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Zinc in PDB 5i2d: Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo

Enzymatic activity of Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo

All present enzymatic activity of Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo, PDB code: 5i2d was solved by Y.Feng, Y.Zhang, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.31 / 4.41
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 171.487, 105.446, 374.585, 90.00, 102.39, 90.00
R / Rfree (%) 24.1 / 28.4

Other elements in 5i2d:

The structure of Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo (pdb code 5i2d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo, PDB code: 5i2d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5i2d

Go back to Zinc Binding Sites List in 5i2d
Zinc binding site 1 out of 4 in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo


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 T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:52.6
occ:1.00
SG D:CYS1112 2.3 63.2 1.0
SG D:CYS1201 2.3 77.4 1.0
SG D:CYS1194 2.3 74.2 1.0
SG D:CYS1204 2.3 0.8 1.0
CB D:CYS1204 3.2 0.6 1.0
CB D:CYS1194 3.2 74.8 1.0
CA D:CYS1194 3.5 73.9 1.0
CB D:CYS1112 3.6 62.8 1.0
CB D:CYS1201 3.6 89.3 1.0
OG1 D:THR1196 3.8 0.2 1.0
N D:GLN1195 3.9 60.8 1.0
C D:CYS1194 4.2 76.3 1.0
N D:CYS1112 4.2 68.6 1.0
N D:CYS1201 4.2 87.1 1.0
CG2 D:THR1114 4.2 78.4 1.0
CA D:CYS1204 4.4 0.4 1.0
N D:CYS1204 4.5 0.2 1.0
CA D:CYS1201 4.5 85.4 1.0
CA D:CYS1112 4.5 69.1 1.0
N D:THR1196 4.6 98.5 1.0
NH2 D:ARG1189 4.7 0.9 1.0
N D:CYS1194 4.7 69.7 1.0
CB D:THR1196 4.9 0.8 1.0

Zinc binding site 2 out of 4 in 5i2d

Go back to Zinc Binding Sites List in 5i2d
Zinc binding site 2 out of 4 in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo


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 T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:49.2
occ:1.00
SG D:CYS73 2.3 62.6 1.0
SG D:CYS76 2.3 86.4 1.0
SG D:CYS60 2.3 51.0 1.0
SG D:CYS58 2.3 57.6 1.0
CB D:CYS73 2.8 53.5 1.0
CB D:CYS58 3.2 60.1 1.0
CB D:CYS76 3.4 84.7 1.0
N D:CYS60 3.7 54.0 1.0
CB D:CYS60 3.7 50.8 1.0
N D:CYS76 4.0 92.9 1.0
N D:GLY61 4.1 73.0 1.0
N D:LYS62 4.1 81.1 1.0
CA D:CYS60 4.1 54.9 1.0
N D:ALA59 4.2 72.4 1.0
CB D:LYS62 4.2 77.3 1.0
CA D:CYS76 4.3 84.1 1.0
CA D:CYS73 4.3 55.0 1.0
CA D:CYS58 4.4 60.2 1.0
C D:CYS58 4.5 58.6 1.0
C D:CYS60 4.5 63.5 1.0
C D:ALA59 4.7 80.5 1.0
CA D:LYS62 4.8 74.3 1.0
CD1 D:TYR63 4.8 72.9 1.0
CB D:ARG75 4.8 94.0 1.0
C D:CYS73 4.9 61.8 1.0
CA D:ALA59 4.9 72.3 1.0

Zinc binding site 3 out of 4 in 5i2d

Go back to Zinc Binding Sites List in 5i2d
Zinc binding site 3 out of 4 in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo


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 T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn2001

b:53.9
occ:1.00
SG O:CYS1112 2.3 59.7 1.0
SG O:CYS1194 2.3 42.1 1.0
SG O:CYS1201 2.3 39.3 1.0
SG O:CYS1204 2.3 77.4 1.0
CB O:CYS1194 3.2 42.7 1.0
CB O:CYS1204 3.2 77.1 1.0
CA O:CYS1194 3.4 41.8 1.0
CB O:CYS1112 3.5 59.2 1.0
CB O:CYS1201 3.6 51.2 1.0
OG1 O:THR1196 3.7 0.5 1.0
N O:GLN1195 3.8 58.1 1.0
C O:CYS1194 4.1 44.1 1.0
N O:CYS1112 4.2 65.1 1.0
CG2 O:THR1114 4.2 51.2 1.0
N O:CYS1201 4.3 49.0 1.0
CA O:CYS1204 4.4 78.9 1.0
N O:CYS1204 4.4 79.7 1.0
CA O:CYS1112 4.5 65.6 1.0
CA O:CYS1201 4.5 47.3 1.0
NH2 O:ARG1189 4.5 88.5 1.0
N O:THR1196 4.6 0.8 1.0
N O:CYS1194 4.7 37.6 1.0
CB O:THR1196 4.9 0.1 1.0
OD1 O:ASP1111 5.0 84.4 1.0

Zinc binding site 4 out of 4 in 5i2d

Go back to Zinc Binding Sites List in 5i2d
Zinc binding site 4 out of 4 in the Crystal Structure of T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo


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 T. Thermophilus TTHB099 Class II Transcription Activation Complex: Tap-Rpo within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn2002

b:65.6
occ:1.00
SG O:CYS60 2.3 93.0 1.0
SG O:CYS73 2.3 56.6 1.0
SG O:CYS76 2.3 0.4 1.0
SG O:CYS58 2.3 69.5 1.0
CB O:CYS73 3.1 47.4 1.0
CB O:CYS58 3.2 72.1 1.0
CB O:CYS76 3.3 0.7 1.0
N O:CYS60 3.6 96.1 1.0
CB O:CYS60 3.6 92.9 1.0
N O:CYS76 3.9 0.9 1.0
N O:GLY61 4.0 89.5 1.0
CA O:CYS60 4.0 96.9 1.0
N O:LYS62 4.1 88.2 1.0
N O:ALA59 4.1 57.5 1.0
CA O:CYS76 4.2 0.1 1.0
CB O:LYS62 4.2 84.4 1.0
C O:CYS60 4.4 0.6 1.0
C O:CYS58 4.4 70.5 1.0
CA O:CYS58 4.4 72.1 1.0
CA O:CYS73 4.5 48.9 1.0
C O:ALA59 4.6 65.6 1.0
CB O:ARG75 4.7 89.3 1.0
CA O:LYS62 4.7 81.4 1.0
CA O:ALA59 4.8 57.4 1.0
CD1 O:TYR63 4.9 50.0 1.0
C O:ARG75 4.9 97.3 1.0
CA O:GLY61 5.0 93.4 1.0

Reference:

Y.Feng, Y.Zhang, R.H.Ebright. Structural Basis of Transcription Activation. Science V. 352 1330 2016.
ISSN: ESSN 1095-9203
PubMed: 27284196
DOI: 10.1126/SCIENCE.AAF4417
Page generated: Sun Oct 27 17:47:45 2024

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