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Iodine in PDB 4v3f: Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde

Enzymatic activity of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde

All present enzymatic activity of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde:
1.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde, PDB code: 4v3f was solved by A.Zarate-Romero, R.A.Munoz-Clares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.97 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.440, 82.256, 88.516, 79.44, 84.89, 77.32
R / Rfree (%) 19.6 / 21.1

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde (pdb code 4v3f). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde, PDB code: 4v3f:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in 4v3f

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Iodine binding site 1 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:41.8
occ:0.88
 O A:HOH2102 3.9 38.7 1.0
CG2 A:ILE155 4.1 27.5 1.0
CA A:GLY219 4.1 24.9 1.0
CA A:GLY215 4.2 26.7 1.0
CD1 A:ILE155 4.4 24.3 1.0
O A:GLY215 4.4 25.6 1.0
CE1 A:PHE233 4.5 25.0 1.0
CG2 A:THR239 4.5 29.7 1.0
NZ A:LYS182 4.6 22.3 1.0
C A:GLY219 4.6 31.5 1.0
C A:GLY215 4.7 25.4 1.0
N A:ALA220 4.9 24.8 1.0
N A:GLY219 5.0 21.3 1.0

Iodine binding site 2 out of 15 in 4v3f

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Iodine binding site 2 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1498

b:49.8
occ:0.63
 O B:HOH2125 3.5 22.6 1.0
N A:PRO136 3.7 42.8 1.0
O A:THR134 3.9 32.0 1.0
C A:LEU135 3.9 41.6 1.0
CD A:PRO136 4.0 31.7 1.0
CG2 A:THR134 4.0 26.3 1.0
CA A:PRO136 4.1 37.2 1.0
O A:LEU135 4.1 38.2 1.0
CG A:PRO136 4.2 39.1 1.0
C A:THR134 4.3 27.3 1.0
CA A:LEU135 4.5 32.0 1.0
NE2 B:GLN453 4.6 27.5 1.0
CG B:GLN453 4.6 27.2 1.0
CB A:PRO136 4.6 43.1 1.0
CB A:THR134 4.6 30.7 1.0
N A:LEU135 4.7 34.2 1.0
CD B:GLN453 4.8 31.6 1.0

Iodine binding site 3 out of 15 in 4v3f

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Iodine binding site 3 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1499

b:42.1
occ:0.66
 O B:HOH2120 3.2 39.3 1.0
OG1 B:THR434 3.5 60.9 1.0
CE1 A:HIS143 3.5 33.1 1.0
CE A:LYS130 3.8 50.0 1.0
CG B:GLU431 3.9 48.4 1.0
NE2 A:HIS143 3.9 47.5 1.0
CD1 A:LEU145 3.9 25.9 1.0
CD B:GLU431 4.3 57.2 1.0
CA B:GLU431 4.4 47.7 1.0
CB B:GLU431 4.4 47.7 1.0
OE2 B:GLU431 4.6 43.1 1.0
CG1 A:VAL482 4.6 28.7 1.0
CG A:LEU145 4.6 32.2 1.0
NZ A:LYS130 4.6 52.8 1.0
O B:GLU431 4.6 46.1 1.0
CD2 A:LEU145 4.7 35.2 1.0
ND1 A:HIS143 4.7 35.8 1.0
OE1 B:GLU431 4.8 56.7 1.0
CB B:THR434 4.8 39.5 1.0
CG2 A:VAL482 4.8 25.5 1.0
CG A:LYS130 4.8 40.6 1.0
CD A:LYS130 4.8 44.0 1.0
CG B:LYS435 4.9 36.1 1.0
CE B:LYS435 4.9 52.9 1.0
C B:GLU431 5.0 46.4 1.0

Iodine binding site 4 out of 15 in 4v3f

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Iodine binding site 4 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1500

b:43.1
occ:0.41
 NZ A:LYS21 3.2 43.5 1.0
ND2 A:ASN23 3.3 33.0 1.0
O A:HOH2016 3.9 37.5 1.0
NE2 D:HIS70 3.9 30.8 1.0
CG2 D:THR66 4.0 40.7 1.0
CA D:ASN62 4.1 23.2 1.0
O A:HOH2012 4.1 43.5 1.0
CB A:LYS21 4.1 37.5 1.0
O D:ASN61 4.2 32.4 1.0
CE1 D:HIS70 4.2 33.7 1.0
CG A:LYS21 4.3 37.6 1.0
CB D:ASN62 4.3 22.0 1.0
CE A:LYS21 4.4 62.2 1.0
CG A:ASN23 4.4 36.1 1.0
CD A:LYS21 4.4 60.5 1.0
CD2 D:HIS70 4.4 26.0 1.0
O D:ASN62 4.5 42.1 1.0
C D:ASN62 4.6 28.5 1.0
OD1 A:ASN23 4.7 36.6 1.0
ND1 D:HIS70 4.8 23.9 1.0
CG D:HIS70 5.0 36.4 1.0

Iodine binding site 5 out of 15 in 4v3f

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Iodine binding site 5 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1501

b:41.7
occ:0.67
 O A:HOH2181 3.3 27.4 1.0
NE2 A:GLN474 3.3 52.0 1.0
CG A:GLN474 3.4 51.0 1.0
CD A:GLN474 3.9 64.3 1.0
CD1 A:LEU477 3.9 38.6 1.0
O A:HOH2067 4.0 29.5 1.0
CD A:ARG146 4.1 25.4 1.0
CD A:LYS128 4.2 41.1 1.0
NH1 A:ARG146 4.2 31.8 1.0
CD1 A:LEU125 4.3 22.1 1.0
CG2 A:ILE473 4.4 22.5 1.0
CE A:LYS128 4.5 46.6 1.0
CB A:ILE473 4.6 17.9 1.0
NZ A:LYS128 4.7 53.0 1.0
CB A:GLN474 4.7 21.0 1.0
N A:GLN474 4.8 16.4 1.0
CA A:GLN474 4.9 23.5 1.0
NE A:ARG146 5.0 54.9 1.0

Iodine binding site 6 out of 15 in 4v3f

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Iodine binding site 6 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:46.5
occ:0.84
 CG2 B:ILE155 4.1 31.0 1.0
CA B:GLY219 4.1 38.6 1.0
CA B:GLY215 4.2 39.8 1.0
CD1 B:ILE155 4.5 34.9 1.0
CE2 B:PHE233 4.6 32.2 1.0
C B:GLY219 4.6 38.9 1.0
CG2 B:THR239 4.7 33.9 1.0
O B:GLY215 4.7 42.6 1.0
C B:GLY215 4.8 36.6 1.0
N B:ALA220 4.9 39.4 1.0
CG1 B:VAL243 5.0 25.1 1.0

Iodine binding site 7 out of 15 in 4v3f

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Iodine binding site 7 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1498

b:38.6
occ:0.58
 O A:HOH2162 3.3 32.9 1.0
CE1 B:HIS143 3.4 35.4 1.0
NE2 B:HIS143 3.6 38.0 1.0
O B:HOH2050 3.6 56.4 1.0
CG A:GLU431 3.6 31.8 1.0
CD1 B:LEU145 4.0 31.1 1.0
CE B:LYS130 4.1 46.8 1.0
CG2 A:THR434 4.2 30.0 1.0
CD2 B:LEU145 4.3 30.4 1.0
CD A:GLU431 4.4 53.4 1.0
CB A:GLU431 4.4 32.5 1.0
CB A:THR434 4.5 34.4 1.0
CA A:GLU431 4.5 41.1 1.0
NZ B:LYS130 4.5 50.9 1.0
CG B:LEU145 4.5 26.8 1.0
ND1 B:HIS143 4.6 42.2 1.0
OE1 A:GLU431 4.6 55.1 1.0
CG1 B:VAL482 4.7 32.2 1.0
O A:GLU431 4.7 30.7 1.0
O B:HOH2061 4.8 36.0 1.0
CG2 B:VAL482 4.9 28.5 1.0
CE A:LYS435 4.9 50.1 1.0
CD2 B:HIS143 5.0 27.8 1.0
OG1 A:THR434 5.0 35.9 1.0
CG B:LYS130 5.0 24.4 1.0
CG A:LYS435 5.0 32.8 1.0

Iodine binding site 8 out of 15 in 4v3f

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Iodine binding site 8 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1499

b:39.2
occ:0.68
 NH1 B:ARG146 3.2 27.4 0.4
O B:HOH2049 3.2 33.1 1.0
NZ B:LYS128 3.7 43.7 1.0
CD1 B:LEU477 3.9 24.4 1.0
O B:HOH2043 4.0 39.0 1.0
O B:HOH2063 4.0 36.1 1.0
CD1 B:LEU125 4.0 30.2 1.0
NE B:ARG146 4.1 26.0 0.6
CD B:ARG146 4.1 26.0 0.6
CE B:LYS128 4.2 35.1 1.0
CD B:LYS128 4.2 28.7 1.0
CG2 B:ILE473 4.3 37.6 1.0
CD B:ARG146 4.3 25.3 0.4
CZ B:ARG146 4.3 24.8 0.4
CB B:ILE473 4.4 30.2 1.0
NE B:ARG146 4.7 24.9 0.4
CB B:GLN474 4.9 19.3 1.0
N B:GLN474 4.9 14.7 1.0

Iodine binding site 9 out of 15 in 4v3f

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Iodine binding site 9 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1500

b:53.9
occ:0.42
 O A:HOH2186 3.0 25.8 1.0
O A:HOH2108 3.4 40.1 1.0
N B:GLY465 3.7 25.6 1.0
CB B:PHE464 3.7 28.0 1.0
CA B:PHE464 3.9 29.2 1.0
NH1 B:ARG466 3.9 21.1 1.0
O B:GLY458 4.0 23.1 1.0
O A:HOH2109 4.3 35.6 1.0
C B:PHE464 4.3 22.1 1.0
NH2 B:ARG466 4.3 32.5 1.0
CZ B:ARG466 4.3 32.5 1.0
CD1 A:LEU149 4.4 27.0 1.0
O A:HOH2091 4.5 23.8 1.0
O A:LEU477 4.5 20.7 1.0
CA B:GLY465 4.7 22.8 1.0
CG2 B:ILE459 4.7 24.1 1.0
O B:GLY463 5.0 27.8 1.0

Iodine binding site 10 out of 15 in 4v3f

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Iodine binding site 10 out of 15 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I503

b:42.3
occ:0.77
 O C:HOH2069 3.3 34.0 1.0
CA C:GLY215 4.0 25.7 1.0
O C:GLY215 4.1 38.8 1.0
CD1 C:ILE155 4.1 32.1 1.0
CA C:GLY219 4.3 32.4 1.0
C C:GLY215 4.3 34.9 1.0
CG2 C:ILE155 4.4 27.7 1.0
C C:GLY219 4.4 31.5 1.0
CG2 C:THR239 4.5 23.2 1.0
CE1 C:PHE233 4.6 24.4 1.0
N C:ALA220 4.7 31.2 1.0
O C:GLY219 4.9 32.5 1.0
O C:HOH2075 4.9 48.5 1.0

Reference:

A.Zarate-Romero, D.S.Murillo-Melo, C.Mujica-Jimenez, C.Montiel, R.A.Munoz-Clares. Reversible, Partial Inactivation of Plant Betaine Aldehyde Dehydrogenase By Betaine Aldehyde: Mechanism and Possible Physiological Implications. Biochem.J. V. 473 873 2016.
ISSN: ISSN 0264-6021
PubMed: 26792760
DOI: 10.1042/BJ20151084
Page generated: Sun Aug 11 19:59:33 2024

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