Zinc in PDB 8xmj: Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation (pdb code 8xmj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation, PDB code: 8xmj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8xmj

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:373.0
occ:1.00
 NE2 B:HIS370 2.1 289.2 1.0
OE2 B:GLU420 2.1 309.8 1.0
NE2 B:HIS387 2.2 298.3 1.0
CE1 B:HIS370 2.2 289.2 1.0
SG B:CYS433 2.3 310.3 1.0
OE1 B:GLU420 2.4 309.8 1.0
CD B:GLU420 2.4 309.8 1.0
CD2 B:HIS387 2.8 298.3 1.0
CB B:CYS433 2.9 310.3 1.0
CA B:CYS433 2.9 310.3 1.0
CE1 B:HIS387 3.2 298.3 1.0
CD2 B:HIS370 3.4 289.2 1.0
ND1 B:HIS370 3.5 289.2 1.0
N B:GLU434 3.6 289.8 1.0
O B:PRO432 3.7 315.2 1.0
C B:CYS433 3.7 310.3 1.0
CG B:GLU420 3.8 309.8 1.0
CG B:HIS387 3.9 298.3 1.0
ND1 B:HIS387 4.0 298.3 1.0
N B:CYS433 4.1 310.3 1.0
CG B:HIS370 4.1 289.2 1.0
C B:PRO432 4.3 315.2 1.0
OE2 B:GLU368 4.4 299.4 1.0
CB B:GLU420 4.6 309.8 1.0
O B:HIS387 4.7 298.3 1.0
CA B:GLU434 4.9 289.8 1.0
O B:CYS433 4.9 310.3 1.0
N B:LEU435 5.0 285.8 1.0

Zinc binding site 2 out of 8 in 8xmj

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:347.7
occ:1.00
 OE2 B:GLU371 2.2 260.6 1.0
O B:CYS446 2.2 299.9 1.0
NE2 B:HIS373 2.2 242.1 1.0
SG B:CYS447 2.3 322.4 1.0
SG B:CYS446 2.4 299.9 1.0
C B:CYS446 2.8 299.9 1.0
OE1 B:GLU371 2.9 260.6 1.0
CD B:GLU371 2.9 260.6 1.0
CE1 B:HIS373 3.0 242.1 1.0
CB B:CYS447 3.3 322.4 1.0
CB B:CYS446 3.3 299.9 1.0
CD2 B:HIS373 3.3 242.1 1.0
N B:CYS447 3.5 322.4 1.0
CA B:CYS446 3.6 299.9 1.0
CA B:CYS447 3.8 322.4 1.0
C B:CYS447 4.2 322.4 1.0
ND1 B:HIS373 4.2 242.1 1.0
N B:CYS446 4.2 299.9 1.0
CG B:GLU371 4.4 260.6 1.0
CG B:HIS373 4.4 242.1 1.0
O B:CYS447 4.9 322.4 1.0
CA B:GLU371 4.9 260.6 1.0
CB B:GLU371 4.9 260.6 1.0

Zinc binding site 3 out of 8 in 8xmj

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:337.6
occ:1.00
 NE2 B:HIS251 1.9 265.6 1.0
OD1 B:ASP255 1.9 276.5 1.0
OD1 B:ASP47 2.0 269.2 1.0
OD2 B:ASP255 2.0 276.5 1.0
CG B:ASP255 2.2 276.5 1.0
CG B:ASP47 2.4 269.2 1.0
CE1 B:HIS251 2.6 265.6 1.0
CD2 B:HIS251 2.7 265.6 1.0
OD2 B:ASP47 2.9 269.2 1.0
CB B:ASP47 3.4 269.2 1.0
ND1 B:HIS251 3.5 265.6 1.0
CG B:HIS251 3.6 265.6 1.0
CB B:ASP255 3.7 276.5 1.0
CA B:ASP47 3.9 269.2 1.0
O B:HIS251 4.0 265.6 1.0
N B:ASP47 4.4 269.2 1.0
CA B:ASP255 4.6 276.5 1.0
C B:HIS251 4.6 265.6 1.0
N B:ASP255 4.8 276.5 1.0
CB B:HIS251 4.9 265.6 1.0
OG B:SER46 4.9 261.9 1.0

Zinc binding site 4 out of 8 in 8xmj

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:324.7
occ:1.00
 SG A:CYS437 2.3 298.1 1.0
NE2 B:HIS408 2.3 296.1 1.0
ND1 B:HIS413 2.4 295.7 1.0
CD2 B:HIS408 2.5 296.1 1.0
CB B:HIS413 2.9 295.7 1.0
CG B:HIS413 3.0 295.7 1.0
CA B:HIS413 3.2 295.7 1.0
CE1 B:HIS408 3.2 296.1 1.0
CB A:CYS437 3.4 298.1 1.0
CG B:HIS408 3.5 296.1 1.0
CE1 B:HIS413 3.6 295.7 1.0
O B:HIS413 3.6 295.7 1.0
ND1 B:HIS408 3.8 296.1 1.0
C B:HIS413 3.9 295.7 1.0
N A:ARG438 3.9 293.4 1.0
CD2 B:HIS413 4.3 295.7 1.0
O B:ILE412 4.3 284.1 1.0
N B:HIS413 4.5 295.7 1.0
NE2 B:HIS413 4.5 295.7 1.0
CB A:ARG438 4.6 293.4 1.0
CB B:HIS408 4.6 296.1 1.0
CA A:CYS437 4.6 298.1 1.0
O A:ARG438 4.6 293.4 1.0
C A:CYS437 4.7 298.1 1.0
CA A:ARG438 4.7 293.4 1.0
N A:CYS441 4.7 280.7 1.0
C B:ILE412 4.9 284.1 1.0
CB A:CYS441 5.0 280.7 1.0
CA A:CYS441 5.0 280.7 1.0

Zinc binding site 5 out of 8 in 8xmj

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:327.5
occ:1.00
 CD2 A:HIS408 1.9 288.2 1.0
SG B:CYS437 2.1 302.5 1.0
ND1 A:HIS413 2.2 280.3 1.0
NE2 A:HIS408 2.5 288.2 1.0
CG A:HIS413 2.6 280.3 1.0
CA A:HIS413 2.7 280.3 1.0
CB A:HIS413 2.8 280.3 1.0
CG A:HIS408 3.1 288.2 1.0
O A:ILE412 3.1 268.3 1.0
CE1 A:HIS413 3.1 280.3 1.0
CD2 A:HIS413 3.5 280.3 1.0
CB B:CYS437 3.6 302.5 1.0
CE1 A:HIS408 3.7 288.2 1.0
N A:HIS413 3.7 280.3 1.0
C A:HIS413 3.7 280.3 1.0
O A:HIS413 3.8 280.3 1.0
C A:ILE412 3.8 268.3 1.0
NE2 A:HIS413 3.8 280.3 1.0
ND1 A:HIS408 3.9 288.2 1.0
CB A:HIS408 4.0 288.2 1.0
CA B:CYS437 4.4 302.5 1.0
CA A:HIS408 4.5 288.2 1.0
N B:ARG438 4.6 302.7 1.0
O A:HIS408 4.8 288.2 1.0
N A:ALA414 5.0 259.4 1.0

Zinc binding site 6 out of 8 in 8xmj

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:351.8
occ:1.00
 OE2 A:GLU420 2.0 311.3 1.0
NE2 A:HIS387 2.0 287.5 1.0
NE2 A:HIS370 2.1 281.8 1.0
SG A:CYS433 2.4 314.8 1.0
CD A:GLU420 2.5 311.3 1.0
CE1 A:HIS387 2.6 287.5 1.0
CB A:CYS433 2.7 314.8 1.0
OE1 A:GLU420 2.7 311.3 1.0
CD2 A:HIS387 2.8 287.5 1.0
CA A:CYS433 2.9 314.8 1.0
CD2 A:HIS370 3.1 281.8 1.0
CE1 A:HIS370 3.1 281.8 1.0
ND1 A:HIS387 3.4 287.5 1.0
CG A:HIS387 3.5 287.5 1.0
N A:GLU434 3.7 314.3 1.0
C A:CYS433 3.7 314.8 1.0
CG A:GLU420 3.7 311.3 1.0
O A:PRO432 3.9 300.6 1.0
CB A:GLU420 4.0 311.3 1.0
N A:CYS433 4.0 314.8 1.0
ND1 A:HIS370 4.2 281.8 1.0
CG A:HIS370 4.2 281.8 1.0
C A:PRO432 4.4 300.6 1.0
O A:CYS433 4.8 314.8 1.0
N A:LEU435 4.8 307.6 1.0
CB A:HIS387 4.9 287.5 1.0
CA A:GLU434 5.0 314.3 1.0

Zinc binding site 7 out of 8 in 8xmj

Go back to Zinc Binding Sites List in 8xmj
Zinc binding site 7 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:344.8
occ:1.00
 O A:CYS447 2.2 298.9 1.0
CE1 A:HIS373 2.2 244.5 1.0
SG A:CYS447 2.3 298.9 1.0
NE2 A:HIS373 2.3 244.5 1.0
SG A:CYS446 2.3 267.5 1.0
OE2 A:GLU371 2.5 251.4 1.0
C A:CYS447 3.0 298.9 1.0
N A:CYS447 3.0 298.9 1.0
C A:CYS446 3.1 267.5 1.0
CA A:CYS447 3.2 298.9 1.0
CB A:CYS447 3.4 298.9 1.0
O A:CYS446 3.4 267.5 1.0
CB A:CYS446 3.4 267.5 1.0
CD A:GLU371 3.5 251.4 1.0
ND1 A:HIS373 3.5 244.5 1.0
CD2 A:HIS373 3.7 244.5 1.0
CA A:CYS446 3.9 267.5 1.0
OE1 A:GLU371 4.0 251.4 1.0
CG A:HIS373 4.2 244.5 1.0
CG A:GLU371 4.4 251.4 1.0
CA A:GLU371 4.8 251.4 1.0

Zinc binding site 8 out of 8 in 8xmj

Go back to Zinc Binding Sites List in 8xmj
Zinc binding site 8 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Human ZNT1 Wt, in the Presence of Zinc, Determined in Heterogeneous Conformations- One Subunit in An Inward- Facing and the Other in An Outward-Facing Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:328.5
occ:1.00
 OD2 A:ASP47 2.0 274.1 1.0
OD2 A:ASP255 2.0 350.5 1.0
NE2 A:HIS43 2.0 258.2 1.0
NE2 A:HIS251 2.0 363.1 1.0
CE1 A:HIS251 2.4 363.1 1.0
OD1 A:ASP255 2.5 350.5 1.0
CG A:ASP255 2.5 350.5 1.0
CG A:ASP47 2.7 274.1 1.0
CE1 A:HIS43 2.7 258.2 1.0
OD1 A:ASP47 2.9 274.1 1.0
CD2 A:HIS251 3.0 363.1 1.0
CD2 A:HIS43 3.1 258.2 1.0
ND1 A:HIS251 3.4 363.1 1.0
CG A:HIS251 3.7 363.1 1.0
ND1 A:HIS43 3.8 258.2 1.0
CB A:ASP47 3.9 274.1 1.0
CB A:ASP255 4.0 350.5 1.0
CG A:HIS43 4.0 258.2 1.0
O A:HIS251 4.5 363.1 1.0
O A:HIS43 4.7 258.2 1.0
CA A:ASP255 4.9 350.5 1.0

Reference:

Y.Long, Z.Zhu, Z.Zhou, C.Yang, Y.Chao, Y.Wang, Q.Zhou, M.W.Wang, Q.Qu. Structural Insights Into Human Zinc Transporter ZNT1 Mediated Zn 2+ Efflux. Embo Rep. 2024.
ISSN: ESSN 1469-3178
PubMed: 39390258
DOI: 10.1038/S44319-024-00287-3
Page generated: Wed Nov 13 13:47:31 2024

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