Chlorine in PDB 5xwm: Human ERP44 Zinc-Bound Form

Protein crystallography data

The structure of Human ERP44 Zinc-Bound Form, PDB code: 5xwm was solved by S.Watanabe, M.Harayama, K.Inaba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.06 / 2.45
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 175.150, 175.150, 407.810, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 21.4

Other elements in 5xwm:

The structure of Human ERP44 Zinc-Bound Form also contains other interesting chemical elements:

Zinc (Zn) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human ERP44 Zinc-Bound Form (pdb code 5xwm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Human ERP44 Zinc-Bound Form, PDB code: 5xwm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5xwm

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Chlorine binding site 1 out of 8 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:58.2
occ:1.00
 ZN A:ZN401 2.9 50.6 1.0
CL C:CL403 3.1 60.1 1.0
N A:TYR78 3.6 48.4 1.0
CD2 A:TYR78 3.7 50.1 1.0
CD2 C:HIS332 3.8 46.3 1.0
CZ3 A:TRP28 3.8 54.5 1.0
CH2 A:TRP28 4.0 59.1 1.0
CA A:LYS77 4.1 46.5 1.0
O A:TYR78 4.2 56.2 1.0
CB A:LYS77 4.3 45.4 1.0
C A:LYS77 4.4 52.0 1.0
NE2 C:HIS333 4.4 48.1 1.0
CG C:HIS332 4.4 46.1 1.0
CE1 C:HIS328 4.4 47.7 1.0
CE2 A:TYR78 4.4 53.1 1.0
CB A:TYR78 4.5 51.1 1.0
CA A:TYR78 4.5 49.7 1.0
CG A:TYR78 4.5 54.0 1.0
SG A:CYS29 4.6 56.0 1.0
CB C:HIS332 4.6 43.3 1.0
NE2 C:HIS332 4.6 46.5 1.0
NE2 C:HIS328 4.7 54.7 1.0
CD2 C:HIS333 4.7 46.3 1.0
CB A:CYS29 4.8 57.3 1.0
ND1 C:HIS328 4.8 43.2 1.0
C A:TYR78 4.8 51.0 1.0
CE3 A:TRP28 4.8 56.9 1.0

Chlorine binding site 2 out of 8 in 5xwm

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Chlorine binding site 2 out of 8 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:75.6
occ:1.00
 ZN C:ZN402 3.0 65.4 1.0
CL C:CL404 3.0 78.3 1.0
CA A:ARG329 3.5 65.0 1.0
CZ3 C:TRP28 3.6 68.7 1.0
NE2 A:HIS333 3.7 82.0 1.0
CB A:ARG329 3.8 63.5 1.0
CD2 A:HIS333 3.8 72.5 1.0
CE3 C:TRP28 3.9 66.8 1.0
CG A:ARG329 4.0 66.7 1.0
SG C:CYS29 4.0 77.7 1.0
N A:ARG329 4.1 68.5 1.0
CA C:CYS29 4.1 80.8 1.0
CB C:CYS29 4.3 67.7 1.0
O A:HIS328 4.5 63.9 1.0
C A:HIS328 4.5 64.2 1.0
O C:TRP28 4.6 75.0 1.0
C A:ARG329 4.7 66.5 1.0
O A:ARG329 4.8 70.7 1.0
CH2 C:TRP28 4.8 61.3 1.0
N C:CYS29 4.8 79.1 1.0
CD A:ARG329 4.9 72.4 1.0
N C:ARG30 4.9 77.5 1.0
CE1 A:HIS333 5.0 68.5 1.0

Chlorine binding site 3 out of 8 in 5xwm

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Chlorine binding site 3 out of 8 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:57.1
occ:1.00
 CL D:CL403 3.1 53.4 1.0
ZN D:ZN401 3.1 46.0 1.0
O D:HOH558 3.1 46.5 1.0
O B:HOH580 3.5 42.1 1.0
CA B:ARG329 3.5 40.1 1.0
CZ3 D:TRP28 3.7 42.1 1.0
CB B:ARG329 3.8 41.1 1.0
CD2 B:HIS333 3.9 44.4 1.0
CA D:CYS29 3.9 43.5 1.0
N B:ARG329 4.0 38.6 1.0
NE2 B:HIS333 4.0 54.3 1.0
CB D:CYS29 4.1 39.2 1.0
CG B:ARG329 4.1 42.8 1.0
CE3 D:TRP28 4.1 40.5 1.0
SG D:CYS29 4.1 38.1 1.0
O D:TRP28 4.5 42.8 1.0
C B:HIS328 4.5 37.7 1.0
O B:HIS328 4.6 38.0 1.0
C B:ARG329 4.7 43.4 1.0
CD B:ARG329 4.8 44.2 1.0
N D:ARG30 4.8 43.4 1.0
N D:CYS29 4.8 41.7 1.0
O B:ARG329 4.9 48.5 1.0
CH2 D:TRP28 4.9 48.7 1.0
C D:CYS29 4.9 45.6 1.0

Chlorine binding site 4 out of 8 in 5xwm

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Chlorine binding site 4 out of 8 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:56.6
occ:1.00
 ZN B:ZN403 2.8 48.9 1.0
CL D:CL404 3.0 62.2 1.0
N B:TYR78 3.5 47.1 1.0
CD2 B:TYR78 3.8 51.9 1.0
CD2 D:HIS332 3.8 49.0 1.0
CZ3 B:TRP28 4.0 53.1 1.0
NE2 D:HIS333 4.0 67.2 1.0
CA B:LYS77 4.0 43.8 1.0
O B:TYR78 4.1 63.6 1.0
CH2 B:TRP28 4.1 55.2 1.0
CB B:LYS77 4.2 43.1 1.0
C B:LYS77 4.3 45.1 1.0
CB B:TYR78 4.3 52.4 1.0
CA B:TYR78 4.3 51.1 1.0
CG D:HIS332 4.3 49.0 1.0
SG B:CYS29 4.4 58.1 1.0
CB D:HIS332 4.4 52.7 1.0
CG B:TYR78 4.5 54.1 1.0
CE1 D:HIS328 4.7 58.4 1.0
CB B:CYS29 4.7 56.5 1.0
C B:TYR78 4.7 50.3 1.0
CE2 B:TYR78 4.7 50.9 1.0
NE2 D:HIS332 4.7 56.4 1.0
NE2 D:HIS328 4.8 67.5 1.0
CE1 D:HIS333 4.8 55.4 1.0
CD2 D:HIS333 4.8 53.7 1.0
CE3 B:TRP28 5.0 59.2 1.0

Chlorine binding site 5 out of 8 in 5xwm

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Chlorine binding site 5 out of 8 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:60.1
occ:1.00
 ZN A:ZN401 3.1 50.6 1.0
CL A:CL404 3.1 58.2 1.0
O A:HOH516 3.2 40.1 1.0
CA C:ARG329 3.4 40.4 1.0
O C:HOH592 3.5 49.7 1.0
CB C:ARG329 3.7 41.2 1.0
CZ3 A:TRP28 3.7 54.5 1.0
N C:ARG329 4.0 38.9 1.0
CD2 C:HIS333 4.0 46.3 1.0
CE3 A:TRP28 4.1 56.9 1.0
CG C:ARG329 4.1 43.1 1.0
CA A:CYS29 4.1 59.6 1.0
CB A:CYS29 4.2 57.3 1.0
SG A:CYS29 4.2 56.0 1.0
NE2 C:HIS333 4.3 48.1 1.0
C C:HIS328 4.5 40.7 1.0
O C:HIS328 4.6 41.8 1.0
C C:ARG329 4.6 48.2 1.0
O A:TRP28 4.7 68.2 1.0
O C:ARG329 4.8 51.7 1.0
CD C:ARG329 4.9 44.0 1.0
CH2 A:TRP28 4.9 59.1 1.0
ND1 C:HIS328 5.0 43.2 1.0
N A:CYS29 5.0 60.6 1.0
N A:ARG30 5.0 63.0 1.0

Chlorine binding site 6 out of 8 in 5xwm

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Chlorine binding site 6 out of 8 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:78.3
occ:1.00
 ZN C:ZN402 3.0 65.4 1.0
CL A:CL405 3.0 75.6 1.0
N C:TYR78 3.6 55.3 1.0
CZ3 C:TRP28 3.7 68.7 1.0
CD2 C:TYR78 3.8 58.4 1.0
CD2 A:HIS332 3.8 59.4 1.0
CH2 C:TRP28 3.9 61.3 1.0
CA C:LYS77 4.0 54.7 1.0
NE2 A:HIS333 4.0 82.0 1.0
O C:TYR78 4.2 77.1 1.0
CB C:LYS77 4.2 52.1 1.0
C C:LYS77 4.3 62.5 1.0
CG A:HIS332 4.3 57.0 1.0
CB C:TYR78 4.4 59.3 1.0
CA C:TYR78 4.4 57.2 1.0
SG C:CYS29 4.4 77.7 1.0
CB A:HIS332 4.5 61.0 1.0
CG C:TYR78 4.5 57.6 1.0
NE2 A:HIS328 4.5 77.2 1.0
CE1 A:HIS328 4.6 69.8 1.0
CE2 C:TYR78 4.6 60.3 1.0
NE2 A:HIS332 4.7 62.6 1.0
CE3 C:TRP28 4.7 66.8 1.0
CD2 A:HIS333 4.7 72.5 1.0
C C:TYR78 4.8 61.1 1.0
CB C:CYS29 4.9 67.7 1.0
CD2 A:HIS328 5.0 69.2 1.0

Chlorine binding site 7 out of 8 in 5xwm

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Chlorine binding site 7 out of 8 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:53.4
occ:1.00
 ZN D:ZN401 3.0 46.0 1.0
CL B:CL404 3.1 57.1 1.0
CZ3 D:TRP28 3.7 42.1 1.0
CD2 B:HIS332 3.7 42.6 1.0
N D:TYR78 3.8 35.9 1.0
CD2 D:TYR78 3.9 38.8 1.0
CH2 D:TRP28 4.0 48.7 1.0
NE2 B:HIS333 4.2 54.3 1.0
CA D:LYS77 4.2 35.8 1.0
CG B:HIS332 4.3 40.2 1.0
CE1 B:HIS328 4.3 38.7 1.0
CB D:LYS77 4.4 32.8 1.0
O D:TYR78 4.4 50.9 1.0
CB B:HIS332 4.5 41.1 1.0
C D:LYS77 4.5 39.5 1.0
NE2 B:HIS328 4.5 45.8 1.0
CE2 D:TYR78 4.6 43.7 1.0
SG D:CYS29 4.6 38.1 1.0
NE2 B:HIS332 4.6 46.8 1.0
CA D:TYR78 4.7 34.5 1.0
CB D:TYR78 4.7 38.6 1.0
ND1 B:HIS328 4.7 42.6 1.0
CD2 B:HIS333 4.7 44.4 1.0
CG D:TYR78 4.7 42.6 1.0
CB D:CYS29 4.7 39.2 1.0
CE3 D:TRP28 4.8 40.5 1.0
C D:TYR78 5.0 34.9 1.0

Chlorine binding site 8 out of 8 in 5xwm

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Chlorine binding site 8 out of 8 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:62.2
occ:1.00
 ZN B:ZN403 2.9 48.9 1.0
CL B:CL405 3.0 56.6 1.0
CA D:ARG329 3.4 49.0 1.0
O B:HOH510 3.5 68.4 1.0
NE2 D:HIS333 3.5 67.2 1.0
CB D:ARG329 3.6 50.1 1.0
CD2 D:HIS333 3.9 53.7 1.0
CZ3 B:TRP28 3.9 53.1 1.0
CG D:ARG329 3.9 58.2 1.0
N D:ARG329 4.0 48.0 1.0
SG B:CYS29 4.1 58.1 1.0
CA B:CYS29 4.1 65.2 1.0
CB B:CYS29 4.2 56.5 1.0
CE3 B:TRP28 4.3 59.2 1.0
C D:HIS328 4.6 51.0 1.0
C D:ARG329 4.6 57.8 1.0
O D:HIS328 4.6 54.9 1.0
O D:ARG329 4.7 62.8 1.0
CD D:ARG329 4.7 56.3 1.0
CE1 D:HIS333 4.7 55.4 1.0
O B:TRP28 4.8 61.7 1.0
N B:ARG30 4.9 62.4 1.0
CH2 B:TRP28 4.9 55.2 1.0

Reference:

S.Watanabe, Y.Amagai, S.Sannino, T.Tempio, T.Anelli, M.Harayama, S.Masui, I.Sorrentino, M.Yamada, R.Sitia, K.Inaba. Zinc Regulates ERP44-Dependent Protein Quality Control in the Early Secretory Pathway. Nat Commun V. 10 603 2019.
ISSN: ESSN 2041-1723
PubMed: 30723194
DOI: 10.1038/S41467-019-08429-1
Page generated: Sat Dec 12 12:39:46 2020

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