
OD1 B:ASN53 3.5 16.1 1.0
CB B:ASN53 3.5 12.0 1.0
N B:PHE54 3.5 11.7 1.0
O B:ASN53 3.6 12.6 1.0
CG B:LEU56 3.6 9.1 1.0
CB B:GLN55 3.6 13.1 1.0
CA B:GLN55 3.8 11.9 1.0
CG B:ASN53 3.9 12.5 1.0
CB B:LEU56 4.1 9.8 1.0
C B:GLN55 4.1 11.5 1.0
CD A:GLN22 4.1 22.4 1.0
C B:PHE54 4.2 11.5 1.0
CG B:GLN55 4.3 14.5 1.0
OE1 B:GLN55 4.3 21.6 1.0
CD1 B:LEU56 4.3 10.8 1.0
CA B:LEU56 4.3 10.1 1.0
CG A:GLN22 4.4 19.8 1.0
CA B:PHE54 4.4 11.1 1.0
CD B:GLN55 4.7 19.0 1.0
N B:ASN53 4.7 13.1 1.0
CD2 B:LEU56 4.7 11.8 1.0
CB A:GLN22 4.9 14.7 1.0
O B:ARG52 4.9 14.5 1.0

Zinc binding site 3 out of 6 in 2xev

Go back to Zinc Binding Sites List in 2xev
Zinc binding site 3 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1126

b:15.9
occ:0.70
OE2 B:GLU88 1.9 24.9 1.0
OE1 B:GLU58 2.1 20.6 1.0
OD1 A:ASP19 2.1 17.1 1.0
OD2 A:ASP19 2.5 17.5 1.0
CG A:ASP19 2.6 17.2 1.0
CD B:GLU88 2.9 22.8 1.0
ZN B:ZN1127 3.0 16.7 0.7
OE1 B:GLU88 3.2 22.0 1.0
CD B:GLU58 3.2 17.4 1.0
OE2 B:GLU58 3.6 17.5 1.0
NZ B:LYS90 3.8 28.9 1.0
O B:HOH2037 4.0 13.8 1.0
CB A:ASP19 4.1 14.2 1.0
CG B:GLU88 4.3 21.5 1.0
CG B:GLN55 4.3 14.5 1.0
CG B:GLU58 4.5 14.1 1.0
CE B:LYS90 4.6 30.0 1.0
O A:HOH2010 4.6 16.9 1.0
NE2 B:GLN55 4.7 18.3 1.0
CB B:GLN55 4.7 13.1 1.0
CA B:GLN55 4.8 11.9 1.0
CD B:LYS90 4.8 27.7 1.0
CA A:ASP19 4.9 14.1 1.0
CB B:GLU58 4.9 12.0 1.0

Zinc binding site 4 out of 6 in 2xev

Go back to Zinc Binding Sites List in 2xev
Zinc binding site 4 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1127

b:16.7
occ:0.70
OE1 B:GLU88 1.9 22.0 1.0
OE2 B:GLU58 2.0 17.5 1.0
OE1 B:GLU93 2.1 23.9 1.0
CD B:GLU58 2.8 17.4 1.0
CD B:GLU93 2.9 25.8 1.0
CD B:GLU88 2.9 22.8 1.0
OE2 B:GLU93 3.0 28.9 1.0
ZN B:ZN1126 3.0 15.9 0.7
OE1 B:GLU58 3.0 20.6 1.0
OE2 B:GLU88 3.2 24.9 1.0
CD B:LYS90 3.6 27.7 1.0
CG B:GLN85 3.7 17.2 1.0
NZ B:LYS90 4.1 28.9 1.0
NE2 B:GLN85 4.1 20.0 1.0
CG B:GLU58 4.2 14.1 1.0
CB B:GLN85 4.3 15.0 1.0
CG B:GLU88 4.3 21.5 1.0
CD B:GLN85 4.3 19.5 1.0
CG B:GLU93 4.3 24.5 1.0
CE B:LYS90 4.3 30.0 1.0
CG B:LYS90 4.5 24.1 1.0
CA B:GLN85 4.6 15.5 1.0
OD2 A:ASP19 4.7 17.5 1.0
CB B:LYS90 4.7 23.4 1.0
NH2 B:ARG62 4.7 30.7 1.0
CB B:GLU88 4.8 20.3 1.0
CB B:GLU93 5.0 22.8 1.0

Zinc binding site 5 out of 6 in 2xev

Go back to Zinc Binding Sites List in 2xev
Zinc binding site 5 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1126

b:12.7
occ:1.00
OE1 C:GLU88 1.9 18.1 1.0
OE1 C:GLU58 2.0 9.2 1.0
OD2 B:ASP19 2.0 8.5 0.5
OD2 B:ASP19 2.0 7.0 0.5
CL C:CL1125 2.2 15.0 1.0
CD C:GLU58 2.8 8.1 1.0
CD C:GLU88 2.8 18.3 1.0
CG B:ASP19 2.9 9.9 0.5
CG B:ASP19 2.9 11.1 0.5
OD1 B:ASP19 3.1 10.1 0.5
OE2 C:GLU58 3.1 11.1 1.0
OE2 C:GLU88 3.1 17.9 1.0
OD1 B:ASP19 3.1 12.9 0.5
NZ B:LYS16 3.7 18.3 1.0
NZ C:LYS90 3.9 17.8 1.0
O C:HOH2032 4.1 10.4 1.0
CG C:GLN55 4.2 13.3 1.0
CG C:GLU88 4.2 20.7 1.0
CG C:GLU58 4.2 10.0 1.0
CG C:GLN85 4.2 12.4 1.0
CB B:ASP19 4.3 10.2 0.5
CB B:ASP19 4.3 10.7 0.5
O B:HOH2015 4.4 30.0 1.0
CB C:GLU58 4.5 10.3 1.0
CG C:LYS90 4.7 20.3 1.0
CE B:LYS16 4.7 19.4 1.0
CA C:GLN55 4.8 10.5 1.0
NE2 C:GLN85 4.9 15.4 1.0
CB C:GLN55 4.9 11.4 1.0
CB C:GLU88 4.9 18.6 1.0
CA C:GLN85 4.9 11.7 1.0

Zinc binding site 6 out of 6 in 2xev

Go back to Zinc Binding Sites List in 2xev
Zinc binding site 6 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1127

b:18.9
occ:1.00
OD1 C:ASP19 2.2 17.5 1.0
OD2 C:ASP19 2.3 17.5 1.0
CG C:ASP19 2.5 15.3 1.0
CB C:ASP19 4.0 14.4 1.0
O C:HOH2011 4.2 28.3 1.0
O C:HOH2014 4.4 19.6 1.0
O C:HOH2013 4.7 22.9 1.0
CA C:ASP19 4.9 14.3 1.0

Reference:

A.M.Krachler, A.Sharma, A.Cauldwell, G.Papadakos, C.Kleanthous. Tola Modulates the Oligomeric Status of Ybgf in the Bacterial Periplasm. J.Mol.Biol. V. 403 270 2010.
ISSN: ISSN 0022-2836
PubMed: 20816983
DOI: 10.1016/J.JMB.2010.08.050
Page generated: Wed Dec 16 03:59:52 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy