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Zinc in PDB 5c7e: Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide

Protein crystallography data

The structure of Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide, PDB code: 5c7e was solved by J.Ke, H.Ma, X.Gu, J.S.Brunzelle, H.E.Xu, K.Melcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 3.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.668, 162.668, 157.250, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 22.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide (pdb code 5c7e). 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 Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide, PDB code: 5c7e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5c7e

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Zinc binding site 1 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:0.8
occ:0.50
NE2 A:HIS202 2.0 0.7 1.0
ND1 A:HIS183 2.0 0.9 1.0
SG A:CYS186 2.2 1.0 1.0
SG A:CYS204 2.3 0.4 1.0
CE1 A:HIS183 2.8 0.8 1.0
CD2 A:HIS202 3.0 0.0 1.0
CE1 A:HIS202 3.0 0.4 1.0
CG A:HIS183 3.1 0.3 1.0
CB A:HIS183 3.6 0.3 1.0
CB A:CYS204 3.7 0.5 1.0
CA A:HIS183 3.7 0.6 1.0
CB A:CYS186 3.9 0.8 1.0
O A:HIS183 3.9 0.6 1.0
N A:CYS204 4.0 0.8 1.0
NE2 A:HIS183 4.0 0.6 1.0
C A:THR203 4.1 0.9 1.0
ND1 A:HIS202 4.1 0.3 1.0
CG A:HIS202 4.1 0.8 1.0
CD2 A:HIS183 4.1 1.0 1.0
CG A:PRO193 4.2 0.1 1.0
C A:HIS183 4.3 0.0 1.0
CA A:CYS204 4.3 0.1 1.0
CA A:THR203 4.5 0.3 1.0
O A:THR203 4.5 0.5 1.0
CB A:PRO193 4.6 0.3 1.0
N A:HIS183 5.0 0.8 1.0

Zinc binding site 2 out of 6 in 5c7e

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Zinc binding site 2 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:0.7
occ:0.50
ND1 B:HIS183 1.9 0.9 1.0
SG B:CYS186 2.2 0.7 1.0
SG B:CYS204 2.2 0.9 1.0
NE2 B:HIS202 2.4 0.2 1.0
CE1 B:HIS183 2.6 0.4 1.0
CG B:HIS183 3.0 0.7 1.0
CB B:CYS186 3.1 0.4 1.0
CD2 B:HIS202 3.4 0.1 1.0
CE1 B:HIS202 3.4 0.1 1.0
CB B:CYS204 3.5 0.9 1.0
CB B:HIS183 3.6 0.1 1.0
O B:HIS183 3.7 0.2 1.0
NE2 B:HIS183 3.7 0.1 1.0
CA B:HIS183 3.7 0.9 1.0
CD2 B:HIS183 4.0 0.5 1.0
CB B:PRO193 4.0 0.7 1.0
N B:CYS204 4.1 0.6 1.0
C B:HIS183 4.2 0.9 1.0
CA B:CYS204 4.4 0.4 1.0
C B:THR203 4.4 0.9 1.0
ND1 B:HIS202 4.5 0.3 1.0
CG B:HIS202 4.5 0.3 1.0
CA B:CYS186 4.5 0.6 1.0
CB B:PRO189 4.6 0.8 1.0
CA B:PRO189 4.6 0.2 1.0
O B:THR203 4.8 0.6 1.0
CG B:PRO193 4.8 0.2 1.0
CA B:THR203 4.9 0.1 1.0
N B:HIS183 5.0 1.0 1.0
N B:CYS186 5.0 0.7 1.0

Zinc binding site 3 out of 6 in 5c7e

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Zinc binding site 3 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn400

b:84.8
occ:0.50
ND1 C:HIS183 1.9 0.0 1.0
SG C:CYS204 2.0 0.5 1.0
SG C:CYS186 2.2 99.8 1.0
NE2 C:HIS202 2.2 98.2 1.0
CE1 C:HIS183 2.6 0.0 1.0
CE1 C:HIS202 3.1 0.5 1.0
CG C:HIS183 3.1 97.7 1.0
CB C:CYS186 3.1 0.3 1.0
CD2 C:HIS202 3.2 98.3 1.0
CB C:CYS204 3.6 0.8 1.0
CB C:HIS183 3.7 93.1 1.0
NE2 C:HIS183 3.8 0.4 1.0
CA C:HIS183 3.8 90.5 1.0
CB C:PRO189 3.9 0.1 1.0
O C:HIS183 3.9 0.3 1.0
N C:CYS204 4.0 0.8 1.0
CB C:PRO193 4.0 0.1 1.0
CD2 C:HIS183 4.0 98.1 1.0
CA C:CYS204 4.2 0.1 1.0
ND1 C:HIS202 4.2 0.6 1.0
CG C:PRO189 4.2 0.9 1.0
CG C:HIS202 4.3 0.6 1.0
C C:HIS183 4.3 95.5 1.0
C C:THR203 4.5 0.0 1.0
CA C:CYS186 4.6 0.8 1.0
CG C:PRO193 4.7 0.8 1.0
CA C:THR203 4.9 0.9 1.0

Zinc binding site 4 out of 6 in 5c7e

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Zinc binding site 4 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn400

b:0.7
occ:0.50
ND1 D:HIS183 1.9 0.6 1.0
NE2 D:HIS202 2.0 0.9 1.0
SG D:CYS204 2.1 0.4 1.0
SG D:CYS186 2.3 94.6 1.0
CE1 D:HIS183 2.5 0.9 1.0
CE1 D:HIS202 2.9 0.8 1.0
CG D:HIS183 3.1 0.4 1.0
CD2 D:HIS202 3.1 0.8 1.0
CB D:CYS204 3.2 0.8 1.0
CB D:CYS186 3.5 0.7 1.0
CB D:HIS183 3.7 0.1 1.0
NE2 D:HIS183 3.7 0.4 1.0
N D:CYS204 3.8 0.5 1.0
CB D:PRO193 3.8 0.2 1.0
CA D:HIS183 3.9 0.9 1.0
CA D:CYS204 4.0 0.2 1.0
CD2 D:HIS183 4.0 0.2 1.0
O D:HIS183 4.0 0.6 1.0
ND1 D:HIS202 4.1 0.0 1.0
C D:THR203 4.1 0.4 1.0
CG D:HIS202 4.2 0.5 1.0
C D:HIS183 4.5 0.3 1.0
CA D:PRO189 4.5 0.5 1.0
O D:THR203 4.6 0.6 1.0
CA D:THR203 4.6 0.2 1.0
CB D:PRO189 4.7 0.1 1.0
CG D:PRO193 4.8 0.9 1.0
N D:ARG190 4.9 0.7 1.0
CA D:CYS186 5.0 0.9 1.0

Zinc binding site 5 out of 6 in 5c7e

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Zinc binding site 5 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn400

b:0.0
occ:0.50
ND1 E:HIS183 1.9 0.1 1.0
SG E:CYS204 2.1 1.0 1.0
NE2 E:HIS202 2.2 0.5 1.0
SG E:CYS186 2.2 0.8 1.0
CE1 E:HIS183 2.8 0.8 1.0
CG E:HIS183 2.9 0.4 1.0
CD2 E:HIS202 3.0 0.8 1.0
CB E:CYS186 3.2 0.3 1.0
CE1 E:HIS202 3.3 0.4 1.0
CB E:HIS183 3.3 0.3 1.0
CA E:HIS183 3.4 0.0 1.0
O E:HIS183 3.5 0.7 1.0
CB E:CYS204 3.7 0.3 1.0
NE2 E:HIS183 3.8 0.3 1.0
CD2 E:HIS183 3.9 0.3 1.0
C E:HIS183 3.9 0.7 1.0
CB E:PRO193 4.1 0.6 1.0
CG E:HIS202 4.2 0.7 1.0
N E:CYS204 4.2 0.9 1.0
ND1 E:HIS202 4.3 0.5 1.0
C E:THR203 4.4 0.3 1.0
CA E:CYS204 4.4 0.4 1.0
CG E:PRO193 4.5 0.5 1.0
N E:HIS183 4.6 0.1 1.0
CA E:CYS186 4.6 0.8 1.0
O E:THR203 4.6 0.1 1.0
CA E:THR203 4.8 0.9 1.0
O E:GLN182 4.9 0.6 1.0

Zinc binding site 6 out of 6 in 5c7e

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Zinc binding site 6 out of 6 in the Crystal Structure of the Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide


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 Rice Topless Related Protein 2 (TPR2) N- Terminal Domain (1-209) in Complex with Arabidopsis IAA10 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn400

b:0.0
occ:0.50
ND1 F:HIS183 1.9 0.6 1.0
NE2 F:HIS202 2.2 0.5 1.0
SG F:CYS186 2.2 0.3 1.0
SG F:CYS204 2.3 0.9 1.0
CE1 F:HIS183 2.7 0.8 1.0
CG F:HIS183 2.9 0.8 1.0
CE1 F:HIS202 3.1 0.4 1.0
CD2 F:HIS202 3.1 0.4 1.0
CB F:CYS186 3.5 0.0 1.0
CB F:HIS183 3.5 0.3 1.0
CA F:HIS183 3.6 1.0 1.0
O F:HIS183 3.7 0.0 1.0
CB F:CYS204 3.7 0.3 1.0
NE2 F:HIS183 3.8 0.1 1.0
CD2 F:HIS183 3.9 0.2 1.0
C F:HIS183 4.1 0.4 1.0
ND1 F:HIS202 4.2 0.1 1.0
CG F:HIS202 4.3 0.2 1.0
N F:CYS204 4.3 0.5 1.0
C F:THR203 4.6 0.3 1.0
CA F:CYS204 4.6 0.4 1.0
N F:HIS183 4.8 0.8 1.0
CA F:CYS186 4.8 0.2 1.0

Reference:

J.Ke, H.Ma, X.Gu, A.Thelen, J.S.Brunzelle, J.Li, H.E.Xu, K.Melcher. Structural Basis For Recognition of Diverse Transcriptional Repressors By the Topless Family of Corepressors. Sci Adv V. 1 00107 2015.
ISSN: ESSN 2375-2548
PubMed: 26601214
DOI: 10.1126/SCIADV.1500107
Page generated: Sun Oct 27 13:55:40 2024

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