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Zinc 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:

Chlorine (Cl) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human ERP44 Zinc-Bound Form (pdb code 5xwm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Human ERP44 Zinc-Bound Form, PDB code: 5xwm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5xwm

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Zinc binding site 1 out of 10 in the Human ERP44 Zinc-Bound Form


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:50.6
occ:1.00
 NE2 C:HIS333 2.0 48.1 1.0
SG A:CYS29 2.2 56.0 1.0
O A:TYR78 2.4 56.2 1.0
CD2 C:HIS333 2.8 46.3 1.0
CL A:CL404 2.9 58.2 1.0
CL C:CL403 3.1 60.1 1.0
CE1 C:HIS333 3.2 56.2 1.0
CB A:CYS29 3.3 57.3 1.0
C A:TYR78 3.4 51.0 1.0
N A:TYR78 3.9 48.4 1.0
CG C:HIS333 4.0 50.9 1.0
CA A:TYR78 4.0 49.7 1.0
ND1 C:HIS333 4.2 48.5 1.0
CA A:CYS29 4.2 59.6 1.0
CB A:TYR78 4.2 51.1 1.0
N A:PRO79 4.4 51.8 1.0
CD A:PRO79 4.7 53.6 1.0
CB A:PHE31 4.8 59.4 1.0
C A:CYS29 4.9 61.9 1.0
CD1 A:PHE31 4.9 67.0 1.0

Zinc binding site 2 out of 10 in 5xwm

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Zinc binding site 2 out of 10 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:80.8
occ:1.00
 NE2 C:HIS281 2.0 0.2 1.0
NE2 C:HIS277 2.0 91.7 1.0
NE2 A:HIS277 2.1 0.5 1.0
NE2 A:HIS281 2.1 98.4 1.0
CE1 A:HIS277 2.5 0.4 1.0
CE1 C:HIS277 2.7 84.9 1.0
CD2 A:HIS281 3.0 93.2 1.0
CE1 C:HIS281 3.0 0.2 1.0
CD2 C:HIS281 3.0 0.9 1.0
CD2 C:HIS277 3.1 85.0 1.0
CE1 A:HIS281 3.1 92.9 1.0
CD2 A:HIS277 3.2 0.1 1.0
ND1 A:HIS277 3.7 0.3 1.0
ND1 C:HIS277 3.8 83.5 1.0
CG C:HIS277 4.0 83.3 1.0
CG A:HIS277 4.0 0.4 1.0
ND1 C:HIS281 4.1 0.8 1.0
CG A:HIS281 4.1 88.8 1.0
CG C:HIS281 4.2 94.4 1.0
ND1 A:HIS281 4.2 92.5 1.0

Zinc binding site 3 out of 10 in 5xwm

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Zinc binding site 3 out of 10 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:53.7
occ:1.00
 NE2 A:HIS332 2.0 62.6 1.0
NE2 A:HIS299 2.0 76.3 1.0
NE2 A:HIS328 2.1 77.2 1.0
O A:HOH533 2.7 43.9 1.0
CE1 A:HIS299 2.8 64.7 1.0
CE1 A:HIS332 2.9 56.1 1.0
CE1 A:HIS328 3.0 69.8 1.0
CD2 A:HIS332 3.0 59.4 1.0
CD2 A:HIS328 3.2 69.2 1.0
CD2 A:HIS299 3.2 66.2 1.0
CD A:ARG298 4.0 0.7 1.0
ND1 A:HIS299 4.0 65.7 1.0
ND1 A:HIS332 4.1 56.0 1.0
O C:SER76 4.1 59.8 1.0
ND1 A:HIS328 4.1 66.9 1.0
CG A:HIS332 4.2 57.0 1.0
CG A:HIS299 4.2 55.1 1.0
CG A:HIS328 4.2 65.6 1.0
NE A:ARG298 4.7 0.9 1.0
O C:HOH618 4.9 57.9 1.0
CG A:ARG298 4.9 99.4 1.0

Zinc binding site 4 out of 10 in 5xwm

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Zinc binding site 4 out of 10 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:72.4
occ:1.00
 NE2 D:HIS277 1.9 85.0 1.0
NE2 D:HIS281 2.0 0.9 1.0
NE2 B:HIS281 2.1 93.4 1.0
NE2 B:HIS277 2.1 87.1 1.0
CE1 B:HIS281 2.8 93.2 1.0
CE1 B:HIS277 2.8 84.4 1.0
CE1 D:HIS277 2.8 86.9 1.0
CE1 D:HIS281 2.9 95.8 1.0
CD2 D:HIS277 3.0 85.6 1.0
CD2 D:HIS281 3.0 97.4 1.0
CD2 B:HIS281 3.1 91.8 1.0
CD2 B:HIS277 3.1 83.4 1.0
ND1 B:HIS281 3.9 91.0 1.0
ND1 B:HIS277 3.9 84.7 1.0
ND1 D:HIS277 4.0 90.1 1.0
CG B:HIS281 4.1 79.8 1.0
ND1 D:HIS281 4.1 97.0 1.0
CG B:HIS277 4.1 83.6 1.0
CG D:HIS277 4.1 84.6 1.0
CG D:HIS281 4.1 94.3 1.0
O B:HIS277 5.0 55.3 1.0

Zinc binding site 5 out of 10 in 5xwm

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Zinc binding site 5 out of 10 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:43.6
occ:1.00
 NE2 B:HIS328 2.0 45.8 1.0
NE2 B:HIS299 2.1 51.4 1.0
NE2 B:HIS332 2.1 46.8 1.0
O B:HOH618 2.5 40.5 1.0
O B:HOH621 2.7 33.6 1.0
CE1 B:HIS328 2.9 38.7 1.0
CE1 B:HIS299 3.0 39.4 1.0
CE1 B:HIS332 3.1 47.5 1.0
CD2 B:HIS332 3.1 42.6 1.0
CD2 B:HIS328 3.1 43.2 1.0
CD2 B:HIS299 3.1 35.3 1.0
O D:SER76 4.1 58.8 1.0
ND1 B:HIS328 4.1 42.6 1.0
ND1 B:HIS299 4.1 39.9 1.0
ND1 B:HIS332 4.2 40.0 1.0
CG B:HIS328 4.2 42.7 1.0
CG B:HIS332 4.2 40.2 1.0
CG B:HIS299 4.2 34.5 1.0
CG B:ARG298 4.8 66.2 1.0
NE B:ARG298 4.9 85.5 1.0
CD B:ARG298 5.0 73.3 1.0

Zinc binding site 6 out of 10 in 5xwm

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Zinc binding site 6 out of 10 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:48.9
occ:1.00
 NE2 D:HIS333 1.9 67.2 1.0
SG B:CYS29 2.2 58.1 1.0
O B:TYR78 2.3 63.6 1.0
CE1 D:HIS333 2.5 55.4 1.0
CL B:CL405 2.8 56.6 1.0
CL D:CL404 2.9 62.2 1.0
CD2 D:HIS333 3.1 53.7 1.0
C B:TYR78 3.3 50.3 1.0
CB B:CYS29 3.4 56.5 1.0
ND1 D:HIS333 3.7 56.6 1.0
N B:TYR78 3.9 47.1 1.0
CA B:TYR78 3.9 51.1 1.0
CG D:HIS333 4.0 61.3 1.0
CB B:TYR78 4.1 52.4 1.0
CA B:CYS29 4.2 65.2 1.0
N B:PRO79 4.4 51.1 1.0
CD1 B:PHE31 4.7 65.4 1.0
CD B:PRO79 4.7 55.7 1.0
CB B:PHE31 4.8 59.4 1.0
C B:CYS29 4.9 65.8 1.0
CB D:PRO354 5.0 75.7 1.0

Zinc binding site 7 out of 10 in 5xwm

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Zinc binding site 7 out of 10 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:51.0
occ:1.00
 NE2 C:HIS332 2.0 46.5 1.0
NE2 C:HIS299 2.1 54.7 1.0
NE2 C:HIS328 2.1 54.7 1.0
O C:HOH629 2.3 41.3 1.0
CE1 C:HIS299 2.9 48.4 1.0
CE1 C:HIS328 2.9 47.7 1.0
CE1 C:HIS332 2.9 50.8 1.0
CD2 C:HIS332 3.0 46.3 1.0
CD2 C:HIS328 3.2 44.6 1.0
CD2 C:HIS299 3.2 48.3 1.0
ND1 C:HIS299 4.1 47.4 1.0
ND1 C:HIS332 4.1 46.7 1.0
ND1 C:HIS328 4.1 43.2 1.0
O A:SER76 4.1 60.9 1.0
CG C:HIS332 4.2 46.1 1.0
CD C:ARG298 4.3 99.0 1.0
CG C:HIS299 4.3 43.2 1.0
CG C:HIS328 4.3 42.4 1.0
CG C:ARG298 4.3 89.5 1.0
NE C:ARG298 5.0 99.2 1.0

Zinc binding site 8 out of 10 in 5xwm

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Zinc binding site 8 out of 10 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:65.4
occ:1.00
 NE2 A:HIS333 1.9 82.0 1.0
SG C:CYS29 2.1 77.7 1.0
O C:TYR78 2.3 77.1 1.0
CE1 A:HIS333 2.7 68.5 1.0
CL A:CL405 3.0 75.6 1.0
CL C:CL404 3.0 78.3 1.0
CD2 A:HIS333 3.1 72.5 1.0
C C:TYR78 3.3 61.1 1.0
CB C:CYS29 3.4 67.7 1.0
ND1 A:HIS333 3.9 69.8 1.0
N C:TYR78 3.9 55.3 1.0
CA C:TYR78 4.0 57.2 1.0
CG A:HIS333 4.1 71.9 1.0
CB C:TYR78 4.1 59.3 1.0
CA C:CYS29 4.1 80.8 1.0
N C:PRO79 4.4 61.6 1.0
CB C:PHE31 4.6 76.2 1.0
CD C:PRO79 4.7 62.4 1.0
C C:CYS29 4.9 83.3 1.0
CB A:PRO354 4.9 66.0 1.0
N C:PHE31 5.0 74.1 1.0

Zinc binding site 9 out of 10 in 5xwm

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Zinc binding site 9 out of 10 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:46.0
occ:1.00
 NE2 B:HIS333 1.9 54.3 1.0
SG D:CYS29 2.2 38.1 1.0
O D:TYR78 2.5 50.9 1.0
CE1 B:HIS333 2.9 47.9 1.0
CD2 B:HIS333 2.9 44.4 1.0
CL D:CL403 3.0 53.4 1.0
CL B:CL404 3.1 57.1 1.0
CB D:CYS29 3.3 39.2 1.0
C D:TYR78 3.4 34.9 1.0
N D:TYR78 3.9 35.9 1.0
ND1 B:HIS333 4.0 46.5 1.0
CA D:TYR78 4.0 34.5 1.0
CG B:HIS333 4.0 47.2 1.0
CB D:TYR78 4.2 38.6 1.0
CA D:CYS29 4.2 43.5 1.0
N D:PRO79 4.4 37.4 1.0
CD D:PRO79 4.6 35.9 1.0
CB D:PHE31 4.7 38.6 1.0
C D:CYS29 4.9 45.6 1.0
CB B:PRO354 4.9 46.2 1.0
N D:PHE31 5.0 45.8 1.0

Zinc binding site 10 out of 10 in 5xwm

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Zinc binding site 10 out of 10 in the Human ERP44 Zinc-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human ERP44 Zinc-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:45.8
occ:1.00
 NE2 D:HIS332 2.0 56.4 1.0
NE2 D:HIS299 2.0 56.0 1.0
NE2 D:HIS328 2.1 67.5 1.0
CE1 D:HIS299 2.8 54.6 1.0
CE1 D:HIS332 2.8 52.5 1.0
O D:HOH639 2.9 50.2 1.0
CE1 D:HIS328 2.9 58.4 1.0
CD2 D:HIS332 3.1 49.0 1.0
CD2 D:HIS328 3.2 58.4 1.0
CD2 D:HIS299 3.2 54.6 1.0
ND1 D:HIS332 4.0 46.9 1.0
ND1 D:HIS299 4.0 55.2 1.0
ND1 D:HIS328 4.1 54.8 1.0
O B:SER76 4.1 61.4 1.0
CG D:HIS332 4.1 49.0 1.0
CD D:ARG298 4.2 0.0 1.0
CG D:HIS299 4.2 50.0 1.0
CG D:HIS328 4.3 55.9 1.0
NE D:ARG298 4.9 0.8 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: Mon Oct 28 15:16:24 2024

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