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Zinc in PDB 4e2f: Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State

Enzymatic activity of Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State

All present enzymatic activity of Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State:
2.1.3.2;

Protein crystallography data

The structure of Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State, PDB code: 4e2f was solved by W.Guo, E.R.Kantrowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.89 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.086, 144.814, 203.359, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 27.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State (pdb code 4e2f). 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 E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State, PDB code: 4e2f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4e2f

Go back to Zinc Binding Sites List in 4e2f
Zinc binding site 1 out of 6 in the Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State


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 E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:59.6
occ:1.00
 SG D:CYS138 2.2 56.6 1.0
SG D:CYS114 2.3 67.3 1.0
SG D:CYS141 2.4 67.3 1.0
SG D:CYS109 2.7 68.0 1.0
CB D:CYS138 2.9 62.4 1.0
CB D:CYS141 3.1 68.9 1.0
CB D:CYS114 3.2 83.0 1.0
N D:CYS141 3.3 67.7 1.0
CB D:CYS109 3.6 56.4 1.0
CA D:CYS141 3.7 62.4 1.0
CB D:TYR140 4.3 64.0 1.0
C D:TYR140 4.4 76.7 1.0
CA D:CYS138 4.4 61.0 1.0
CA D:CYS114 4.5 44.4 1.0
C D:CYS141 4.6 77.7 1.0
OG D:SER116 4.6 67.9 1.0
CA D:TYR140 4.7 77.5 1.0
N D:GLU142 4.7 72.8 1.0
CB D:ASN111 4.7 57.7 1.0
N D:TYR140 4.7 69.6 1.0
C D:CYS138 4.9 78.7 1.0

Zinc binding site 2 out of 6 in 4e2f

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Zinc binding site 2 out of 6 in the Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State


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 E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:59.5
occ:1.00
 SG B:CYS138 2.3 50.2 1.0
SG B:CYS141 2.3 58.3 1.0
SG B:CYS109 2.3 56.5 1.0
SG B:CYS114 2.4 59.9 1.0
CB B:CYS138 3.0 56.9 1.0
CB B:CYS114 3.2 64.4 1.0
CB B:CYS141 3.2 71.2 1.0
CB B:CYS109 3.2 64.7 1.0
N B:CYS141 3.7 55.6 1.0
CA B:CYS141 4.0 61.2 1.0
CB B:ASN111 4.4 65.7 1.0
CA B:CYS138 4.5 60.4 1.0
CA B:CYS114 4.5 55.0 1.0
CA B:CYS109 4.6 69.9 1.0
OG B:SER116 4.7 70.0 1.0
CB B:TYR140 4.7 40.7 1.0
C B:TYR140 4.8 59.6 1.0
C B:CYS141 4.8 63.2 1.0
ND2 B:ASN111 4.9 38.0 1.0
N B:GLU142 5.0 62.2 1.0

Zinc binding site 3 out of 6 in 4e2f

Go back to Zinc Binding Sites List in 4e2f
Zinc binding site 3 out of 6 in the Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State


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 E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:75.4
occ:1.00
 SG J:CYS114 2.2 68.2 1.0
SG J:CYS138 2.3 65.2 1.0
SG J:CYS109 2.3 79.4 1.0
SG J:CYS141 2.4 80.9 1.0
CB J:CYS114 2.8 90.8 1.0
CB J:CYS141 3.1 79.2 1.0
CB J:CYS138 3.2 58.3 1.0
CB J:CYS109 3.3 72.1 1.0
N J:CYS141 3.6 57.6 1.0
CA J:CYS141 3.9 54.6 1.0
CA J:CYS114 4.2 55.9 1.0
CB J:ASN111 4.3 73.2 1.0
OG J:SER116 4.6 66.8 1.0
CA J:CYS138 4.7 67.8 1.0
CB J:TYR140 4.7 46.7 1.0
C J:CYS141 4.8 78.5 1.0
CA J:CYS109 4.8 88.2 1.0
C J:TYR140 4.8 68.1 1.0
ND2 J:ASN111 4.8 72.7 1.0
CG J:ASN111 4.9 81.3 1.0

Zinc binding site 4 out of 6 in 4e2f

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Zinc binding site 4 out of 6 in the Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State


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 E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:57.7
occ:1.00
 SG L:CYS109 2.2 80.0 1.0
SG L:CYS114 2.2 77.8 1.0
SG L:CYS141 2.3 62.0 1.0
SG L:CYS138 2.4 62.5 1.0
CB L:CYS114 3.0 73.9 1.0
CB L:CYS138 3.2 48.9 1.0
CB L:CYS109 3.2 67.2 1.0
CB L:CYS141 3.2 64.1 1.0
N L:CYS141 3.8 59.4 1.0
CA L:CYS141 4.0 50.5 1.0
CB L:ASN111 4.2 71.6 1.0
CA L:CYS114 4.4 62.6 1.0
CA L:CYS109 4.6 69.9 1.0
OG L:SER116 4.7 73.0 1.0
CA L:CYS138 4.7 52.1 1.0
CB L:TYR140 4.8 59.8 1.0
C L:CYS141 4.8 75.3 1.0
ND2 L:ASN111 4.9 82.8 1.0
C L:TYR140 4.9 65.5 1.0
CG L:ASN111 5.0 68.1 1.0

Zinc binding site 5 out of 6 in 4e2f

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Zinc binding site 5 out of 6 in the Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State


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 E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:98.6
occ:1.00
 SG H:CYS141 2.1 70.9 1.0
SG H:CYS138 2.3 69.2 1.0
SG H:CYS114 2.4 70.2 1.0
SG H:CYS109 2.5 77.5 1.0
CB H:CYS141 2.9 74.8 1.0
CB H:CYS138 3.0 63.9 1.0
CB H:CYS114 3.1 97.4 1.0
N H:CYS141 3.4 75.1 1.0
CB H:CYS109 3.6 71.5 1.0
CA H:CYS141 3.7 81.8 1.0
CA H:CYS114 4.4 69.5 1.0
CB H:ASN111 4.4 83.6 1.0
CA H:CYS138 4.5 68.5 1.0
C H:CYS141 4.5 85.0 1.0
C H:TYR140 4.6 79.3 1.0
CB H:TYR140 4.7 65.6 1.0
N H:GLU142 4.7 80.6 1.0
ND2 H:ASN111 4.8 71.1 1.0
OG H:SER116 4.9 96.7 1.0
CA H:TYR140 5.0 82.4 1.0

Zinc binding site 6 out of 6 in 4e2f

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Zinc binding site 6 out of 6 in the Crystal Structure of E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State


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 E. Coli Aspartate Transcarbamoylase K164E/E239K Mutant in An Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:58.2
occ:1.00
 SG F:CYS138 2.3 52.8 1.0
SG F:CYS109 2.3 60.8 1.0
SG F:CYS114 2.3 45.4 1.0
SG F:CYS141 2.4 67.2 1.0
CB F:CYS114 3.1 61.6 1.0
CB F:CYS138 3.1 55.9 1.0
CB F:CYS141 3.2 59.7 1.0
CB F:CYS109 3.2 69.5 1.0
N F:CYS141 3.7 41.5 1.0
CA F:CYS141 4.0 51.7 1.0
CB F:ASN111 4.3 65.1 1.0
CA F:CYS114 4.4 57.9 1.0
CA F:CYS138 4.6 61.0 1.0
CA F:CYS109 4.6 78.5 1.0
OG F:SER116 4.7 60.9 1.0
ND2 F:ASN111 4.8 77.1 1.0
CB F:TYR140 4.8 57.9 1.0
C F:CYS141 4.9 66.3 1.0
C F:TYR140 4.9 54.7 1.0
CG F:ASN111 5.0 59.1 1.0

Reference:

W.Guo, J.M.West, A.S.Dutton, H.Tsuruta, E.R.Kantrowitz. Trapping and Structure Determination of An Intermediate in the Allosteric Transition of Aspartate Transcarbamoylase. Proc.Natl.Acad.Sci.Usa V. 109 7741 2012.
ISSN: ISSN 0027-8424
PubMed: 22547808
DOI: 10.1073/PNAS.1119683109
Page generated: Wed Dec 16 05:15:24 2020

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