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Zinc in PDB 1zkm: Structural Analysis of Escherichia Coli Thif

Protein crystallography data

The structure of Structural Analysis of Escherichia Coli Thif, PDB code: 1zkm was solved by D.M.Duda, H.Walden, J.Sfondouris, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.95
Space group F 41 3 2 3
Cell size a, b, c (Å), α, β, γ (°) 360.168, 360.168, 360.168, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Analysis of Escherichia Coli Thif (pdb code 1zkm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Analysis of Escherichia Coli Thif, PDB code: 1zkm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1zkm

Go back to Zinc Binding Sites List in 1zkm
Zinc binding site 1 out of 4 in the Structural Analysis of Escherichia Coli Thif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Analysis of Escherichia Coli Thif within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn252

b:81.3
occ:1.00
 SG A:CYS172 2.5 98.5 1.0
SG A:CYS169 2.6 74.5 1.0
CB A:CYS243 2.6 0.1 1.0
SG A:CYS240 2.8 0.2 1.0
O A:VAL242 3.0 0.9 1.0
SG A:CYS243 3.3 0.1 1.0
CB A:CYS240 3.3 0.2 1.0
N A:CYS169 3.4 69.7 1.0
CB A:CYS169 3.7 74.5 1.0
C A:VAL242 3.7 0.9 1.0
CB A:CYS172 3.8 98.5 1.0
CA A:CYS243 3.9 1.0 1.0
CA A:CYS169 4.0 69.7 1.0
N A:CYS243 4.1 1.0 1.0
N A:CYS172 4.2 0.7 1.0
CA A:CYS172 4.2 0.7 1.0
C A:ARG171 4.2 0.0 1.0
O A:ARG171 4.3 0.0 1.0
C A:GLY168 4.3 77.8 1.0
CA A:GLY168 4.3 77.8 1.0
C A:CYS169 4.6 69.7 1.0
O A:CYS169 4.6 69.7 1.0
CB A:VAL242 4.6 79.9 1.0
C A:CYS243 4.6 1.0 1.0
CA A:VAL242 4.7 0.9 1.0
CA A:CYS240 4.8 0.8 1.0
CB A:ARG236 4.8 0.1 1.0
CB A:ARG171 4.9 0.5 1.0
N A:VAL242 4.9 0.9 1.0
CA A:ARG171 5.0 0.0 1.0
CG1 A:VAL242 5.0 79.9 1.0

Zinc binding site 2 out of 4 in 1zkm

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Zinc binding site 2 out of 4 in the Structural Analysis of Escherichia Coli Thif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Analysis of Escherichia Coli Thif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn252

b:81.3
occ:1.00
 SG B:CYS172 2.2 68.2 1.0
SG B:CYS240 2.3 0.6 1.0
SG B:CYS169 2.4 77.3 1.0
SG B:CYS243 2.5 0.9 1.0
CB B:CYS240 3.0 0.6 1.0
CB B:CYS169 3.1 77.3 1.0
CB B:CYS243 3.2 0.9 1.0
N B:CYS243 3.4 0.8 1.0
N B:CYS169 3.5 87.8 1.0
CB B:CYS172 3.6 68.2 1.0
N B:CYS172 3.8 0.5 1.0
CA B:CYS243 3.9 0.8 1.0
CA B:CYS169 3.9 87.8 1.0
CG2 B:VAL242 3.9 83.3 1.0
CA B:CYS172 4.1 0.5 1.0
CB B:VAL242 4.3 83.3 1.0
CA B:CYS240 4.4 0.8 1.0
C B:GLY168 4.4 78.2 1.0
C B:VAL242 4.4 0.7 1.0
C B:CYS169 4.5 87.8 1.0
N B:VAL242 4.6 0.7 1.0
CA B:GLY168 4.6 78.2 1.0
CA B:VAL242 4.7 0.7 1.0
C B:CYS240 4.7 0.8 1.0
O B:CYS169 4.8 87.8 1.0
C B:ARG171 4.9 0.2 1.0
O B:CYS240 4.9 0.8 1.0
CB B:ARG171 5.0 0.8 1.0

Zinc binding site 3 out of 4 in 1zkm

Go back to Zinc Binding Sites List in 1zkm
Zinc binding site 3 out of 4 in the Structural Analysis of Escherichia Coli Thif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Analysis of Escherichia Coli Thif within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn252

b:81.3
occ:1.00
 SG C:CYS172 2.4 88.6 1.0
SG C:CYS240 2.5 0.5 1.0
SG C:CYS169 2.5 90.1 1.0
SG C:CYS243 2.7 0.9 1.0
CB C:CYS243 3.3 0.9 1.0
CB C:CYS240 3.5 0.5 1.0
CB C:CYS169 3.6 90.1 1.0
N C:CYS243 3.7 87.5 1.0
CB C:CYS172 3.8 88.6 1.0
N C:CYS169 3.8 87.7 1.0
C C:VAL242 3.9 0.9 1.0
N C:CYS172 3.9 78.5 1.0
CA C:CYS243 3.9 87.5 1.0
CB C:VAL242 4.2 92.0 1.0
O C:VAL242 4.2 0.9 1.0
CA C:CYS172 4.2 78.5 1.0
CA C:CYS169 4.3 87.7 1.0
C C:CYS243 4.3 87.5 1.0
CA C:VAL242 4.4 0.9 1.0
C C:ARG171 4.4 90.7 1.0
N C:VAL242 4.5 0.9 1.0
CB C:ARG171 4.7 0.1 1.0
C C:CYS169 4.7 87.7 1.0
O C:CYS169 4.8 87.7 1.0
CA C:CYS240 4.9 0.6 1.0
CA C:ARG171 4.9 90.7 1.0
N C:ARG171 4.9 90.7 1.0
C C:GLY168 4.9 73.8 1.0
CG1 C:VAL242 5.0 92.0 1.0

Zinc binding site 4 out of 4 in 1zkm

Go back to Zinc Binding Sites List in 1zkm
Zinc binding site 4 out of 4 in the Structural Analysis of Escherichia Coli Thif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Analysis of Escherichia Coli Thif within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn252

b:81.3
occ:1.00
 SG D:CYS172 2.4 78.8 1.0
SG D:CYS243 2.6 0.1 1.0
SG D:CYS169 2.6 94.6 1.0
SG D:CYS240 2.6 0.7 1.0
CB D:CYS240 3.2 0.7 1.0
CB D:CYS169 3.2 94.6 1.0
CB D:CYS243 3.3 0.1 1.0
N D:CYS243 3.5 0.8 1.0
CG1 D:VAL242 3.6 88.8 1.0
N D:CYS172 3.8 77.5 1.0
CB D:CYS172 3.8 78.8 1.0
CA D:CYS243 4.0 0.8 1.0
CA D:CYS172 4.2 77.5 1.0
N D:CYS169 4.3 75.5 1.0
CA D:CYS169 4.3 75.5 1.0
CB D:ARG171 4.4 0.6 1.0
C D:ARG171 4.5 0.2 1.0
C D:VAL242 4.6 0.5 1.0
CB D:VAL242 4.6 88.8 1.0
CA D:CYS240 4.6 0.9 1.0
N D:VAL242 4.7 0.5 1.0
C D:CYS169 4.8 75.5 1.0
C D:GLY168 4.8 76.6 1.0
CA D:VAL242 4.8 0.5 1.0
CA D:ARG171 4.8 0.2 1.0
N D:ARG171 4.8 0.2 1.0
N D:GLY244 4.9 93.5 1.0
CG2 D:VAL242 4.9 88.8 1.0
O D:CYS169 4.9 75.5 1.0

Reference:

D.M.Duda, H.Walden, J.Sfondouris, B.A.Schulman. Structural Analysis of Escherichia Coli Thif. J.Mol.Biol. V. 349 774 2005.
ISSN: ISSN 0022-2836
PubMed: 15896804
DOI: 10.1016/J.JMB.2005.04.011
Page generated: Wed Oct 16 21:16:39 2024

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