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Iodine in PDB 6jze: Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C

Enzymatic activity of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C

All present enzymatic activity of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C:
3.4.17.17;

Protein crystallography data

The structure of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C, PDB code: 6jze was solved by Z.Chen, Y.Ling, G.Zeyuan, L.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.73 / 2.51
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.690, 111.115, 126.454, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26.6

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C (pdb code 6jze). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C, PDB code: 6jze:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 6jze

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Iodine binding site 1 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:77.8
occ:0.84
 I3 A:I3C401 0.0 77.8 0.8
C6 A:I3C401 2.2 0.5 0.8
C1 A:I3C401 3.1 98.9 0.8
C5 A:I3C401 3.1 96.0 0.8
N13 A:I3C401 3.3 91.3 0.8
C7 A:I3C401 3.4 0.6 0.8
CE A:LYS247 3.6 49.1 1.0
ND1 A:HIS192 3.7 56.5 1.0
NZ A:LYS247 3.7 58.1 1.0
CD A:LYS247 3.7 40.5 1.0
O8 A:I3C401 3.8 0.2 0.8
O A:PHE182 4.0 36.5 1.0
O9 A:I3C401 4.0 0.6 0.8
CB A:SER181 4.1 30.2 1.0
C A:PHE182 4.1 35.5 1.0
CB A:LYS183 4.1 47.5 1.0
CG A:LYS247 4.2 45.4 1.0
N A:LYS183 4.2 40.2 1.0
CE1 A:HIS192 4.3 59.9 1.0
C2 A:I3C401 4.5 88.6 0.8
C4 A:I3C401 4.5 86.7 0.8
N A:PHE182 4.5 27.7 1.0
CA A:LYS183 4.6 40.0 1.0
C A:SER181 4.6 33.4 1.0
CA A:PHE182 4.8 27.5 1.0
CG A:HIS192 4.8 50.5 1.0
O A:SER181 5.0 32.9 1.0
C3 A:I3C401 5.0 90.8 0.8

Iodine binding site 2 out of 12 in 6jze

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Iodine binding site 2 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:57.6
occ:0.84
 I2 A:I3C401 0.0 57.6 0.8
C4 A:I3C401 2.1 86.7 0.8
C3 A:I3C401 3.0 90.8 0.8
C10 A:I3C401 3.1 95.7 0.8
C5 A:I3C401 3.2 96.0 0.8
O12 A:I3C401 3.3 96.7 0.8
N13 A:I3C401 3.4 91.3 0.8
O11 A:I3C401 3.6 97.2 0.8
CG1 A:VAL194 3.9 29.4 1.0
O A:HIS192 3.9 35.2 1.0
C A:HIS192 4.1 33.3 1.0
CB A:HIS192 4.1 31.7 1.0
CB A:VAL194 4.2 28.1 1.0
N A:HIS193 4.2 35.1 1.0
C A:HIS193 4.3 34.9 1.0
C2 A:I3C401 4.4 88.6 0.8
CA A:HIS193 4.4 32.7 1.0
SG A:CYS158 4.4 34.8 1.0
N A:VAL194 4.4 30.7 1.0
C6 A:I3C401 4.5 0.5 0.8
O A:HIS193 4.7 37.9 1.0
CA A:HIS192 4.7 32.5 1.0
C1 A:I3C401 4.9 98.9 0.8
CA A:VAL194 5.0 28.8 1.0
NZ A:LYS135 5.0 48.5 1.0

Iodine binding site 3 out of 12 in 6jze

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Iodine binding site 3 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:82.5
occ:0.84
 I1 A:I3C401 0.0 82.5 0.8
C2 A:I3C401 2.1 88.6 0.8
C1 A:I3C401 3.0 98.9 0.8
C7 A:I3C401 3.1 0.6 0.8
C3 A:I3C401 3.1 90.8 0.8
O9 A:I3C401 3.4 0.6 0.8
C10 A:I3C401 3.4 95.7 0.8
O A:HOH540 3.5 53.2 1.0
O8 A:I3C401 3.5 0.2 0.8
O11 A:I3C401 3.6 97.2 0.8
NZ A:LYS135 3.9 48.5 1.0
O12 A:I3C401 4.0 96.7 0.8
C6 A:I3C401 4.4 0.5 0.8
C4 A:I3C401 4.4 86.7 0.8
NZ A:LYS265 4.5 69.7 1.0
C5 A:I3C401 4.9 96.0 0.8

Iodine binding site 4 out of 12 in 6jze

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Iodine binding site 4 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:0.1
occ:0.50
 I3 A:I3C402 0.0 0.1 0.5
C6 A:I3C402 2.1 0.8 0.5
C1 A:I3C402 3.0 0.2 0.5
C7 A:I3C402 3.0 1.0 0.5
O8 A:I3C402 3.1 0.3 0.5
C5 A:I3C402 3.1 0.1 0.5
N13 A:I3C402 3.3 0.3 0.5
O9 A:I3C402 3.7 0.6 0.5
O A:LYS92 4.1 46.2 1.0
C2 A:I3C402 4.3 0.6 0.5
CB A:ALA91 4.4 62.9 1.0
C4 A:I3C402 4.4 0.1 0.5
CA A:PRO93 4.5 43.0 1.0
C A:LYS92 4.6 50.4 1.0
N A:PRO93 4.8 44.8 1.0
C3 A:I3C402 4.9 0.3 0.5
N A:SER94 5.0 43.3 1.0

Iodine binding site 5 out of 12 in 6jze

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Iodine binding site 5 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:0.3
occ:0.50
 I2 A:I3C402 0.0 0.3 0.5
C4 A:I3C402 2.1 0.1 0.5
C3 A:I3C402 3.0 0.3 0.5
C5 A:I3C402 3.1 0.1 0.5
C10 A:I3C402 3.2 0.4 0.5
N13 A:I3C402 3.3 0.3 0.5
O11 A:I3C402 3.6 0.5 0.5
O12 A:I3C402 3.7 0.6 0.5
NE2 A:GLN122 4.3 34.7 1.0
C2 A:I3C402 4.3 0.6 0.5
C6 A:I3C402 4.4 0.8 0.5
O A:HOH539 4.5 37.8 1.0
C1 A:I3C402 4.9 0.2 0.5

Iodine binding site 6 out of 12 in 6jze

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Iodine binding site 6 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:0.5
occ:0.50
 I1 A:I3C402 0.0 0.5 0.5
C2 A:I3C402 2.1 0.6 0.5
C1 A:I3C402 3.0 0.2 0.5
C3 A:I3C402 3.0 0.3 0.5
C10 A:I3C402 3.2 0.4 0.5
C7 A:I3C402 3.2 1.0 0.5
O9 A:I3C402 3.3 0.6 0.5
O12 A:I3C402 3.5 0.6 0.5
O B:TYR40 3.6 38.5 1.0
O11 A:I3C402 3.6 0.5 0.5
C B:TYR40 3.7 39.7 1.0
N B:ALA41 3.7 37.5 1.0
CA B:ALA41 3.9 43.1 1.0
O8 A:I3C402 3.9 0.3 0.5
CB B:TYR40 4.0 33.6 1.0
C6 A:I3C402 4.3 0.8 0.5
C4 A:I3C402 4.3 0.1 0.5
CB B:ALA41 4.4 37.8 1.0
CA B:TYR40 4.5 38.0 1.0
CG A:PRO93 4.7 42.9 1.0
C5 A:I3C402 4.9 0.1 0.5
O B:ALA37 4.9 44.8 1.0

Iodine binding site 7 out of 12 in 6jze

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Iodine binding site 7 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:0.5
occ:0.76
 I3 A:I3C403 0.0 0.5 0.8
C6 A:I3C403 2.1 0.7 0.8
C1 A:I3C403 3.0 0.6 0.8
C5 A:I3C403 3.0 0.4 0.8
C7 A:I3C403 3.1 0.5 0.8
N13 A:I3C403 3.2 0.6 0.8
O9 A:I3C403 3.5 0.3 0.8
O8 A:I3C403 3.6 0.2 0.8
C4 A:I3C403 4.3 0.8 0.8
C2 A:I3C403 4.3 0.6 0.8
CE1 A:PHE259 4.6 85.9 1.0
CD1 A:PHE259 4.6 77.7 1.0
C3 A:I3C403 4.8 1.0 0.8

Iodine binding site 8 out of 12 in 6jze

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Iodine binding site 8 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:0.5
occ:0.76
 I2 A:I3C403 0.0 0.5 0.8
C4 A:I3C403 2.1 0.8 0.8
C5 A:I3C403 3.0 0.4 0.8
C3 A:I3C403 3.1 1.0 0.8
N13 A:I3C403 3.1 0.6 0.8
C10 A:I3C403 3.3 0.4 0.8
O11 A:I3C403 3.7 0.2 0.8
O12 A:I3C403 3.7 1.0 0.8
O A:HOH525 3.8 44.3 1.0
C6 A:I3C403 4.3 0.7 0.8
C2 A:I3C403 4.4 0.6 0.8
NH2 A:ARG134 4.5 79.4 1.0
O A:MET136 4.6 50.8 1.0
CA A:ARG137 4.7 57.6 1.0
C1 A:I3C403 4.9 0.6 0.8

Iodine binding site 9 out of 12 in 6jze

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Iodine binding site 9 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:0.9
occ:0.76
 I1 A:I3C403 0.0 0.9 0.8
C2 A:I3C403 2.1 0.6 0.8
C1 A:I3C403 3.0 0.6 0.8
C3 A:I3C403 3.1 1.0 0.8
C7 A:I3C403 3.2 0.5 0.8
C10 A:I3C403 3.3 0.4 0.8
O12 A:I3C403 3.6 1.0 0.8
O11 A:I3C403 3.6 0.2 0.8
O8 A:I3C403 3.7 0.2 0.8
O9 A:I3C403 3.7 0.3 0.8
C6 A:I3C403 4.4 0.7 0.8
C4 A:I3C403 4.4 0.8 0.8
C5 A:I3C403 4.9 0.4 0.8

Iodine binding site 10 out of 12 in 6jze

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Iodine binding site 10 out of 12 in the Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of VASH2-Svbp Complex with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:77.7
occ:0.74
 I3 B:I3C101 0.0 77.7 0.7
C6 B:I3C101 2.1 90.3 0.7
O9 B:I3C101 3.1 94.4 0.7
C1 B:I3C101 3.1 89.7 0.7
C5 B:I3C101 3.1 0.1 0.7
C7 B:I3C101 3.2 92.1 0.7
N13 B:I3C101 3.3 0.9 0.7
O B:HOH202 3.6 47.8 1.0
OE2 B:GLU38 3.6 59.0 1.0
CG B:ARG34 3.7 47.1 1.0
O8 B:I3C101 4.0 88.3 0.7
CD1 B:LEU31 4.1 62.5 1.0
CD B:GLU38 4.2 55.4 1.0
C4 B:I3C101 4.4 0.2 0.7
C2 B:I3C101 4.4 90.4 0.7
OE1 B:GLU38 4.4 58.0 1.0
CG B:GLN35 4.5 49.7 1.0
CB B:ARG34 4.5 46.8 1.0
NE1 A:TRP63 4.6 60.5 1.0
CZ2 A:TRP63 4.7 54.2 1.0
NE B:ARG34 4.7 47.1 1.0
CE2 A:TRP63 4.8 56.2 1.0
CD B:ARG34 4.9 46.7 1.0
N B:GLN35 4.9 43.0 1.0
C3 B:I3C101 4.9 98.4 0.7
O B:HOH201 4.9 72.8 1.0
C B:ARG34 5.0 46.9 1.0

Reference:

C.Zhou, L.Yan, W.H.Zhang, Z.Liu. Structural Basis of Tubulin Detyrosination By VASH2/Svbp Heterodimer. Nat Commun V. 10 3212 2019.
ISSN: ESSN 2041-1723
PubMed: 31324789
DOI: 10.1038/S41467-019-11277-8
Page generated: Fri Aug 8 21:33:12 2025

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