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Chlorine in PDB 5eqa: Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245, PDB code: 5eqa was solved by M.Ruszkowski, Z.Dauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.20 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.240, 89.390, 92.240, 90.00, 96.93, 90.00
R / Rfree (%) 12.4 / 16.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 (pdb code 5eqa). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245, PDB code: 5eqa:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 5eqa

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Chlorine binding site 1 out of 9 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:32.0
occ:1.00
 OG A:SER122 2.8 20.8 1.0
O A:HOH789 3.0 42.2 1.0
O A:HOH526 3.2 52.3 1.0
N A:SER122 3.2 16.5 1.0
N A:PRO121 3.5 19.4 1.0
CA A:PHE120 3.5 18.0 1.0
CB A:SER122 3.5 19.0 1.0
CD A:PRO121 3.5 22.6 1.0
C A:PHE120 3.6 17.8 1.0
CA A:SER122 4.0 15.8 1.0
CG A:PRO121 4.0 27.0 1.0
CB A:PHE120 4.2 18.4 1.0
C A:PRO121 4.2 18.7 1.0
O A:PHE120 4.3 17.4 1.0
CA A:PRO121 4.4 20.4 1.0
CD1 A:PHE120 4.4 19.9 1.0
CD2 A:HIS123 4.5 13.9 1.0
O A:ASN119 4.5 22.7 1.0
O A:HOH779 4.5 46.7 1.0
O A:HOH638 4.7 27.1 1.0
C A:SER122 4.7 14.4 1.0
N A:PHE120 4.7 20.2 1.0
N A:HIS123 4.7 14.6 1.0
NE2 A:HIS123 4.8 14.1 1.0
CG A:PHE120 4.8 16.8 1.0
CB A:PRO121 4.9 25.2 1.0

Chlorine binding site 2 out of 9 in 5eqa

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Chlorine binding site 2 out of 9 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:29.2
occ:1.00
 O A:HOH744 2.6 30.5 1.0
O A:HOH682 3.0 17.0 1.0
N A:TRP288 3.0 12.9 1.0
CB A:TRP288 3.5 14.6 1.0
CB A:ASP287 3.5 14.4 1.0
CB A:ASN307 3.6 13.8 1.0
CA A:TRP288 3.7 14.3 1.0
CD1 A:TRP326 3.8 20.2 1.0
NE1 A:TRP326 3.8 20.3 1.0
CG A:ASP287 3.8 17.1 1.0
O A:ASN307 3.9 14.1 1.0
ND2 A:ASN307 4.0 24.3 1.0
C A:ASP287 4.0 13.9 1.0
O A:HOH662 4.0 28.7 1.0
OD2 A:ASP287 4.1 18.6 1.0
CG A:TRP288 4.1 13.7 1.0
N A:LYS289 4.2 17.2 1.0
CA A:ASP287 4.2 13.6 1.0
CG A:ASN307 4.3 15.3 1.0
N A:ASN307 4.3 12.5 1.0
OD1 A:ASP287 4.3 17.2 1.0
CA A:ASN307 4.3 12.7 1.0
C A:TRP288 4.4 15.5 1.0
C A:ASN307 4.4 12.1 1.0
CD1 A:TRP288 4.6 13.3 1.0
O A:HOH532 4.7 19.7 1.0
CG A:TRP326 4.8 19.2 1.0
CD2 A:TRP288 4.9 13.4 1.0
CE2 A:TRP326 4.9 20.3 1.0

Chlorine binding site 3 out of 9 in 5eqa

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Chlorine binding site 3 out of 9 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:20.6
occ:1.00
 OG A:SER264 2.7 18.0 0.5
O A:HOH752 2.9 16.8 1.0
N A:LEU222 3.1 14.3 1.0
OG A:SER264 3.2 13.6 0.5
CB A:PRO220 3.4 18.2 1.0
CB A:LEU222 3.6 16.6 1.0
N A:HIS221 3.6 13.5 1.0
CA A:LEU222 3.6 15.6 1.0
N A:SER224 3.7 15.4 1.0
CB A:SER224 3.7 17.1 1.0
C A:LEU222 3.7 14.8 1.0
N A:PHE223 3.7 14.1 1.0
C A:PRO220 3.8 13.2 1.0
CB A:SER264 3.8 18.6 0.5
CA A:PRO220 3.8 14.6 1.0
CB A:SER264 3.8 12.5 0.5
O A:SER264 4.0 13.6 1.0
C A:SER264 4.0 12.2 1.0
C A:HIS221 4.2 14.7 1.0
N A:GLY265 4.3 12.3 1.0
CA A:SER224 4.3 15.5 1.0
CA A:GLY265 4.4 13.0 1.0
O A:PRO220 4.4 14.4 1.0
O A:LEU222 4.5 15.8 1.0
CA A:HIS221 4.5 13.6 1.0
CA A:SER264 4.5 13.5 0.5
CB A:ALA227 4.5 17.1 1.0
CA A:SER264 4.6 11.7 0.5
CG A:LEU222 4.6 18.0 1.0
O A:HOH605 4.6 18.1 1.0
C A:PHE223 4.7 14.0 1.0
CG A:PRO220 4.7 22.4 1.0
CA A:PHE223 4.7 14.9 1.0
O A:HOH801 4.8 15.4 1.0
O A:HOH696 4.8 28.4 1.0
OG A:SER224 4.9 19.9 1.0

Chlorine binding site 4 out of 9 in 5eqa

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Chlorine binding site 4 out of 9 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:26.2
occ:1.00
 OG B:SER122 2.8 20.3 1.0
O B:HOH790 3.1 42.2 1.0
O B:HOH770 3.1 39.6 1.0
N B:SER122 3.3 15.2 1.0
CB B:SER122 3.5 17.9 1.0
N B:PRO121 3.5 14.0 1.0
CA B:PHE120 3.5 13.2 1.0
CD B:PRO121 3.5 17.3 1.0
C B:PHE120 3.6 12.6 1.0
CA B:SER122 3.9 15.3 1.0
CB B:PHE120 4.1 13.6 1.0
CG B:PRO121 4.2 24.1 1.0
C B:PRO121 4.3 15.3 1.0
O B:PHE120 4.3 14.5 1.0
CD1 B:PHE120 4.3 16.9 1.0
CA B:PRO121 4.4 16.4 1.0
CD2 B:HIS123 4.5 13.6 1.0
O B:ASN119 4.5 17.6 1.0
O B:HOH681 4.7 25.2 1.0
C B:SER122 4.7 13.9 1.0
N B:PHE120 4.7 14.1 1.0
CG B:PHE120 4.7 12.9 1.0
NE2 B:HIS123 4.8 12.8 1.0
N B:HIS123 4.8 12.8 1.0
CB B:PRO121 4.8 18.7 1.0

Chlorine binding site 5 out of 9 in 5eqa

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Chlorine binding site 5 out of 9 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:29.5
occ:1.00
 O B:HOH739 2.6 33.8 1.0
O B:HOH700 3.0 20.1 1.0
N B:TRP288 3.1 13.6 1.0
CB B:TRP288 3.5 15.9 1.0
CB B:ASP287 3.6 14.9 1.0
CB B:ASN307 3.6 13.8 1.0
CD1 B:TRP326 3.7 22.1 1.0
CA B:TRP288 3.8 15.0 1.0
NE1 B:TRP326 3.8 23.1 1.0
CG B:ASP287 3.8 16.6 1.0
O B:HOH670 3.9 30.0 1.0
O D:HOH629 3.9 33.3 1.0
O B:ASN307 3.9 17.3 1.0
C B:ASP287 4.1 14.5 1.0
ND2 B:ASN307 4.1 26.4 1.0
OD2 B:ASP287 4.1 20.9 1.0
CG B:TRP288 4.1 15.3 1.0
CA B:ASP287 4.2 14.2 1.0
N B:LYS289 4.2 18.0 1.0
OD1 B:ASP287 4.3 17.8 1.0
CG B:ASN307 4.3 14.9 1.0
N B:ASN307 4.3 13.9 1.0
CA B:ASN307 4.3 12.5 1.0
C B:TRP288 4.4 17.5 1.0
C B:ASN307 4.5 14.1 1.0
CD1 B:TRP288 4.7 13.7 1.0
O B:HOH538 4.7 21.8 1.0
CG B:TRP326 4.8 20.2 1.0
CD2 B:TRP288 4.9 14.6 1.0
CE2 B:TRP326 4.9 21.1 1.0

Chlorine binding site 6 out of 9 in 5eqa

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Chlorine binding site 6 out of 9 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:22.8
occ:1.00
 OG B:SER264 2.7 20.7 0.7
O B:HOH754 2.9 19.5 1.0
OG B:SER264 3.1 11.9 0.3
N B:LEU222 3.2 15.6 1.0
CB B:PRO220 3.3 18.8 1.0
N B:HIS221 3.6 14.6 1.0
CB B:LEU222 3.7 17.0 1.0
CA B:LEU222 3.7 16.3 1.0
CB B:SER224 3.7 18.7 1.0
N B:SER224 3.7 18.2 1.0
CB B:SER264 3.7 19.0 0.7
N B:PHE223 3.8 14.9 1.0
C B:LEU222 3.8 14.6 1.0
C B:PRO220 3.8 14.6 1.0
CA B:PRO220 3.8 16.2 1.0
CB B:SER264 3.8 13.9 0.3
O B:SER264 4.0 14.4 1.0
C B:SER264 4.0 13.1 1.0
N B:GLY265 4.2 13.4 1.0
C B:HIS221 4.3 16.1 1.0
CA B:SER224 4.3 18.5 1.0
CA B:GLY265 4.4 13.9 1.0
O B:PRO220 4.4 15.2 1.0
CA B:HIS221 4.5 15.2 1.0
CB B:ALA227 4.5 18.9 1.0
O B:LEU222 4.5 17.1 1.0
CA B:SER264 4.5 12.9 0.7
CG B:LEU222 4.6 19.6 1.0
CA B:SER264 4.6 13.6 0.3
O B:HOH607 4.6 20.5 1.0
CG B:PRO220 4.7 23.7 1.0
C B:PHE223 4.7 16.0 1.0
O B:HOH694 4.7 30.2 1.0
CA B:PHE223 4.7 15.9 1.0
O B:HOH807 4.8 17.5 1.0
OG B:SER224 4.9 21.6 1.0
OD1 B:ASN307 5.0 17.4 1.0

Chlorine binding site 7 out of 9 in 5eqa

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Chlorine binding site 7 out of 9 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:31.2
occ:1.00
 O C:HOH655 3.0 31.2 1.0
N C:TRP288 3.2 16.4 1.0
CD1 C:TRP326 3.5 34.1 1.0
CB C:ASP287 3.6 18.2 1.0
CB C:TRP288 3.7 17.0 1.0
NE1 C:TRP326 3.7 38.9 1.0
ND2 C:ASN307 3.7 35.9 1.0
CB C:ASN307 3.7 19.9 1.0
CG C:ASP287 3.8 20.3 1.0
CA C:TRP288 3.9 18.8 1.0
O C:HOH647 3.9 39.1 1.0
C C:ASP287 4.1 17.0 1.0
OD2 C:ASP287 4.2 25.3 1.0
N C:LYS289 4.2 21.0 1.0
CG C:ASN307 4.2 22.8 1.0
OD1 C:ASP287 4.2 20.6 1.0
O C:ASN307 4.2 20.1 1.0
CA C:ASP287 4.3 16.9 1.0
CG C:TRP288 4.3 16.7 1.0
C C:TRP288 4.4 20.2 1.0
N C:ASN307 4.6 17.9 1.0
CA C:ASN307 4.6 17.0 1.0
CG C:TRP326 4.7 41.3 1.0
O C:HOH562 4.7 37.1 1.0
C C:ASN307 4.8 16.6 1.0
CE2 C:TRP326 4.8 41.3 1.0
CG C:LYS289 4.9 33.4 1.0
CD1 C:TRP288 4.9 17.3 1.0

Chlorine binding site 8 out of 9 in 5eqa

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Chlorine binding site 8 out of 9 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:29.6
occ:1.00
 OG D:SER122 2.8 21.3 1.0
O D:HOH729 3.0 51.8 1.0
N D:SER122 3.2 17.8 1.0
CB D:SER122 3.4 20.2 1.0
CD D:PRO121 3.5 19.4 1.0
N D:PRO121 3.5 17.7 1.0
CA D:PHE120 3.5 17.9 1.0
C D:PHE120 3.6 15.9 1.0
CA D:SER122 3.9 18.6 1.0
CB D:PHE120 4.1 16.3 1.0
CG D:PRO121 4.2 24.8 1.0
C D:PRO121 4.2 18.3 1.0
O D:PHE120 4.3 16.9 1.0
CD1 D:PHE120 4.4 20.2 1.0
CA D:PRO121 4.4 19.5 1.0
CD2 D:HIS123 4.5 15.6 1.0
O D:ASN119 4.5 20.7 1.0
C D:SER122 4.7 17.7 1.0
O D:HOH648 4.7 29.1 1.0
N D:PHE120 4.7 16.4 1.0
N D:HIS123 4.7 16.3 1.0
CG D:PHE120 4.7 16.5 1.0
NE2 D:HIS123 4.8 16.9 1.0
O D:HOH702 4.8 43.8 1.0
CB D:PRO121 4.8 20.7 1.0

Chlorine binding site 9 out of 9 in 5eqa

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Chlorine binding site 9 out of 9 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Phosphatase (Mthpp) with Intermolecular Cross-Link Between LYS158 and CYS245 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:33.0
occ:1.00
 O D:HOH657 3.0 29.1 1.0
N D:TRP288 3.3 19.6 1.0
CD1 D:TRP326 3.4 36.0 1.0
NE1 D:TRP326 3.5 36.1 1.0
CB D:ASP287 3.7 18.7 1.0
ND2 D:ASN307 3.7 33.9 1.0
CB D:TRP288 3.8 20.5 1.0
CB D:ASN307 3.8 22.0 1.0
CG D:ASP287 3.8 21.4 1.0
CA D:TRP288 4.0 21.1 1.0
OD2 D:ASP287 4.0 25.7 1.0
N D:LYS289 4.1 25.0 1.0
CG D:ASN307 4.2 25.3 1.0
C D:ASP287 4.2 19.2 1.0
OD1 D:ASP287 4.3 24.4 1.0
O D:ASN307 4.3 21.8 1.0
CA D:ASP287 4.4 18.5 1.0
C D:TRP288 4.4 21.8 1.0
CG D:TRP288 4.5 21.4 1.0
CG D:LYS289 4.6 32.6 1.0
N D:ASN307 4.6 19.6 1.0
CA D:ASN307 4.6 19.5 1.0
CG D:TRP326 4.6 31.9 1.0
O D:HOH545 4.7 31.6 1.0
CE2 D:TRP326 4.7 32.8 1.0
C D:ASN307 4.8 18.0 1.0

Reference:

M.Ruszkowski, Z.Dauter. Structural Studies of Medicago Truncatula Histidinol Phosphate Phosphatase From Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants. J.Biol.Chem. V. 291 9960 2016.
ISSN: ESSN 1083-351X
PubMed: 26994138
DOI: 10.1074/JBC.M115.708727
Page generated: Fri Jul 26 07:26:35 2024

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